diff --git a/src/extensions/rcsb/graphql/types.ts b/src/extensions/rcsb/graphql/types.ts
index c0efb6f1fbc0fb79e0b6c5059c6759f4ee5ffcf4..0a01028acc812d9f728bbc47b8c5b923cf3e51e6 100644
--- a/src/extensions/rcsb/graphql/types.ts
+++ b/src/extensions/rcsb/graphql/types.ts
@@ -1,7 +1,9 @@
/* eslint-disable */
export type Maybe<T> = T | null;
export type Exact<T extends { [key: string]: unknown }> = { [K in keyof T]: T[K] };
-// Generated on 2020-09-13T02:52:22-07:00
+export type MakeOptional<T, K extends keyof T> = Omit<T, K> & { [SubKey in K]?: Maybe<T[SubKey]> };
+export type MakeMaybe<T, K extends keyof T> = Omit<T, K> & { [SubKey in K]: Maybe<T[SubKey]> };
+// Generated on 2021-09-12T13:31:40-07:00
/** All built-in and custom scalars, mapped to their actual values */
export type Scalars = {
@@ -12,3585 +14,3674 @@ export type Scalars = {
Float: number;
/** Built-in scalar representing an instant in time */
Date: any;
- /** Unrepresentable type */
+ /** Built-in scalar for dynamic values */
+ ObjectScalar: any;
+ /** Use SPQR's SchemaPrinter to remove this from SDL */
UNREPRESENTABLE: any;
};
-export type PdbxDatabasePdbObsSpr = {
+export type AuditAuthor = {
/**
- * The date of replacement.
- *
+ * The Open Researcher and Contributor ID (ORCID).
+ *
* Examples:
- * 1997-03-30
- */
- readonly date?: Maybe<Scalars['Date']>;
- /** Details related to the replaced or replacing entry. */
- readonly details?: Maybe<Scalars['String']>;
- /**
- * Identifier for the type of obsolete entry to be added to this entry.
- *
- * Allowable values:
- * OBSLTE, SPRSDE
+ * 0000-0002-6681-547X
+ *
*/
- readonly id?: Maybe<Scalars['String']>;
+ readonly identifier_ORCID?: Maybe<Scalars['String']>;
/**
- * The new PDB identifier for the replaced entry.
- *
+ * The name of an author of this data block. If there are multiple
+ * authors, _audit_author.name is looped with _audit_author.address.
+ * The family name(s), followed by a comma and including any
+ * dynastic components, precedes the first name(s) or initial(s).
+ *
* Examples:
- * 2ABC
+ * Jones, T.J., Bleary, Percival R., O'Neil, F.K., Van den Bossche, G., Yang, D.-L., Simonov, Yu.A
+ *
*/
- readonly pdb_id: Scalars['String'];
+ readonly name?: Maybe<Scalars['String']>;
/**
- * The PDB identifier for the replaced (OLD) entry/entries.
- *
- * Examples:
- * 3ABC
+ * This data item defines the order of the author's name in the
+ * list of audit authors.
*/
- readonly replace_pdb_id: Scalars['String'];
+ readonly pdbx_ordinal: Scalars['Int'];
};
-export type PdbxStructSpecialSymmetry = {
+export type Cell = {
/**
- * Part of the identifier for the molecular component.
- *
- * This data item is a pointer to _atom_site.pdbx_PDB_model_num in the
- * ATOM_SITE category.
+ * The number of the polymeric chains in a unit cell. In the case
+ * of heteropolymers, Z is the number of occurrences of the most
+ * populous chain.
+ *
+ * This data item is provided for compatibility with the original
+ * Protein Data Bank format, and only for that purpose.
*/
- readonly PDB_model_num?: Maybe<Scalars['Int']>;
+ readonly Z_PDB?: Maybe<Scalars['Int']>;
+ /** Unit-cell angle alpha of the reported structure in degrees. */
+ readonly angle_alpha?: Maybe<Scalars['Float']>;
+ /** Unit-cell angle beta of the reported structure in degrees. */
+ readonly angle_beta?: Maybe<Scalars['Float']>;
+ /** Unit-cell angle gamma of the reported structure in degrees. */
+ readonly angle_gamma?: Maybe<Scalars['Float']>;
/**
- * Part of the identifier for the molecular component.
- *
- * This data item is a pointer to _atom_site.auth_seq_id in the
- * ATOM_SITE category.
+ * The number of the formula units in the unit cell as specified
+ * by _chemical_formula.structural, _chemical_formula.moiety or
+ * _chemical_formula.sum.
*/
- readonly auth_seq_id?: Maybe<Scalars['String']>;
+ readonly formula_units_Z?: Maybe<Scalars['Int']>;
/**
- * The value of _pdbx_struct_special_symmetry.id must uniquely identify
- * each item in the PDBX_STRUCT_SPECIAL_SYMMETRY list.
- *
- * This is an integer serial number.
+ * Unit-cell length a corresponding to the structure reported in
+ * angstroms.
*/
- readonly id: Scalars['Int'];
+ readonly length_a?: Maybe<Scalars['Float']>;
/**
- * Part of the identifier for the molecular component.
- *
- * This data item is a pointer to _atom_site.label_asym_id in the
- * ATOM_SITE category.
+ * Unit-cell length b corresponding to the structure reported in
+ * angstroms.
*/
- readonly label_asym_id?: Maybe<Scalars['String']>;
+ readonly length_b?: Maybe<Scalars['Float']>;
/**
- * Part of the identifier for the molecular component.
- *
- * This data item is a pointer to _atom_site.label_comp_id in the
- * ATOM_SITE category.
+ * Unit-cell length c corresponding to the structure reported in
+ * angstroms.
*/
- readonly label_comp_id?: Maybe<Scalars['String']>;
+ readonly length_c?: Maybe<Scalars['Float']>;
+ /**
+ * To further identify unique axis if necessary. E.g., P 21 with
+ * an unique C axis will have 'C' in this field.
+ */
+ readonly pdbx_unique_axis?: Maybe<Scalars['String']>;
+ /**
+ * Cell volume V in angstroms cubed.
+ *
+ * V = a b c (1 - cos^2^~alpha~ - cos^2^~beta~ - cos^2^~gamma~
+ * + 2 cos~alpha~ cos~beta~ cos~gamma~)^1/2^
+ *
+ * a = _cell.length_a
+ * b = _cell.length_b
+ * c = _cell.length_c
+ * alpha = _cell.angle_alpha
+ * beta = _cell.angle_beta
+ * gamma = _cell.angle_gamma
+ */
+ readonly volume?: Maybe<Scalars['Float']>;
};
-export type PdbxChemCompAudit = {
+export type ChemComp = {
/**
- * The action associated with this audit record.
- *
+ * The formula for the chemical component. Formulae are written
+ * according to the following rules:
+ *
+ * (1) Only recognized element symbols may be used.
+ *
+ * (2) Each element symbol is followed by a 'count' number. A count
+ * of '1' may be omitted.
+ *
+ * (3) A space or parenthesis must separate each cluster of
+ * (element symbol + count), but in general parentheses are
+ * not used.
+ *
+ * (4) The order of elements depends on whether carbon is
+ * present or not. If carbon is present, the order should be:
+ * C, then H, then the other elements in alphabetical order
+ * of their symbol. If carbon is not present, the elements
+ * are listed purely in alphabetic order of their symbol. This
+ * is the 'Hill' system used by Chemical Abstracts.
+ *
+ * Examples:
+ * C18 H19 N7 O8 S
+ *
+ */
+ readonly formula?: Maybe<Scalars['String']>;
+ /**
+ * Formula mass of the chemical component.
+ *
+ * Examples:
+ * null, null
+ *
+ */
+ readonly formula_weight?: Maybe<Scalars['Float']>;
+ /**
+ * The value of _chem_comp.id must uniquely identify each item in
+ * the CHEM_COMP list.
+ *
+ * For protein polymer entities, this is the three-letter code for
+ * the amino acid.
+ *
+ * For nucleic acid polymer entities, this is the one-letter code
+ * for the base.
+ *
+ * Examples:
+ * ALA, VAL, DG, C
+ *
+ */
+ readonly id: Scalars['String'];
+ /**
+ * The identifier for the parent component of the nonstandard
+ * component. May be be a comma separated list if this component
+ * is derived from multiple components.
+ *
+ * Items in this indirectly point to _chem_comp.id in
+ * the CHEM_COMP category.
+ */
+ readonly mon_nstd_parent_comp_id?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
+ /**
+ * The full name of the component.
+ *
+ * Examples:
+ * alanine, valine, adenine, cytosine
+ *
+ */
+ readonly name?: Maybe<Scalars['String']>;
+ /**
+ * For standard polymer components, the one-letter code for
+ * the component. For non-standard polymer components, the
+ * one-letter code for parent component if this exists;
+ * otherwise, the one-letter code should be given as 'X'.
+ *
+ * Components that derived from multiple parents components
+ * are described by a sequence of one-letter-codes.
+ *
+ * Examples:
+ * A, B, R, N, D, C, Q, E, Z, G, H, I, L, K, M, F, P, S, T, W, Y, V, U, O, X
+ *
+ */
+ readonly one_letter_code?: Maybe<Scalars['String']>;
+ /**
+ * A preliminary classification used by PDB to indicate
+ * that the chemistry of this component while described
+ * as clearly as possible is still ambiguous. Software
+ * tools may not be able to process this component
+ * definition.
+ */
+ readonly pdbx_ambiguous_flag?: Maybe<Scalars['String']>;
+ /**
+ * The net integer charge assigned to this component. This is the
+ * formal charge assignment normally found in chemical diagrams.
+ */
+ readonly pdbx_formal_charge?: Maybe<Scalars['Int']>;
+ /** Date component was added to database. */
+ readonly pdbx_initial_date?: Maybe<Scalars['Date']>;
+ /** Date component was last modified. */
+ readonly pdbx_modified_date?: Maybe<Scalars['Date']>;
+ /**
+ * This data item identifies the deposition site that processed
+ * this chemical component defintion.
+ *
* Allowable values:
- * Create component, Initial release, Modify aromatic_flag, Modify atom id, Modify charge, Modify component atom id, Modify component comp_id, Modify coordinates, Modify descriptor, Modify formal charge, Modify formula, Modify identifier, Modify internal type, Modify leaving atom flag, Modify linking type, Modify model coordinates code, Modify name, Modify one letter code, Modify parent residue, Modify processing site, Modify subcomponent list, Modify synonyms, Modify value order, Obsolete component, Other modification
+ * EBI, PDBC, PDBE, PDBJ, RCSB
+ *
*/
- readonly action_type?: Maybe<Scalars['String']>;
+ readonly pdbx_processing_site?: Maybe<Scalars['String']>;
/**
- * This data item is a pointer to _chem_comp.id in the CHEM_COMP
- * category.
+ * This data item holds the current release status for the component.
+ *
+ * Allowable values:
+ * DEL, HOLD, HPUB, OBS, REF_ONLY, REL
+ *
*/
- readonly comp_id?: Maybe<Scalars['String']>;
- /** The date associated with this audit record. */
- readonly date?: Maybe<Scalars['Date']>;
+ readonly pdbx_release_status?: Maybe<Scalars['String']>;
/**
- * Additional details decribing this change.
- *
+ * Identifies the _chem_comp.id of the component that
+ * has replaced this component.
+ *
* Examples:
- * Added C14 as a leaving atom.
+ * q11, tvx
+ *
*/
- readonly details?: Maybe<Scalars['String']>;
+ readonly pdbx_replaced_by?: Maybe<Scalars['String']>;
/**
- * This data item is an ordinal index for the
- * PDBX_CHEM_COMP_AUDIT category.
+ * Identifies the _chem_comp.id's of the components
+ * which have been replaced by this component.
+ * Multiple id codes should be separated by commas.
+ *
+ * Examples:
+ * q11, tvx,atv
+ *
*/
- readonly ordinal: Scalars['Int'];
+ readonly pdbx_replaces?: Maybe<Scalars['String']>;
+ /**
+ * The list of subcomponents contained in this component.
+ *
+ * Examples:
+ * TSM DPH HIS CHF EMR
+ *
+ */
+ readonly pdbx_subcomponent_list?: Maybe<Scalars['String']>;
+ /**
+ * For standard polymer components, the common three-letter code for
+ * the component. Non-standard polymer components and non-polymer
+ * components are also assigned three-letter-codes.
+ *
+ * For ambiguous polymer components three-letter code should
+ * be given as 'UNK'. Ambiguous ions are assigned the code 'UNX'.
+ * Ambiguous non-polymer components are assigned the code 'UNL'.
+ *
+ * Examples:
+ * ALA, ARG, ASN, ASP, ASX, CYS, GLN, GLU, GLY, GLX, HIS, ILE, LEU, LYS, MET, PHE, PRO, SER, THR, TRP, TYR, VAL, 1MA, 5MC, OMC, 1MG, 2MG, M2G, 7MG, 0MG, H2U, 5MU, PSU, ACE, FOR, HOH, UNK
+ *
+ */
+ readonly three_letter_code?: Maybe<Scalars['String']>;
+ /**
+ * For standard polymer components, the type of the monomer.
+ * Note that monomers that will form polymers are of three types:
+ * linking monomers, monomers with some type of N-terminal (or 5')
+ * cap and monomers with some type of C-terminal (or 3') cap.
+ *
+ * Allowable values:
+ * D-beta-peptide, C-gamma linking, D-gamma-peptide, C-delta linking, D-peptide COOH carboxy terminus, D-peptide NH3 amino terminus, D-peptide linking, D-saccharide, D-saccharide, alpha linking, D-saccharide, beta linking, DNA OH 3 prime terminus, DNA OH 5 prime terminus, DNA linking, L-DNA linking, L-RNA linking, L-beta-peptide, C-gamma linking, L-gamma-peptide, C-delta linking, L-peptide COOH carboxy terminus, L-peptide NH3 amino terminus, L-peptide linking, L-saccharide, L-saccharide, alpha linking, L-saccharide, beta linking, RNA OH 3 prime terminus, RNA OH 5 prime terminus, RNA linking, non-polymer, other, peptide linking, peptide-like, saccharide
+ *
+ */
+ readonly type?: Maybe<Scalars['String']>;
};
-/** Query root */
-export type Query = {
- /** Get a PDB polymer entity instance (chain), given the PDB ID and ENTITY INSTANCE ID. Here ENTITY INSTANCE ID identifies structural element in the asymmetric unit, e.g. 'A', 'B', etc. */
- readonly polymer_entity_instance?: Maybe<CorePolymerEntityInstance>;
- /** Get a list of PDB non-polymer entities given a list of ENTITY IDs. Here ENTITY ID is a compound identifier that includes entry_id and entity_id separated by '_', e.g. 1XXX_1. */
- readonly nonpolymer_entities?: Maybe<ReadonlyArray<Maybe<CoreNonpolymerEntity>>>;
- /** Get a list of PDB polymer entities given a list of ENTITY IDs. Here ENTITY ID is a compound identifier that includes entry_id and entity_id separated by '_', e.g. 1XXX_1. */
- readonly polymer_entities?: Maybe<ReadonlyArray<Maybe<CorePolymerEntity>>>;
- /** Get a PDB polymer entity, given the PDB ID and ENTITY ID. Here ENTITY ID is a '1', '2', '3', etc. */
- readonly polymer_entity?: Maybe<CorePolymerEntity>;
- /** Get literature information from PubMed database given the PubMed identifier. */
- readonly pubmed?: Maybe<CorePubmed>;
- /** Get an assembly given the PDB ID and ASSEMBLY ID. Here ASSEMBLY ID is '1', '2', '3', etc. or 'deposited' for deposited coordinates. */
- readonly assembly?: Maybe<CoreAssembly>;
- /** Get a list of PDB branched entity instances (chains), given the list of ENTITY INSTANCE IDs. Here ENTITY INSTANCE ID identifies structural element in the asymmetric unit, e.g. 'A', 'B', etc. */
- readonly branched_entity_instances?: Maybe<ReadonlyArray<Maybe<CoreBranchedEntityInstance>>>;
- /** Get a list of PDB polymer entity instances (chains), given the list of ENTITY INSTANCE IDs. Here ENTITY INSTANCE ID identifies structural element in the asymmetric unit, e.g. 'A', 'B', etc. */
- readonly polymer_entity_instances?: Maybe<ReadonlyArray<Maybe<CorePolymerEntityInstance>>>;
- /** Get a list of assemblies given the list of ASSEMBLY IDs. Here an ASSEMBLY ID is a compound identifier that includes entry_id and assembly_id separated by '-', e.g. 1XXX-1. */
- readonly assemblies?: Maybe<ReadonlyArray<Maybe<CoreAssembly>>>;
- /** Get a PDB branched entity, given the PDB ID and ENTITY ID. Here ENTITY ID is a '1', '2', '3', etc. */
- readonly branched_entity?: Maybe<CoreBranchedEntity>;
- /** Get a PDB branched entity instance (chain), given the PDB ID and ENTITY INSTANCE ID. Here ENTITY INSTANCE ID identifies structural element in the asymmetric unit, e.g. 'A', 'B', etc. */
- readonly branched_entity_instance?: Maybe<CoreBranchedEntityInstance>;
- /** Get a PDB non-polymer entity instance (chain), given the PDB ID and ENTITY INSTANCE ID. Here ENTITY INSTANCE ID identifies structural element in the asymmetric unit, e.g. 'A', 'B', etc. */
- readonly nonpolymer_entity_instance?: Maybe<CoreNonpolymerEntityInstance>;
- /** Get a chemical component given the CHEMICAL COMPONENT ID, e.g. 'CFF', 'HEM', 'FE'.For nucleic acid polymer entities, use the one-letter code for the base. */
- readonly chem_comp?: Maybe<CoreChemComp>;
- /** Get PDB entry given the PDB id. */
- readonly entry?: Maybe<CoreEntry>;
- /** Get a list of PDB entries given a list of PDB IDs. */
- readonly entries?: Maybe<ReadonlyArray<Maybe<CoreEntry>>>;
- /** Get a list of PDB branched entities given a list of ENTITY IDs. Here ENTITY ID is a compound identifier that includes entry_id and entity_id separated by '_', e.g. 1XXX_1. */
- readonly branched_entities?: Maybe<ReadonlyArray<Maybe<CoreBranchedEntity>>>;
- /** Get UniProt KB entry given the UniProt primary accession. */
- readonly uniprot?: Maybe<CoreUniprot>;
- /** Get a list of PDB non-polymer entity instances (chains), given the list of ENTITY INSTANCE IDs. Here ENTITY INSTANCE ID identifies structural element in the asymmetric unit, e.g. 'A', 'B', etc. */
- readonly nonpolymer_entity_instances?: Maybe<ReadonlyArray<Maybe<CoreNonpolymerEntityInstance>>>;
- /** Get a PDB non-polymer entity, given the PDB ID and ENTITY ID. Here ENTITY ID is a '1', '2', '3', etc. */
- readonly nonpolymer_entity?: Maybe<CoreNonpolymerEntity>;
-};
-
-
-/** Query root */
-export type QueryPolymer_Entity_InstanceArgs = {
- asym_id: Scalars['String'];
- entry_id: Scalars['String'];
-};
-
-
-/** Query root */
-export type QueryNonpolymer_EntitiesArgs = {
- entity_ids: ReadonlyArray<Scalars['String']>;
-};
-
-
-/** Query root */
-export type QueryPolymer_EntitiesArgs = {
- entity_ids: ReadonlyArray<Scalars['String']>;
-};
-
-
-/** Query root */
-export type QueryPolymer_EntityArgs = {
- entity_id: Scalars['String'];
- entry_id: Scalars['String'];
-};
-
-
-/** Query root */
-export type QueryPubmedArgs = {
- pubmed_id: Scalars['Int'];
-};
-
-
-/** Query root */
-export type QueryAssemblyArgs = {
- assembly_id: Scalars['String'];
- entry_id: Scalars['String'];
-};
-
-
-/** Query root */
-export type QueryBranched_Entity_InstancesArgs = {
- instance_ids: ReadonlyArray<Maybe<Scalars['String']>>;
-};
-
-
-/** Query root */
-export type QueryPolymer_Entity_InstancesArgs = {
- instance_ids: ReadonlyArray<Maybe<Scalars['String']>>;
-};
-
-
-/** Query root */
-export type QueryAssembliesArgs = {
- assembly_ids: ReadonlyArray<Maybe<Scalars['String']>>;
-};
-
-
-/** Query root */
-export type QueryBranched_EntityArgs = {
- entity_id: Scalars['String'];
- entry_id: Scalars['String'];
-};
-
-
-/** Query root */
-export type QueryBranched_Entity_InstanceArgs = {
- asym_id: Scalars['String'];
- entry_id: Scalars['String'];
-};
-
-
-/** Query root */
-export type QueryNonpolymer_Entity_InstanceArgs = {
- asym_id: Scalars['String'];
- entry_id: Scalars['String'];
-};
-
-
-/** Query root */
-export type QueryChem_CompArgs = {
- comp_id: Scalars['String'];
-};
-
-
-/** Query root */
-export type QueryEntryArgs = {
- entry_id: Scalars['String'];
-};
-
-
-/** Query root */
-export type QueryEntriesArgs = {
- entry_ids: ReadonlyArray<Scalars['String']>;
-};
-
-
-/** Query root */
-export type QueryBranched_EntitiesArgs = {
- entity_ids: ReadonlyArray<Scalars['String']>;
-};
-
-
-/** Query root */
-export type QueryUniprotArgs = {
- uniprot_id: Scalars['String'];
-};
-
-
-/** Query root */
-export type QueryNonpolymer_Entity_InstancesArgs = {
- instance_ids: ReadonlyArray<Maybe<Scalars['String']>>;
-};
-
-
-/** Query root */
-export type QueryNonpolymer_EntityArgs = {
- entity_id: Scalars['String'];
- entry_id: Scalars['String'];
-};
-
-export type EntityPoly = {
+export type Citation = {
/**
- * A flag to indicate whether the polymer contains at least
- * one monomer-to-monomer link different from that implied by
- * _entity_poly.type.
- *
- * Allowable values:
- * n, no, y, yes
+ * The International Standard Book Number (ISBN) code assigned to
+ * the book cited; relevant for books or book chapters.
*/
- readonly nstd_linkage?: Maybe<Scalars['String']>;
+ readonly book_id_ISBN?: Maybe<Scalars['String']>;
/**
- * A flag to indicate whether the polymer contains at least
- * one monomer that is not considered standard.
- *
+ * The name of the publisher of the citation; relevant
+ * for books or book chapters.
+ *
+ * Examples:
+ * John Wiley and Sons
+ *
+ */
+ readonly book_publisher?: Maybe<Scalars['String']>;
+ /**
+ * The location of the publisher of the citation; relevant
+ * for books or book chapters.
+ *
+ * Examples:
+ * London
+ *
+ */
+ readonly book_publisher_city?: Maybe<Scalars['String']>;
+ /**
+ * The title of the book in which the citation appeared; relevant
+ * for books or book chapters.
+ */
+ readonly book_title?: Maybe<Scalars['String']>;
+ /**
+ * _citation.coordinate_linkage states whether this citation
+ * is concerned with precisely the set of coordinates given in the
+ * data block. If, for instance, the publication described the same
+ * structure, but the coordinates had undergone further refinement
+ * prior to the creation of the data block, the value of this data
+ * item would be 'no'.
+ *
* Allowable values:
* n, no, y, yes
+ *
*/
- readonly nstd_monomer?: Maybe<Scalars['String']>;
+ readonly coordinate_linkage?: Maybe<Scalars['String']>;
/**
- * Chemical sequence expressed as string of one-letter
- * amino acid codes. Modifications and non-standard
- * amino acids are coded as X.
- *
- * Examples:
- * HHHH(MSE)AKQRSG or AUCGGAAU, A for alanine or adenine
- * B for ambiguous asparagine/aspartic-acid
- * R for arginine
- * N for asparagine
- * D for aspartic-acid
- * C for cysteine or cystine or cytosine
- * Q for glutamine
- * E for glutamic-acid
- * Z for ambiguous glutamine/glutamic acid
- * G for glycine or guanine
- * H for histidine
- * I for isoleucine
- * L for leucine
- * K for lysine
- * M for methionine
- * F for phenylalanine
- * P for proline
- * S for serine
- * T for threonine or thymine
- * W for tryptophan
- * Y for tyrosine
- * V for valine
- * U for uracil
- * O for water
- * X for other
+ * The country/region of publication; relevant for books
+ * and book chapters.
*/
- readonly pdbx_seq_one_letter_code?: Maybe<Scalars['String']>;
+ readonly country?: Maybe<Scalars['String']>;
/**
- * Cannonical chemical sequence expressed as string of
- * one-letter amino acid codes. Modifications are coded
- * as the parent amino acid where possible.
- *
- * A for alanine or adenine
- * B for ambiguous asparagine/aspartic-acid
- * R for arginine
- * N for asparagine
- * D for aspartic-acid
- * C for cysteine or cystine or cytosine
- * Q for glutamine
- * E for glutamic-acid
- * Z for ambiguous glutamine/glutamic acid
- * G for glycine or guanine
- * H for histidine
- * I for isoleucine
- * L for leucine
- * K for lysine
- * M for methionine
- * F for phenylalanine
- * P for proline
- * S for serine
- * T for threonine or thymine
- * W for tryptophan
- * Y for tyrosine
- * V for valine
- * U for uracil
- *
+ * The value of _citation.id must uniquely identify a record in the
+ * CITATION list.
+ *
+ * The _citation.id 'primary' should be used to indicate the
+ * citation that the author(s) consider to be the most pertinent to
+ * the contents of the data block.
+ *
+ * Note that this item need not be a number; it can be any unique
+ * identifier.
+ *
* Examples:
- * MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGAAFNVEFD
+ * primary, 1, 2
+ *
*/
- readonly pdbx_seq_one_letter_code_can?: Maybe<Scalars['String']>;
+ readonly id: Scalars['String'];
/**
- * The PDB strand/chain id(s) corresponding to this polymer entity.
- *
+ * Abbreviated name of the cited journal as given in the
+ * Chemical Abstracts Service Source Index.
+ *
* Examples:
- * A,B, A, B, A,B,C
+ * J.Mol.Biol., J. Mol. Biol.
+ *
*/
- readonly pdbx_strand_id?: Maybe<Scalars['String']>;
+ readonly journal_abbrev?: Maybe<Scalars['String']>;
/**
- * For Structural Genomics entries, the sequence's target identifier registered at the TargetTrack database.
- *
+ * The American Society for Testing and Materials (ASTM) code
+ * assigned to the journal cited (also referred to as the CODEN
+ * designator of the Chemical Abstracts Service); relevant for
+ * journal articles.
+ */
+ readonly journal_id_ASTM?: Maybe<Scalars['String']>;
+ /**
+ * The Cambridge Structural Database (CSD) code assigned to the
+ * journal cited; relevant for journal articles. This is also the
+ * system used at the Protein Data Bank (PDB).
+ *
* Examples:
- * JCSG-11211, 356560
+ * 0070
+ *
*/
- readonly pdbx_target_identifier?: Maybe<Scalars['String']>;
+ readonly journal_id_CSD?: Maybe<Scalars['String']>;
/**
- * Number of regions in the sample sequence identified as expression tags, linkers, or
- * cloning artifacts.
+ * The International Standard Serial Number (ISSN) code assigned to
+ * the journal cited; relevant for journal articles.
*/
- readonly rcsb_artifact_monomer_count?: Maybe<Scalars['Int']>;
- /** Number of monomer conflicts relative to the reference sequence. */
- readonly rcsb_conflict_count?: Maybe<Scalars['Int']>;
- /** Number of monomer deletions relative to the reference sequence. */
- readonly rcsb_deletion_count?: Maybe<Scalars['Int']>;
+ readonly journal_id_ISSN?: Maybe<Scalars['String']>;
/**
- * A coarse-grained polymer entity type.
- *
- * Allowable values:
- * DNA, NA-hybrid, Other, Protein, RNA
+ * Issue number of the journal cited; relevant for journal
+ * articles.
+ *
+ * Examples:
+ * 2
+ *
*/
- readonly rcsb_entity_polymer_type?: Maybe<Scalars['String']>;
- /** Number of monomer insertions relative to the reference sequence. */
- readonly rcsb_insertion_count?: Maybe<Scalars['Int']>;
- /** Number of engineered mutations engineered in the sample sequence. */
- readonly rcsb_mutation_count?: Maybe<Scalars['Int']>;
- /** Number of non-standard monomers in the sample sequence. */
- readonly rcsb_non_std_monomer_count?: Maybe<Scalars['Int']>;
- /** Unique list of non-standard monomer chemical component identifiers in the sample sequence. */
- readonly rcsb_non_std_monomers?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
- /** For polymer BIRD molecules the BIRD identifier for the entity. */
- readonly rcsb_prd_id?: Maybe<Scalars['String']>;
- /** The monomer length of the sample sequence. */
- readonly rcsb_sample_sequence_length?: Maybe<Scalars['Int']>;
+ readonly journal_issue?: Maybe<Scalars['String']>;
/**
- * The type of the polymer.
- *
- * Allowable values:
- * cyclic-pseudo-peptide, other, peptide nucleic acid, polydeoxyribonucleotide, polydeoxyribonucleotide/polyribonucleotide hybrid, polypeptide(D), polypeptide(L), polyribonucleotide
+ * Volume number of the journal cited; relevant for journal
+ * articles.
+ *
+ * Examples:
+ * 174
+ *
*/
- readonly type?: Maybe<Scalars['String']>;
-};
-
-export type CorePolymerEntity = {
- /** Get all unique monomers described in this molecular entity. */
- readonly chem_comp_monomers?: Maybe<ReadonlyArray<Maybe<CoreChemComp>>>;
- /** Get all unique non-standard monomers described in this molecular entity. */
- readonly chem_comp_nstd_monomers?: Maybe<ReadonlyArray<Maybe<CoreChemComp>>>;
- readonly entity_poly?: Maybe<EntityPoly>;
- readonly entity_src_gen?: Maybe<ReadonlyArray<Maybe<EntitySrcGen>>>;
- readonly entity_src_nat?: Maybe<ReadonlyArray<Maybe<EntitySrcNat>>>;
- /** Get PDB entry that contains this molecular entity. */
- readonly entry?: Maybe<CoreEntry>;
- readonly pdbx_entity_src_syn?: Maybe<ReadonlyArray<Maybe<PdbxEntitySrcSyn>>>;
- /** Get all unique Pfam annotations associated with this molecular entity. */
- readonly pfams?: Maybe<ReadonlyArray<Maybe<CorePfam>>>;
- /** Get all unique polymer instances (chains) for this molecular entity. */
- readonly polymer_entity_instances?: Maybe<ReadonlyArray<Maybe<CorePolymerEntityInstance>>>;
- /** Get a BIRD chemical components described in this molecular entity. */
- readonly prd?: Maybe<CoreChemComp>;
- /** Indicates intrinsic flexibility of protein structures determined from structural variations between different depositions and chains in asymmetric units of the same protein in PDB (95% sequence identity). */
- readonly rcsb_cluster_flexibility?: Maybe<RcsbClusterFlexibility>;
- readonly rcsb_cluster_membership?: Maybe<ReadonlyArray<Maybe<RcsbClusterMembership>>>;
- readonly rcsb_entity_host_organism?: Maybe<ReadonlyArray<Maybe<RcsbEntityHostOrganism>>>;
- readonly rcsb_entity_source_organism?: Maybe<ReadonlyArray<Maybe<RcsbEntitySourceOrganism>>>;
- readonly rcsb_genomic_lineage?: Maybe<ReadonlyArray<Maybe<RcsbGenomicLineage>>>;
+ readonly journal_volume?: Maybe<Scalars['String']>;
/**
- * A unique identifier for each object in this entity container formed by
- * an underscore separated concatenation of entry and entity identifiers.
+ * Language in which the cited article is written.
+ *
+ * Examples:
+ * German
+ *
*/
- readonly rcsb_id: Scalars['String'];
- readonly rcsb_latest_revision?: Maybe<RcsbLatestRevision>;
- /** Members of the membrane protein classification lineage. */
- readonly rcsb_membrane_lineage?: Maybe<ReadonlyArray<Maybe<RcsbMembraneLineage>>>;
+ readonly language?: Maybe<Scalars['String']>;
/**
- * Mpstruc keyword denotes original annotation, Homology keyword denotes annotation inferred by homology.
- *
- * Allowable values:
- * Mpstruc, Homology
+ * The first page of the citation; relevant for journal
+ * articles, books and book chapters.
*/
- readonly rcsb_membrane_lineage_provenance_code?: Maybe<Scalars['String']>;
- readonly rcsb_polymer_entity?: Maybe<RcsbPolymerEntity>;
- readonly rcsb_polymer_entity_align?: Maybe<ReadonlyArray<Maybe<RcsbPolymerEntityAlign>>>;
- readonly rcsb_polymer_entity_annotation?: Maybe<ReadonlyArray<Maybe<RcsbPolymerEntityAnnotation>>>;
- readonly rcsb_polymer_entity_container_identifiers: RcsbPolymerEntityContainerIdentifiers;
- readonly rcsb_polymer_entity_feature?: Maybe<ReadonlyArray<Maybe<RcsbPolymerEntityFeature>>>;
- readonly rcsb_polymer_entity_feature_summary?: Maybe<ReadonlyArray<Maybe<RcsbPolymerEntityFeatureSummary>>>;
- readonly rcsb_polymer_entity_keywords?: Maybe<RcsbPolymerEntityKeywords>;
- readonly rcsb_polymer_entity_name_com?: Maybe<ReadonlyArray<Maybe<RcsbPolymerEntityNameCom>>>;
- readonly rcsb_polymer_entity_name_sys?: Maybe<ReadonlyArray<Maybe<RcsbPolymerEntityNameSys>>>;
- /** Get all unique UniProt KB annotations associated with this molecular entity. */
- readonly uniprots?: Maybe<ReadonlyArray<Maybe<CoreUniprot>>>;
-};
-
-export type PdbxSolnScatterModel = {
+ readonly page_first?: Maybe<Scalars['String']>;
/**
- * A description of the conformer selection criteria
- * used.
- *
- * Examples:
- * The modelled scattering curves were assessed by calculation of the
- * RG, RSX-1 and RXS-2 values in the same Q ranges
- * used in the experimental Guinier fits. models were
- * then ranked using a goodness-of-fit R-factor
- * defined by analogy with protein crystallography
- * and based on the experimental curves in the Q range
- * extending to 1.4 nm-1.
+ * The last page of the citation; relevant for journal
+ * articles, books and book chapters.
*/
- readonly conformer_selection_criteria?: Maybe<Scalars['String']>;
+ readonly page_last?: Maybe<Scalars['String']>;
/**
- * A description of any additional details concerning the experiment.
- *
+ * Document Object Identifier used by doi.org to uniquely
+ * specify bibliographic entry.
+ *
* Examples:
- * Homology models were built for
- * the 17 SCR domains and energy minimisations were
- * performed to improve the connectivity in the fh model.
- * triantennary complex-type carbohydrate structures
- * (MAN3GLCNAC6GAL3FUC3NEUNAC1) were added to each of the
- * N-linked glycosylation sites. a library of linker peptide
- * conformations was used in domain modelling constrained
- * by the solution scattering fits. modelling with the
- * scattering data was also carried out by rotational
- * search methods. the x-ray and neutron scattering curve
- * I(Q) was calculated assuming a uniform scattering density
- * for the spheres using the debye equation as adapted to
- * spheres. x-ray curves were calculated from the hydrated
- * sphere models without corrections for wavelength spread or
- * beam divergence, while these corrections were applied for
- * the neutron curves but now using unhydrated models.
+ * 10.2345/S1384107697000225
+ *
*/
- readonly details?: Maybe<Scalars['String']>;
+ readonly pdbx_database_id_DOI?: Maybe<Scalars['String']>;
/**
- * A list of the entries used to fit the model
- * to the scattering data
- *
- * Examples:
- * PDB CODE 1HFI, 1HCC, 1HFH, 1VCC
+ * Ascession number used by PubMed to categorize a specific
+ * bibliographic entry.
*/
- readonly entry_fitting_list?: Maybe<Scalars['String']>;
+ readonly pdbx_database_id_PubMed?: Maybe<Scalars['Int']>;
/**
- * The value of _pdbx_soln_scatter_model.id must
- * uniquely identify the sample in the category PDBX_SOLN_SCATTER_MODEL
+ * Names of the authors of the citation; relevant for journal
+ * articles, books and book chapters. Names are separated by vertical bars.
+ *
+ * The family name(s), followed by a comma and including any
+ * dynastic components, precedes the first name(s) or initial(s).
*/
- readonly id: Scalars['String'];
+ readonly rcsb_authors?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
/**
- * A description of the methods used in the modelling
- *
- * Examples:
- * Constrained scattering fitting of homology models
+ * Flag to indicate a primary citation.
+ *
+ * Allowable values:
+ * N, Y
+ *
*/
- readonly method?: Maybe<Scalars['String']>;
- /** The number of model conformers calculated. */
- readonly num_conformers_calculated?: Maybe<Scalars['Int']>;
- /** The number of model conformers submitted in the entry */
- readonly num_conformers_submitted?: Maybe<Scalars['Int']>;
- /** The index of the representative conformer among the submitted conformers for the entry */
- readonly representative_conformer?: Maybe<Scalars['Int']>;
- /** This data item is a pointer to _pdbx_soln_scatter.id in the PDBX_SOLN_SCATTER category. */
- readonly scatter_id: Scalars['String'];
+ readonly rcsb_is_primary?: Maybe<Scalars['String']>;
/**
- * A list of the software authors
- *
+ * Normalized journal abbreviation.
+ *
* Examples:
- * MSI
+ * Nat Struct Mol Biol
+ *
*/
- readonly software_author_list?: Maybe<Scalars['String']>;
+ readonly rcsb_journal_abbrev?: Maybe<Scalars['String']>;
/**
- * A list of the software used in the modeeling
- *
+ * The title of the citation; relevant for journal articles, books
+ * and book chapters.
+ *
* Examples:
- * INSIGHT II, HOMOLOGY, DISCOVERY, BIOPOLYMER, DELPHI
+ * Structure of diferric duck ovotransferrin
+ * at 2.35 Angstroms resolution.
+ *
*/
- readonly software_list?: Maybe<Scalars['String']>;
-};
-
-export type RcsbUniprotFeature = {
- /** Identifies the version of the feature assignment. */
- readonly assignment_version?: Maybe<Scalars['String']>;
- /** A description for the feature. */
- readonly description?: Maybe<Scalars['String']>;
- /** An identifier for the feature. */
- readonly feature_id?: Maybe<Scalars['String']>;
- readonly feature_positions?: Maybe<ReadonlyArray<Maybe<RcsbUniprotFeatureFeaturePositions>>>;
- /** A name for the feature. */
- readonly name?: Maybe<Scalars['String']>;
+ readonly title?: Maybe<Scalars['String']>;
/**
- * Code identifying the individual, organization or program that
- * assigned the feature.
+ * Flag to indicate that this citation will not be published.
+ *
+ * Allowable values:
+ * N, Y
+ *
*/
- readonly provenance_source?: Maybe<Scalars['String']>;
- /** Code residue coordinate system for the assigned feature. */
- readonly reference_scheme?: Maybe<Scalars['String']>;
+ readonly unpublished_flag?: Maybe<Scalars['String']>;
/**
- * A type or category of the feature.
- *
- * Allowable values:
- * ACTIVE_SITE, BINDING_SITE, CALCIUM_BINDING_REGION, CHAIN, COMPOSITIONALLY_BIASED_REGION, CROSS_LINK, DNA_BINDING_REGION, DOMAIN, GLYCOSYLATION_SITE, INITIATOR_METHIONINE, LIPID_MOIETY_BINDING_REGION, METAL_ION_BINDING_SITE, MODIFIED_RESIDUE, MUTAGENESIS_SITE, NON_CONSECUTIVE_RESIDUES, NON_TERMINAL_RESIDUE, NUCLEOTIDE_PHOSPHATE_BINDING_REGION, PEPTIDE, PROPEPTIDE, REGION_OF_INTEREST, REPEAT, NON_STANDARD_AMINO_ACID, SEQUENCE_CONFLICT, SEQUENCE_VARIANT, SHORT_SEQUENCE_MOTIF, SIGNAL_PEPTIDE, SITE, SPLICE_VARIANT, TOPOLOGICAL_DOMAIN, TRANSIT_PEPTIDE, TRANSMEMBRANE_REGION, UNSURE_RESIDUE, ZINC_FINGER_REGION, INTRAMEMBRANE_REGION
+ * The year of the citation; relevant for journal articles, books
+ * and book chapters.
*/
- readonly type?: Maybe<Scalars['String']>;
+ readonly year?: Maybe<Scalars['Int']>;
};
-export type Em3dFittingList = {
- /**
- * The value of _em_3d_fitting_list.3d_fitting_id is a pointer
- * to _em_3d_fitting.id in the 3d_fitting category
- */
- readonly _3d_fitting_id: Scalars['String'];
- /** Details about the model used in fitting. */
- readonly details?: Maybe<Scalars['String']>;
- /** This data item is a unique identifier. */
- readonly id: Scalars['String'];
- /**
- * The ID of the biopolymer chain used for fitting, e.g., A. Please note that
- * only one chain can be specified per instance. If all chains of a particular
- * structure have been used for fitting, this field can be left blank.
- */
- readonly pdb_chain_id?: Maybe<Scalars['String']>;
- /** The molecular entities represented in this fitting description. */
- readonly pdb_chain_residue_range?: Maybe<Scalars['String']>;
+export type ClustersMembers = {
+ /** Internal chain ID used in mmCIF files to uniquely identify structural elements in the asymmetric unit. */
+ readonly asym_id: Scalars['String'];
+ /** Optional list of operator ids (pdbx_struct_oper_list.id) as appears in pdbx_struct_assembly_gen.oper_expression. One operator id per operand in the expression (most cases have only 1 operator). If it's not given then identity operator is assumed. */
+ readonly pdbx_struct_oper_list_ids?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
+};
+
+export type CoreAssembly = {
+ /** Get PDB entry that includes this assembly. */
+ readonly entry?: Maybe<CoreEntry>;
+ readonly pdbx_struct_assembly?: Maybe<PdbxStructAssembly>;
+ readonly pdbx_struct_assembly_auth_evidence?: Maybe<ReadonlyArray<Maybe<PdbxStructAssemblyAuthEvidence>>>;
+ readonly pdbx_struct_assembly_gen?: Maybe<ReadonlyArray<Maybe<PdbxStructAssemblyGen>>>;
+ readonly pdbx_struct_assembly_prop?: Maybe<ReadonlyArray<Maybe<PdbxStructAssemblyProp>>>;
+ readonly pdbx_struct_oper_list?: Maybe<ReadonlyArray<Maybe<PdbxStructOperList>>>;
+ readonly rcsb_assembly_container_identifiers: RcsbAssemblyContainerIdentifiers;
+ readonly rcsb_assembly_info?: Maybe<RcsbAssemblyInfo>;
/**
- * The PDB code for the entry used in fitting.
- *
+ * A unique identifier for each object in this assembly container formed by
+ * a dash separated concatenation of entry and assembly identifiers.
+ *
* Examples:
- * PDB entry 1EHZ
+ * 1KIP-1
+ *
*/
- readonly pdb_entry_id?: Maybe<Scalars['String']>;
+ readonly rcsb_id: Scalars['String'];
+ readonly rcsb_latest_revision?: Maybe<RcsbLatestRevision>;
+ readonly rcsb_struct_symmetry?: Maybe<ReadonlyArray<Maybe<RcsbStructSymmetry>>>;
+ readonly rcsb_struct_symmetry_lineage?: Maybe<ReadonlyArray<Maybe<RcsbStructSymmetryLineage>>>;
+ /** The title and version of software package used for symmetry calculations. */
+ readonly rcsb_struct_symmetry_provenance_code?: Maybe<Scalars['String']>;
};
-export type EmDiffraction = {
+export type CoreBranchedEntity = {
+ /** Get all unique branched instances (chains) for this molecular entity. */
+ readonly branched_entity_instances?: Maybe<ReadonlyArray<Maybe<CoreBranchedEntityInstance>>>;
+ /** Get all unique monomers described in this branched entity. */
+ readonly chem_comp_monomers?: Maybe<ReadonlyArray<Maybe<CoreChemComp>>>;
+ /** Get PDB entry that contains this branched entity. */
+ readonly entry?: Maybe<CoreEntry>;
+ readonly pdbx_entity_branch?: Maybe<PdbxEntityBranch>;
+ readonly pdbx_entity_branch_descriptor?: Maybe<ReadonlyArray<Maybe<PdbxEntityBranchDescriptor>>>;
+ /** Get a BIRD chemical components described in this branched entity. */
+ readonly prd?: Maybe<CoreChemComp>;
+ readonly rcsb_branched_entity?: Maybe<RcsbBranchedEntity>;
+ readonly rcsb_branched_entity_annotation?: Maybe<ReadonlyArray<Maybe<RcsbBranchedEntityAnnotation>>>;
+ readonly rcsb_branched_entity_container_identifiers?: Maybe<RcsbBranchedEntityContainerIdentifiers>;
+ readonly rcsb_branched_entity_feature?: Maybe<ReadonlyArray<Maybe<RcsbBranchedEntityFeature>>>;
+ readonly rcsb_branched_entity_feature_summary?: Maybe<ReadonlyArray<Maybe<RcsbBranchedEntityFeatureSummary>>>;
+ readonly rcsb_branched_entity_keywords?: Maybe<RcsbBranchedEntityKeywords>;
+ readonly rcsb_branched_entity_name_com?: Maybe<RcsbBranchedEntityNameCom>;
+ readonly rcsb_branched_entity_name_sys?: Maybe<ReadonlyArray<Maybe<RcsbBranchedEntityNameSys>>>;
/**
- * TODO
- *
+ * A unique identifier for each object in this entity container formed by
+ * an underscore separated concatenation of entry and entity identifiers.
+ *
* Examples:
- * 800
+ * 2HYV_2
+ *
*/
- readonly camera_length?: Maybe<Scalars['Float']>;
- /** Primary key */
- readonly id: Scalars['String'];
- /** Foreign key to the EM_IMAGING category */
- readonly imaging_id?: Maybe<Scalars['String']>;
+ readonly rcsb_id: Scalars['String'];
+ readonly rcsb_latest_revision?: Maybe<RcsbLatestRevision>;
+};
+
+export type CoreBranchedEntityInstance = {
+ /** Get branched entity for this branched entity instance. */
+ readonly branched_entity?: Maybe<CoreBranchedEntity>;
+ readonly pdbx_struct_special_symmetry?: Maybe<ReadonlyArray<Maybe<PdbxStructSpecialSymmetry>>>;
+ readonly rcsb_branched_entity_instance_container_identifiers?: Maybe<RcsbBranchedEntityInstanceContainerIdentifiers>;
+ readonly rcsb_branched_instance_annotation?: Maybe<ReadonlyArray<Maybe<RcsbBranchedInstanceAnnotation>>>;
+ readonly rcsb_branched_instance_feature?: Maybe<ReadonlyArray<Maybe<RcsbBranchedInstanceFeature>>>;
+ readonly rcsb_branched_instance_feature_summary?: Maybe<ReadonlyArray<Maybe<RcsbBranchedInstanceFeatureSummary>>>;
+ readonly rcsb_branched_struct_conn?: Maybe<ReadonlyArray<Maybe<RcsbBranchedStructConn>>>;
/**
- * Comma-separated list of tilt angles (in degrees) used in the electron diffraction experiment.
- *
+ * A unique identifier for each object in this entity instance container formed by
+ * an 'dot' (.) separated concatenation of entry and entity instance identifiers.
+ *
* Examples:
- * 20,40,50,55
+ * 1KIP.A
+ *
*/
- readonly tilt_angle_list?: Maybe<Scalars['String']>;
+ readonly rcsb_id: Scalars['String'];
+ readonly rcsb_latest_revision?: Maybe<RcsbLatestRevision>;
+ readonly rcsb_ligand_neighbors?: Maybe<ReadonlyArray<Maybe<RcsbLigandNeighbors>>>;
};
-export type RcsbChemCompRelated = {
- /**
- * The value of _rcsb_chem_comp_related.comp_id is a reference to
- * a chemical component definition.
- */
- readonly comp_id: Scalars['String'];
- /**
- * The value of _rcsb_chem_comp_related.ordinal distinguishes
- * related examples for each chemical component.
- */
- readonly ordinal: Scalars['Int'];
- /**
- * The method used to establish the resource correspondence.
- *
- * Allowable values:
- * assigned by DrugBank resource, assigned by PDB, assigned by PubChem resource, matching ChEMBL ID in Pharos, matching InChIKey in DrugBank, matching InChIKey in PubChem, matching InChIKey-prefix in DrugBank, matching by RESID resource
- */
- readonly related_mapping_method?: Maybe<Scalars['String']>;
+export type CoreChemComp = {
+ readonly chem_comp?: Maybe<ChemComp>;
+ /** Get DrubBank entry associated with this chemical component. */
+ readonly drugbank?: Maybe<CoreDrugbank>;
+ readonly pdbx_chem_comp_audit?: Maybe<ReadonlyArray<Maybe<PdbxChemCompAudit>>>;
+ readonly pdbx_chem_comp_descriptor?: Maybe<ReadonlyArray<Maybe<PdbxChemCompDescriptor>>>;
+ readonly pdbx_chem_comp_feature?: Maybe<ReadonlyArray<Maybe<PdbxChemCompFeature>>>;
+ readonly pdbx_chem_comp_identifier?: Maybe<ReadonlyArray<Maybe<PdbxChemCompIdentifier>>>;
+ readonly pdbx_family_prd_audit?: Maybe<ReadonlyArray<Maybe<PdbxFamilyPrdAudit>>>;
+ readonly pdbx_prd_audit?: Maybe<ReadonlyArray<Maybe<PdbxPrdAudit>>>;
+ readonly pdbx_reference_entity_list?: Maybe<ReadonlyArray<Maybe<PdbxReferenceEntityList>>>;
+ readonly pdbx_reference_entity_poly?: Maybe<ReadonlyArray<Maybe<PdbxReferenceEntityPoly>>>;
+ readonly pdbx_reference_entity_poly_link?: Maybe<ReadonlyArray<Maybe<PdbxReferenceEntityPolyLink>>>;
+ readonly pdbx_reference_entity_poly_seq?: Maybe<ReadonlyArray<Maybe<PdbxReferenceEntityPolySeq>>>;
+ readonly pdbx_reference_entity_sequence?: Maybe<ReadonlyArray<Maybe<PdbxReferenceEntitySequence>>>;
+ readonly pdbx_reference_entity_src_nat?: Maybe<ReadonlyArray<Maybe<PdbxReferenceEntitySrcNat>>>;
+ readonly pdbx_reference_molecule?: Maybe<PdbxReferenceMolecule>;
+ readonly pdbx_reference_molecule_annotation?: Maybe<ReadonlyArray<Maybe<PdbxReferenceMoleculeAnnotation>>>;
+ readonly pdbx_reference_molecule_details?: Maybe<ReadonlyArray<Maybe<PdbxReferenceMoleculeDetails>>>;
+ readonly pdbx_reference_molecule_family?: Maybe<PdbxReferenceMoleculeFamily>;
+ readonly pdbx_reference_molecule_features?: Maybe<ReadonlyArray<Maybe<PdbxReferenceMoleculeFeatures>>>;
+ readonly pdbx_reference_molecule_list?: Maybe<ReadonlyArray<Maybe<PdbxReferenceMoleculeList>>>;
+ readonly pdbx_reference_molecule_related_structures?: Maybe<ReadonlyArray<Maybe<PdbxReferenceMoleculeRelatedStructures>>>;
+ readonly pdbx_reference_molecule_synonyms?: Maybe<ReadonlyArray<Maybe<PdbxReferenceMoleculeSynonyms>>>;
+ readonly rcsb_bird_citation?: Maybe<ReadonlyArray<Maybe<RcsbBirdCitation>>>;
+ readonly rcsb_chem_comp_annotation?: Maybe<ReadonlyArray<Maybe<RcsbChemCompAnnotation>>>;
+ readonly rcsb_chem_comp_container_identifiers?: Maybe<RcsbChemCompContainerIdentifiers>;
+ readonly rcsb_chem_comp_descriptor?: Maybe<RcsbChemCompDescriptor>;
+ readonly rcsb_chem_comp_info?: Maybe<RcsbChemCompInfo>;
+ readonly rcsb_chem_comp_related?: Maybe<ReadonlyArray<Maybe<RcsbChemCompRelated>>>;
+ readonly rcsb_chem_comp_synonyms?: Maybe<ReadonlyArray<Maybe<RcsbChemCompSynonyms>>>;
+ readonly rcsb_chem_comp_target?: Maybe<ReadonlyArray<Maybe<RcsbChemCompTarget>>>;
/**
- * The resource identifier code for the related chemical reference.
- *
+ * A unique identifier for the chemical definition in this container.
+ *
* Examples:
- * 124832
+ * ATP, PRD_000010
+ *
*/
- readonly resource_accession_code?: Maybe<Scalars['String']>;
+ readonly rcsb_id: Scalars['String'];
+ readonly rcsb_schema_container_identifiers?: Maybe<ReadonlyArray<Maybe<RcsbSchemaContainerIdentifiers>>>;
+};
+
+export type CoreDrugbank = {
+ readonly drugbank_container_identifiers?: Maybe<DrugbankContainerIdentifiers>;
+ readonly drugbank_info?: Maybe<DrugbankInfo>;
+ readonly drugbank_target?: Maybe<ReadonlyArray<Maybe<DrugbankTarget>>>;
+};
+
+export type CoreEntityAlignmentsAlignedRegions = {
+ /** Aligned region length */
+ readonly length: Scalars['Int'];
+ /** Entity seqeunce start position */
+ readonly query_begin: Scalars['Int'];
+ /** NCBI sequence start position */
+ readonly target_begin: Scalars['Int'];
+};
+
+export type CoreEntityAlignmentsCoreEntityIdentifiers = {
+ readonly entity_id: Scalars['String'];
+ readonly entry_id: Scalars['String'];
+};
+
+export type CoreEntityAlignmentsScores = {
+ readonly query_coverage: Scalars['Int'];
+ readonly query_length: Scalars['Int'];
+ readonly target_coverage: Scalars['Int'];
+ readonly target_length: Scalars['Int'];
+};
+
+export type CoreEntry = {
+ /** Get all assemblies for this PDB entry. */
+ readonly assemblies?: Maybe<ReadonlyArray<Maybe<CoreAssembly>>>;
+ readonly audit_author?: Maybe<ReadonlyArray<Maybe<AuditAuthor>>>;
+ /** Get all branched entities for this PDB entry. */
+ readonly branched_entities?: Maybe<ReadonlyArray<Maybe<CoreBranchedEntity>>>;
+ readonly cell?: Maybe<Cell>;
+ readonly citation?: Maybe<ReadonlyArray<Maybe<Citation>>>;
+ readonly diffrn?: Maybe<ReadonlyArray<Maybe<Diffrn>>>;
+ readonly diffrn_detector?: Maybe<ReadonlyArray<Maybe<DiffrnDetector>>>;
+ readonly diffrn_radiation?: Maybe<ReadonlyArray<Maybe<DiffrnRadiation>>>;
+ readonly diffrn_source?: Maybe<ReadonlyArray<Maybe<DiffrnSource>>>;
+ readonly em_2d_crystal_entity?: Maybe<ReadonlyArray<Maybe<Em2dCrystalEntity>>>;
+ readonly em_3d_crystal_entity?: Maybe<ReadonlyArray<Maybe<Em3dCrystalEntity>>>;
+ readonly em_3d_fitting?: Maybe<ReadonlyArray<Maybe<Em3dFitting>>>;
+ readonly em_3d_fitting_list?: Maybe<ReadonlyArray<Maybe<Em3dFittingList>>>;
+ readonly em_3d_reconstruction?: Maybe<ReadonlyArray<Maybe<Em3dReconstruction>>>;
+ readonly em_ctf_correction?: Maybe<ReadonlyArray<Maybe<EmCtfCorrection>>>;
+ readonly em_diffraction?: Maybe<ReadonlyArray<Maybe<EmDiffraction>>>;
+ readonly em_diffraction_shell?: Maybe<ReadonlyArray<Maybe<EmDiffractionShell>>>;
+ readonly em_diffraction_stats?: Maybe<ReadonlyArray<Maybe<EmDiffractionStats>>>;
+ readonly em_embedding?: Maybe<ReadonlyArray<Maybe<EmEmbedding>>>;
+ readonly em_entity_assembly?: Maybe<ReadonlyArray<Maybe<EmEntityAssembly>>>;
+ readonly em_experiment?: Maybe<EmExperiment>;
+ readonly em_helical_entity?: Maybe<ReadonlyArray<Maybe<EmHelicalEntity>>>;
+ readonly em_image_recording?: Maybe<ReadonlyArray<Maybe<EmImageRecording>>>;
+ readonly em_imaging?: Maybe<ReadonlyArray<Maybe<EmImaging>>>;
+ readonly em_particle_selection?: Maybe<ReadonlyArray<Maybe<EmParticleSelection>>>;
+ readonly em_single_particle_entity?: Maybe<ReadonlyArray<Maybe<EmSingleParticleEntity>>>;
+ readonly em_software?: Maybe<ReadonlyArray<Maybe<EmSoftware>>>;
+ readonly em_specimen?: Maybe<ReadonlyArray<Maybe<EmSpecimen>>>;
+ readonly em_staining?: Maybe<ReadonlyArray<Maybe<EmStaining>>>;
+ readonly em_vitrification?: Maybe<ReadonlyArray<Maybe<EmVitrification>>>;
+ readonly entry?: Maybe<Entry>;
+ readonly exptl?: Maybe<ReadonlyArray<Maybe<Exptl>>>;
+ readonly exptl_crystal?: Maybe<ReadonlyArray<Maybe<ExptlCrystal>>>;
+ readonly exptl_crystal_grow?: Maybe<ReadonlyArray<Maybe<ExptlCrystalGrow>>>;
+ /** Get all non-polymer (non-solvent) entities for this PDB entry. */
+ readonly nonpolymer_entities?: Maybe<ReadonlyArray<Maybe<CoreNonpolymerEntity>>>;
+ readonly pdbx_SG_project?: Maybe<ReadonlyArray<Maybe<PdbxSgProject>>>;
+ readonly pdbx_audit_revision_category?: Maybe<ReadonlyArray<Maybe<PdbxAuditRevisionCategory>>>;
+ readonly pdbx_audit_revision_details?: Maybe<ReadonlyArray<Maybe<PdbxAuditRevisionDetails>>>;
+ readonly pdbx_audit_revision_group?: Maybe<ReadonlyArray<Maybe<PdbxAuditRevisionGroup>>>;
+ readonly pdbx_audit_revision_history?: Maybe<ReadonlyArray<Maybe<PdbxAuditRevisionHistory>>>;
+ readonly pdbx_audit_revision_item?: Maybe<ReadonlyArray<Maybe<PdbxAuditRevisionItem>>>;
+ readonly pdbx_audit_support?: Maybe<ReadonlyArray<Maybe<PdbxAuditSupport>>>;
+ readonly pdbx_database_PDB_obs_spr?: Maybe<ReadonlyArray<Maybe<PdbxDatabasePdbObsSpr>>>;
+ readonly pdbx_database_related?: Maybe<ReadonlyArray<Maybe<PdbxDatabaseRelated>>>;
+ readonly pdbx_database_status?: Maybe<PdbxDatabaseStatus>;
+ readonly pdbx_deposit_group?: Maybe<ReadonlyArray<Maybe<PdbxDepositGroup>>>;
+ readonly pdbx_molecule_features?: Maybe<ReadonlyArray<Maybe<PdbxMoleculeFeatures>>>;
+ readonly pdbx_nmr_details?: Maybe<PdbxNmrDetails>;
+ readonly pdbx_nmr_ensemble?: Maybe<PdbxNmrEnsemble>;
+ readonly pdbx_nmr_exptl?: Maybe<ReadonlyArray<Maybe<PdbxNmrExptl>>>;
+ readonly pdbx_nmr_exptl_sample_conditions?: Maybe<ReadonlyArray<Maybe<PdbxNmrExptlSampleConditions>>>;
+ readonly pdbx_nmr_refine?: Maybe<ReadonlyArray<Maybe<PdbxNmrRefine>>>;
+ readonly pdbx_nmr_representative?: Maybe<PdbxNmrRepresentative>;
+ readonly pdbx_nmr_sample_details?: Maybe<ReadonlyArray<Maybe<PdbxNmrSampleDetails>>>;
+ readonly pdbx_nmr_software?: Maybe<ReadonlyArray<Maybe<PdbxNmrSoftware>>>;
+ readonly pdbx_nmr_spectrometer?: Maybe<ReadonlyArray<Maybe<PdbxNmrSpectrometer>>>;
+ readonly pdbx_related_exp_data_set?: Maybe<ReadonlyArray<Maybe<PdbxRelatedExpDataSet>>>;
+ readonly pdbx_serial_crystallography_data_reduction?: Maybe<ReadonlyArray<Maybe<PdbxSerialCrystallographyDataReduction>>>;
+ readonly pdbx_serial_crystallography_measurement?: Maybe<ReadonlyArray<Maybe<PdbxSerialCrystallographyMeasurement>>>;
+ readonly pdbx_serial_crystallography_sample_delivery?: Maybe<ReadonlyArray<Maybe<PdbxSerialCrystallographySampleDelivery>>>;
+ readonly pdbx_serial_crystallography_sample_delivery_fixed_target?: Maybe<ReadonlyArray<Maybe<PdbxSerialCrystallographySampleDeliveryFixedTarget>>>;
+ readonly pdbx_serial_crystallography_sample_delivery_injection?: Maybe<ReadonlyArray<Maybe<PdbxSerialCrystallographySampleDeliveryInjection>>>;
+ readonly pdbx_soln_scatter?: Maybe<ReadonlyArray<Maybe<PdbxSolnScatter>>>;
+ readonly pdbx_soln_scatter_model?: Maybe<ReadonlyArray<Maybe<PdbxSolnScatterModel>>>;
+ readonly pdbx_vrpt_summary?: Maybe<PdbxVrptSummary>;
+ /** Get all polymer entities for this PDB entry. */
+ readonly polymer_entities?: Maybe<ReadonlyArray<Maybe<CorePolymerEntity>>>;
+ /** Get literature information from PubMed database. */
+ readonly pubmed?: Maybe<CorePubmed>;
+ readonly rcsb_accession_info?: Maybe<RcsbAccessionInfo>;
+ /** The list of content types associated with this entry. */
+ readonly rcsb_associated_holdings?: Maybe<CurrentEntry>;
+ readonly rcsb_binding_affinity?: Maybe<ReadonlyArray<Maybe<RcsbBindingAffinity>>>;
+ readonly rcsb_entry_container_identifiers: RcsbEntryContainerIdentifiers;
+ readonly rcsb_entry_info: RcsbEntryInfo;
+ readonly rcsb_external_references?: Maybe<ReadonlyArray<Maybe<RcsbExternalReferences>>>;
/**
- * The resource name for the related chemical reference.
- *
- * Allowable values:
- * CAS, CCDC/CSD, ChEBI, ChEMBL, DrugBank, Pharos, PubChem, RESID
+ * A unique identifier for each object in this entry container.
+ *
+ * Examples:
+ * 1KIP
+ *
*/
- readonly resource_name?: Maybe<Scalars['String']>;
+ readonly rcsb_id: Scalars['String'];
+ readonly rcsb_primary_citation?: Maybe<RcsbPrimaryCitation>;
+ readonly refine?: Maybe<ReadonlyArray<Maybe<Refine>>>;
+ readonly refine_analyze?: Maybe<ReadonlyArray<Maybe<RefineAnalyze>>>;
+ readonly refine_hist?: Maybe<ReadonlyArray<Maybe<RefineHist>>>;
+ readonly refine_ls_restr?: Maybe<ReadonlyArray<Maybe<RefineLsRestr>>>;
+ readonly reflns?: Maybe<ReadonlyArray<Maybe<Reflns>>>;
+ readonly reflns_shell?: Maybe<ReadonlyArray<Maybe<ReflnsShell>>>;
+ readonly software?: Maybe<ReadonlyArray<Maybe<Software>>>;
+ readonly struct?: Maybe<Struct>;
+ readonly struct_keywords?: Maybe<StructKeywords>;
+ readonly symmetry?: Maybe<Symmetry>;
};
-export type PdbxNmrSpectrometer = {
- /** A text description of the NMR spectrometer. */
- readonly details?: Maybe<Scalars['String']>;
+export type CoreNonpolymerEntity = {
+ /** Get PDB entry that contains this non-polymer entity. */
+ readonly entry?: Maybe<CoreEntry>;
+ /** Get a non-polymer chemical components described in this molecular entity. */
+ readonly nonpolymer_comp?: Maybe<CoreChemComp>;
+ /** Get all unique non-polymer instances (chains) for this non-polymer entity. */
+ readonly nonpolymer_entity_instances?: Maybe<ReadonlyArray<Maybe<CoreNonpolymerEntityInstance>>>;
+ readonly pdbx_entity_nonpoly?: Maybe<PdbxEntityNonpoly>;
+ /** Get a BIRD chemical components described in this molecular entity. */
+ readonly prd?: Maybe<CoreChemComp>;
/**
- * Select the field strength for protons in MHz.
- *
+ * A unique identifier for each object in this entity container formed by
+ * an underscore separated concatenation of entry and entity identifiers.
+ *
* Examples:
- * 360, 400, 500, 600, 750, 800, 850, 900, 950, 1000
+ * 6EL3_1
+ *
*/
- readonly field_strength?: Maybe<Scalars['Float']>;
+ readonly rcsb_id: Scalars['String'];
+ readonly rcsb_latest_revision?: Maybe<RcsbLatestRevision>;
+ readonly rcsb_nonpolymer_entity?: Maybe<RcsbNonpolymerEntity>;
+ readonly rcsb_nonpolymer_entity_annotation?: Maybe<ReadonlyArray<Maybe<RcsbNonpolymerEntityAnnotation>>>;
+ readonly rcsb_nonpolymer_entity_container_identifiers?: Maybe<RcsbNonpolymerEntityContainerIdentifiers>;
+ readonly rcsb_nonpolymer_entity_feature?: Maybe<ReadonlyArray<Maybe<RcsbNonpolymerEntityFeature>>>;
+ readonly rcsb_nonpolymer_entity_feature_summary?: Maybe<ReadonlyArray<Maybe<RcsbNonpolymerEntityFeatureSummary>>>;
+ readonly rcsb_nonpolymer_entity_keywords?: Maybe<RcsbNonpolymerEntityKeywords>;
+ readonly rcsb_nonpolymer_entity_name_com?: Maybe<ReadonlyArray<Maybe<RcsbNonpolymerEntityNameCom>>>;
+};
+
+export type CoreNonpolymerEntityInstance = {
+ /** Get non-polymer entity for this non-polymer entity instance. */
+ readonly nonpolymer_entity?: Maybe<CoreNonpolymerEntity>;
+ readonly pdbx_struct_special_symmetry?: Maybe<ReadonlyArray<Maybe<PdbxStructSpecialSymmetry>>>;
/**
- * The name of the manufacturer of the spectrometer.
- *
+ * A unique identifier for each object in this entity instance container formed by
+ * an 'dot' (.) separated concatenation of entry and entity instance identifiers.
+ *
* Examples:
- * Varian, Bruker, JEOL, GE
+ * 1KIP.A
+ *
*/
- readonly manufacturer?: Maybe<Scalars['String']>;
+ readonly rcsb_id: Scalars['String'];
+ readonly rcsb_latest_revision?: Maybe<RcsbLatestRevision>;
+ readonly rcsb_nonpolymer_entity_instance_container_identifiers?: Maybe<RcsbNonpolymerEntityInstanceContainerIdentifiers>;
+ readonly rcsb_nonpolymer_instance_annotation?: Maybe<ReadonlyArray<Maybe<RcsbNonpolymerInstanceAnnotation>>>;
+ readonly rcsb_nonpolymer_instance_feature?: Maybe<ReadonlyArray<Maybe<RcsbNonpolymerInstanceFeature>>>;
+ readonly rcsb_nonpolymer_instance_feature_summary?: Maybe<ReadonlyArray<Maybe<RcsbNonpolymerInstanceFeatureSummary>>>;
+ readonly rcsb_nonpolymer_instance_validation_score?: Maybe<ReadonlyArray<Maybe<RcsbNonpolymerInstanceValidationScore>>>;
+ readonly rcsb_nonpolymer_struct_conn?: Maybe<ReadonlyArray<Maybe<RcsbNonpolymerStructConn>>>;
+ readonly rcsb_target_neighbors?: Maybe<ReadonlyArray<Maybe<RcsbTargetNeighbors>>>;
+};
+
+export type CorePfam = {
+ /** Accession number of Pfam entry. */
+ readonly rcsb_id: Scalars['String'];
/**
- * The model of the NMR spectrometer.
- *
+ * The unique accession code of protein families and domains in the Pfam database.
+ *
* Examples:
- * AVANCE, AVANCE II, AVANCE III, AVANCE III HD, WH, WM, AM, AMX, DMX, DRX, MSL, OMEGA, OMEGA PSG, GX, GSX, A, AL, EC, EX, LA, ECP, VXRS, UNITY, UNITYPLUS, INOVA
+ * PF00621, PF00637, PF00656
+ *
*/
- readonly model?: Maybe<Scalars['String']>;
+ readonly rcsb_pfam_accession: Scalars['String'];
+ /** Details of the Pfam clan to which the entity belongs. */
+ readonly rcsb_pfam_clan_id?: Maybe<Scalars['String']>;
+ /** Textual description of the family. */
+ readonly rcsb_pfam_comment?: Maybe<Scalars['String']>;
+ readonly rcsb_pfam_container_identifiers: RcsbPfamContainerIdentifiers;
/**
- * Assign a numerical ID to each instrument.
- *
+ * A human-readable name of protein families and domains.
+ *
* Examples:
- * 1, 2, 3
+ * Lectin like domain, Cell division control protein 24, OB domain 2, Protein of unknown function (DUF722)
+ *
*/
- readonly spectrometer_id: Scalars['String'];
+ readonly rcsb_pfam_description?: Maybe<Scalars['String']>;
/**
- * Select the instrument manufacturer(s) and the model(s) of the NMR(s)
- * used for this work.
- *
+ * The unique identifier of protein families and domains in the Pfam database.
+ *
* Examples:
- * Bruker WH, Bruker WM, Bruker AM, Bruker AMX, Bruker DMX, Bruker DRX, Bruker MSL, Bruker AVANCE, GE Omega, GE Omega PSG, JEOL GX, JEOL GSX, JEOL A, JEOL AL, JEOL EC, JEOL EX, JEOL LA, JEOL ECP, Varian VXRS, Varian UNITY, Varian UNITYplus, Varian INOVA, other
+ * RhoGEF, Clathrin, Peptidase_C14
+ *
*/
- readonly type?: Maybe<Scalars['String']>;
-};
-
-export type PdbxAuditRevisionHistory = {
+ readonly rcsb_pfam_identifier?: Maybe<Scalars['String']>;
/**
- * The type of file that the pdbx_audit_revision_history record refers to.
- *
+ * Pfam-A is the manually curated portion of the Pfam database.
+ *
* Allowable values:
- * Chemical component, NMR restraints, NMR shifts, Structure factors, Structure model
- */
- readonly data_content_type: Scalars['String'];
- /**
- * The major version number of deposition release.
- *
- * Examples:
- * 1
+ * Pfam-A
+ *
*/
- readonly major_revision?: Maybe<Scalars['Int']>;
+ readonly rcsb_pfam_provenance_code?: Maybe<Scalars['String']>;
/**
- * The minor version number of deposition release.
- *
- * Examples:
- * 1
+ * Pfam entries are classified into six different categories, depending on the length and nature of the sequence regions included in the entry: family, domain, repeats, motifs, coiled-coil, and disordered.
+ *
+ * Allowable values:
+ * Family, Domain, Repeat, Motif, Disordered, Coiled-coil
+ *
*/
- readonly minor_revision?: Maybe<Scalars['Int']>;
- /**
- * A unique identifier for the pdbx_audit_revision_history record.
- *
+ readonly rcsb_pfam_seed_source?: Maybe<Scalars['String']>;
+};
+
+export type CorePolymerEntity = {
+ /** Get all unique monomers described in this molecular entity. */
+ readonly chem_comp_monomers?: Maybe<ReadonlyArray<Maybe<CoreChemComp>>>;
+ /** Get all unique non-standard monomers described in this molecular entity. */
+ readonly chem_comp_nstd_monomers?: Maybe<ReadonlyArray<Maybe<CoreChemComp>>>;
+ readonly entity_poly?: Maybe<EntityPoly>;
+ readonly entity_src_gen?: Maybe<ReadonlyArray<Maybe<EntitySrcGen>>>;
+ readonly entity_src_nat?: Maybe<ReadonlyArray<Maybe<EntitySrcNat>>>;
+ /** Get PDB entry that contains this molecular entity. */
+ readonly entry?: Maybe<CoreEntry>;
+ readonly pdbx_entity_src_syn?: Maybe<ReadonlyArray<Maybe<PdbxEntitySrcSyn>>>;
+ /** Get all unique Pfam annotations associated with this molecular entity. */
+ readonly pfams?: Maybe<ReadonlyArray<Maybe<CorePfam>>>;
+ /** Get all unique polymer instances (chains) for this molecular entity. */
+ readonly polymer_entity_instances?: Maybe<ReadonlyArray<Maybe<CorePolymerEntityInstance>>>;
+ /** Get a BIRD chemical components described in this molecular entity. */
+ readonly prd?: Maybe<CoreChemComp>;
+ /** Indicates intrinsic flexibility of protein structures determined from structural variations between different depositions and chains in asymmetric units of the same protein in PDB (95% sequence identity). */
+ readonly rcsb_cluster_flexibility?: Maybe<RcsbClusterFlexibility>;
+ readonly rcsb_cluster_membership?: Maybe<ReadonlyArray<Maybe<RcsbClusterMembership>>>;
+ readonly rcsb_entity_host_organism?: Maybe<ReadonlyArray<Maybe<RcsbEntityHostOrganism>>>;
+ readonly rcsb_entity_source_organism?: Maybe<ReadonlyArray<Maybe<RcsbEntitySourceOrganism>>>;
+ readonly rcsb_genomic_lineage?: Maybe<ReadonlyArray<Maybe<RcsbGenomicLineage>>>;
+ /**
+ * A unique identifier for each object in this entity container formed by
+ * an underscore separated concatenation of entry and entity identifiers.
+ *
* Examples:
- * 1
+ * 6EL3_1
+ *
*/
- readonly ordinal: Scalars['Int'];
+ readonly rcsb_id: Scalars['String'];
+ readonly rcsb_latest_revision?: Maybe<RcsbLatestRevision>;
+ /** Members of the membrane protein classification lineage. */
+ readonly rcsb_membrane_lineage?: Maybe<ReadonlyArray<Maybe<RcsbMembraneLineage>>>;
/**
- * The release date of the revision
- *
+ * Mpstruc keyword denotes original annotation, Homology keyword denotes annotation inferred by homology.
+ *
+ * Allowable values:
+ * Mpstruc, Homology
+ *
+ */
+ readonly rcsb_membrane_lineage_provenance_code?: Maybe<Scalars['String']>;
+ readonly rcsb_polymer_entity?: Maybe<RcsbPolymerEntity>;
+ readonly rcsb_polymer_entity_align?: Maybe<ReadonlyArray<Maybe<RcsbPolymerEntityAlign>>>;
+ readonly rcsb_polymer_entity_annotation?: Maybe<ReadonlyArray<Maybe<RcsbPolymerEntityAnnotation>>>;
+ readonly rcsb_polymer_entity_container_identifiers: RcsbPolymerEntityContainerIdentifiers;
+ readonly rcsb_polymer_entity_feature?: Maybe<ReadonlyArray<Maybe<RcsbPolymerEntityFeature>>>;
+ readonly rcsb_polymer_entity_feature_summary?: Maybe<ReadonlyArray<Maybe<RcsbPolymerEntityFeatureSummary>>>;
+ readonly rcsb_polymer_entity_keywords?: Maybe<RcsbPolymerEntityKeywords>;
+ readonly rcsb_polymer_entity_name_com?: Maybe<ReadonlyArray<Maybe<RcsbPolymerEntityNameCom>>>;
+ readonly rcsb_polymer_entity_name_sys?: Maybe<ReadonlyArray<Maybe<RcsbPolymerEntityNameSys>>>;
+ readonly rcsb_related_target_references?: Maybe<ReadonlyArray<Maybe<RcsbRelatedTargetReferences>>>;
+ readonly rcsb_target_cofactors?: Maybe<ReadonlyArray<Maybe<RcsbTargetCofactors>>>;
+ /** Get all unique UniProt KB annotations associated with this molecular entity. */
+ readonly uniprots?: Maybe<ReadonlyArray<Maybe<CoreUniprot>>>;
+};
+
+export type CorePolymerEntityInstance = {
+ readonly pdbx_struct_special_symmetry?: Maybe<ReadonlyArray<Maybe<PdbxStructSpecialSymmetry>>>;
+ /** Get polymer entity for this polymer entity instance. */
+ readonly polymer_entity?: Maybe<CorePolymerEntity>;
+ /**
+ * A unique identifier for each object in this entity instance container formed by
+ * an 'dot' (.) separated concatenation of entry and entity instance identifiers.
+ *
* Examples:
- * 2017-03-08
+ * 1KIP.A
+ *
*/
- readonly revision_date?: Maybe<Scalars['Date']>;
+ readonly rcsb_id: Scalars['String'];
+ readonly rcsb_latest_revision?: Maybe<RcsbLatestRevision>;
+ readonly rcsb_ligand_neighbors?: Maybe<ReadonlyArray<Maybe<RcsbLigandNeighbors>>>;
+ readonly rcsb_polymer_entity_instance_container_identifiers?: Maybe<RcsbPolymerEntityInstanceContainerIdentifiers>;
+ readonly rcsb_polymer_instance_annotation?: Maybe<ReadonlyArray<Maybe<RcsbPolymerInstanceAnnotation>>>;
+ readonly rcsb_polymer_instance_feature?: Maybe<ReadonlyArray<Maybe<RcsbPolymerInstanceFeature>>>;
+ readonly rcsb_polymer_instance_feature_summary?: Maybe<ReadonlyArray<Maybe<RcsbPolymerInstanceFeatureSummary>>>;
+ readonly rcsb_polymer_struct_conn?: Maybe<ReadonlyArray<Maybe<RcsbPolymerStructConn>>>;
};
-export type RcsbBranchedEntityAnnotationAnnotationLineage = {
- /** Members of the annotation lineage as parent lineage depth (1-N) */
- readonly depth?: Maybe<Scalars['Int']>;
- /** Members of the annotation lineage as parent class identifiers. */
- readonly id?: Maybe<Scalars['String']>;
- /** Members of the annotation lineage as parent class names. */
- readonly name?: Maybe<Scalars['String']>;
+export type CorePubmed = {
+ /** Unique integer value assigned to each PubMed record. */
+ readonly rcsb_id?: Maybe<Scalars['String']>;
+ /** A concise, accurate and factual mini-version of the paper contents. */
+ readonly rcsb_pubmed_abstract_text?: Maybe<Scalars['String']>;
+ /** The institution(s) that the author is affiliated with. Multiple affiliations per author are allowed. */
+ readonly rcsb_pubmed_affiliation_info?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
+ /** Unique integer value assigned to each PubMed Central record. */
+ readonly rcsb_pubmed_central_id?: Maybe<Scalars['String']>;
+ readonly rcsb_pubmed_container_identifiers: RcsbPubmedContainerIdentifiers;
+ /** Persistent identifier used to provide a link to an article location on the Internet. */
+ readonly rcsb_pubmed_doi?: Maybe<Scalars['String']>;
+ /** NLM controlled vocabulary, Medical Subject Headings (MeSH), is used to characterize the content of the articles represented by MEDLINE citations. */
+ readonly rcsb_pubmed_mesh_descriptors?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
+ /** Members of the MeSH classification lineage. */
+ readonly rcsb_pubmed_mesh_descriptors_lineage?: Maybe<ReadonlyArray<Maybe<RcsbPubmedMeshDescriptorsLineage>>>;
};
-export type DiffrnSource = {
- /** A description of special aspects of the radiation source used. */
- readonly details?: Maybe<Scalars['String']>;
- /**
- * This data item is a pointer to _diffrn.id in the DIFFRN
- * category.
- */
- readonly diffrn_id: Scalars['String'];
- /** Synchrotron beamline. */
- readonly pdbx_synchrotron_beamline?: Maybe<Scalars['String']>;
- /** Synchrotron site. */
- readonly pdbx_synchrotron_site?: Maybe<Scalars['String']>;
- /** Wavelength of radiation. */
- readonly pdbx_wavelength?: Maybe<Scalars['String']>;
+export type CoreUniprot = {
+ /** Primary accession number of a given UniProtKB entry. */
+ readonly rcsb_id?: Maybe<Scalars['String']>;
+ /** List of UniProtKB accession numbers where original accession numbers are retained as ‘secondary’ accession numbers. */
+ readonly rcsb_uniprot_accession?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
+ /** UniProt pairwise sequence alignments. */
+ readonly rcsb_uniprot_alignments?: Maybe<RcsbUniprotAlignments>;
+ readonly rcsb_uniprot_annotation?: Maybe<ReadonlyArray<Maybe<RcsbUniprotAnnotation>>>;
+ readonly rcsb_uniprot_container_identifiers: RcsbUniprotContainerIdentifiers;
+ /** A list of unique identifiers (former IDs), often containing biologically relevant information. */
+ readonly rcsb_uniprot_entry_name?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
+ readonly rcsb_uniprot_external_reference?: Maybe<ReadonlyArray<Maybe<RcsbUniprotExternalReference>>>;
+ readonly rcsb_uniprot_feature?: Maybe<ReadonlyArray<Maybe<RcsbUniprotFeature>>>;
+ /** Keywords constitute a controlled vocabulary that summarises the content of a UniProtKB entry. */
+ readonly rcsb_uniprot_keyword?: Maybe<ReadonlyArray<Maybe<RcsbUniprotKeyword>>>;
+ readonly rcsb_uniprot_protein?: Maybe<RcsbUniprotProtein>;
+};
+
+export type CurrentEntry = {
/**
- * Comma separated list of wavelengths or wavelength range.
- *
+ * The RCSB entry identifier.
+ *
* Examples:
- * 0.987 or 0.987, 0.988, 1.0 or 0.99-1.5
+ * 1KIP
+ *
*/
- readonly pdbx_wavelength_list?: Maybe<Scalars['String']>;
+ readonly rcsb_id: Scalars['String'];
+ readonly rcsb_repository_holdings_current?: Maybe<RcsbRepositoryHoldingsCurrent>;
+ readonly rcsb_repository_holdings_current_entry_container_identifiers?: Maybe<RcsbRepositoryHoldingsCurrentEntryContainerIdentifiers>;
+};
+
+export type Diffrn = {
/**
- * The general class of the radiation source.
- *
- * Examples:
- * sealed X-ray tube, nuclear reactor, spallation source, electron microscope, rotating-anode X-ray tube, synchrotron
+ * The mean hydrostatic pressure in kilopascals at which the
+ * intensities were measured.
*/
- readonly source?: Maybe<Scalars['String']>;
+ readonly ambient_pressure?: Maybe<Scalars['Float']>;
/**
- * The make, model or name of the source of radiation.
- *
- * Examples:
- * NSLS beamline X8C, Rigaku RU200
+ * The mean temperature in kelvins at which the intensities were
+ * measured.
*/
- readonly type?: Maybe<Scalars['String']>;
-};
-
-export type PdbxStructAssemblyGen = {
+ readonly ambient_temp?: Maybe<Scalars['Float']>;
/**
- * This data item is a pointer to _pdbx_struct_assembly.id in the
- * PDBX_STRUCT_ASSEMBLY category.
+ * A description of special aspects of temperature control during
+ * data collection.
*/
- readonly assembly_id?: Maybe<Scalars['String']>;
+ readonly ambient_temp_details?: Maybe<Scalars['String']>;
/**
- * This data item is a pointer to _struct_asym.id in
- * the STRUCT_ASYM category.
- *
- * This item may be expressed as a comma separated list of identifiers.
+ * This data item is a pointer to _exptl_crystal.id in the
+ * EXPTL_CRYSTAL category.
*/
- readonly asym_id_list?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
+ readonly crystal_id?: Maybe<Scalars['String']>;
/**
- * Identifies the operation of collection of operations
- * from category PDBX_STRUCT_OPER_LIST.
- *
- * Operation expressions may have the forms:
- *
- * (1) the single operation 1
- * (1,2,5) the operations 1, 2, 5
- * (1-4) the operations 1,2,3 and 4
- * (1,2)(3,4) the combinations of operations
- * 3 and 4 followed by 1 and 2 (i.e.
- * the cartesian product of parenthetical
- * groups applied from right to left)
- *
+ * The physical device used to support the crystal during data
+ * collection.
+ *
* Examples:
- * (1), (1,2,5), (1-60), (1-60)(61)
+ * glass capillary, quartz capillary, fiber, metal loop
+ *
*/
- readonly oper_expression?: Maybe<Scalars['String']>;
+ readonly crystal_support?: Maybe<Scalars['String']>;
/**
- * This data item is an ordinal index for the
- * PDBX_STRUCT_ASSEMBLY category.
+ * Special details of the diffraction measurement process. Should
+ * include information about source instability, crystal motion,
+ * degradation and so on.
*/
- readonly ordinal: Scalars['Int'];
-};
-
-export type PdbxNmrExptl = {
+ readonly details?: Maybe<Scalars['String']>;
/**
- * The number to identify the set of sample conditions.
- *
+ * This data item uniquely identifies a set of diffraction
+ * data.
+ */
+ readonly id: Scalars['String'];
+ /**
+ * Y/N if using serial crystallography experiment in which multiple crystals contribute to each diffraction frame in the experiment.
+ *
* Examples:
- * 1, 2, 3
+ * Y, N
+ *
*/
- readonly conditions_id: Scalars['String'];
+ readonly pdbx_serial_crystal_experiment?: Maybe<Scalars['String']>;
+};
+
+export type DiffrnDetector = {
+ /** A description of special aspects of the radiation detector. */
+ readonly details?: Maybe<Scalars['String']>;
/**
- * A numerical ID for each experiment.
- *
+ * The general class of the radiation detector.
+ *
* Examples:
- * 1, 2, 3
+ * photographic film, scintillation counter, CCD plate, BF~3~ counter
+ *
*/
- readonly experiment_id: Scalars['String'];
+ readonly detector?: Maybe<Scalars['String']>;
/**
- * Physical state of the sample either anisotropic or isotropic.
- *
- * Allowable values:
- * anisotropic, isotropic
+ * This data item is a pointer to _diffrn.id in the DIFFRN
+ * category.
*/
- readonly sample_state?: Maybe<Scalars['String']>;
+ readonly diffrn_id: Scalars['String'];
/**
- * The solution_id from the Experimental Sample to identify the sample
- * that these conditions refer to.
- *
- * [Remember to save the entries here before returning to the
- * Experimental Sample form]
- *
+ * The date of data collection.
+ *
* Examples:
- * 1, 2, 3
+ * 1996-12-25
+ *
*/
- readonly solution_id: Scalars['String'];
- /** Pointer to '_pdbx_nmr_spectrometer.spectrometer_id' */
- readonly spectrometer_id?: Maybe<Scalars['Int']>;
+ readonly pdbx_collection_date?: Maybe<Scalars['Date']>;
+ /** The operating frequency of the detector (Hz) used in data collection. */
+ readonly pdbx_frequency?: Maybe<Scalars['Float']>;
/**
- * The type of NMR experiment.
- *
+ * The make, model or name of the detector device used.
+ *
* Examples:
- * 2D NOESY, 3D_15N-separated_NOESY, 3D_13C-separated_NOESY, 4D_13C-separated_NOESY, 4D_13C/15N-separated_NOESY, 3D_15N-separated_ROESY, 3D_13C-separated_ROESY, HNCA-J, HNHA, DQF-COSY, P-COSY, PE-COSY, E-COSY
+ * DECTRIS PILATUS 12M, RAYONIX MX-325
+ *
*/
readonly type?: Maybe<Scalars['String']>;
};
-export type RcsbChemCompInfo = {
- /** Chemical component total atom count */
- readonly atom_count?: Maybe<Scalars['Int']>;
- /** Chemical component chiral atom count */
- readonly atom_count_chiral?: Maybe<Scalars['Int']>;
- /** Chemical component heavy atom count */
- readonly atom_count_heavy?: Maybe<Scalars['Int']>;
- /** Chemical component total bond count */
- readonly bond_count?: Maybe<Scalars['Int']>;
- /** Chemical component aromatic bond count */
- readonly bond_count_aromatic?: Maybe<Scalars['Int']>;
- /** The chemical component identifier. */
- readonly comp_id: Scalars['String'];
- /** The initial date the chemical definition was released in the PDB repository. */
- readonly initial_release_date?: Maybe<Scalars['Date']>;
+export type DiffrnRadiation = {
/**
- * The release status of the chemical definition.
- *
- * Allowable values:
- * DEL, HOLD, HPUB, OBS, REF_ONLY, REL
+ * The collimation or focusing applied to the radiation.
+ *
+ * Examples:
+ * 0.3 mm double-pinhole, 0.5 mm, focusing mirrors
+ *
*/
- readonly release_status?: Maybe<Scalars['String']>;
- /** The date of last revision of the chemical definition. */
- readonly revision_date?: Maybe<Scalars['Date']>;
-};
-
-export type RcsbPolymerEntityInstanceContainerIdentifiers = {
- /** Instance identifier for this container. */
- readonly asym_id: Scalars['String'];
- /** Author instance identifier for this container. */
- readonly auth_asym_id?: Maybe<Scalars['String']>;
+ readonly collimation?: Maybe<Scalars['String']>;
/**
- * Residue index mappings between author provided and entity polymer sequence positions.
- *
- * Author residue indices (auth_seq_num) include insertion codes when present.
- * The array indices correspond to the indices (1-based) of the deposited sample
- * sequence (entity_poly_seq). Unmodelled residues are represented with a "?" value.
+ * This data item is a pointer to _diffrn.id in the DIFFRN
+ * category.
*/
- readonly auth_to_entity_poly_seq_mapping?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
- /** Entity identifier for the container. */
- readonly entity_id?: Maybe<Scalars['String']>;
- /** Entry identifier for the container. */
- readonly entry_id: Scalars['String'];
+ readonly diffrn_id: Scalars['String'];
/**
- * A unique identifier for each object in this entity instance container formed by
- * an 'dot' (.) separated concatenation of entry and entity instance identifiers.
+ * The method used to obtain monochromatic radiation. If a mono-
+ * chromator crystal is used, the material and the indices of the
+ * Bragg reflection are specified.
+ *
+ * Examples:
+ * Zr filter, Ge 220, none, equatorial mounted graphite
+ *
*/
- readonly rcsb_id?: Maybe<Scalars['String']>;
-};
-
-export type RcsbBranchedEntityNameSys = {
- /** The systematic name for the branched entity. */
- readonly name: Scalars['String'];
- /** The system used to generate the systematic name of the branched entity. */
- readonly system?: Maybe<Scalars['String']>;
-};
-
-export type RcsbBranchedEntityAnnotation = {
- /** An identifier for the annotation. */
- readonly annotation_id?: Maybe<Scalars['String']>;
- readonly annotation_lineage?: Maybe<ReadonlyArray<Maybe<RcsbBranchedEntityAnnotationAnnotationLineage>>>;
- /** Identifies the version of the annotation assignment. */
- readonly assignment_version?: Maybe<Scalars['String']>;
- /** A description for the annotation. */
- readonly description?: Maybe<Scalars['String']>;
- /** A name for the annotation. */
- readonly name?: Maybe<Scalars['String']>;
+ readonly monochromator?: Maybe<Scalars['String']>;
/**
- * Code identifying the individual, organization or program that
- * assigned the annotation.
+ * SINGLE WAVELENGTH, LAUE, or MAD.
+ *
+ * Examples:
+ * SINGLE WAVELENGTH, MONOCHROMATIC, LAUE, MAD, OTHER
+ *
*/
- readonly provenance_source?: Maybe<Scalars['String']>;
- /** A type or category of the annotation. */
- readonly type?: Maybe<Scalars['String']>;
-};
-
-export type RcsbBranchedInstanceFeatureFeaturePositions = {
- /** An identifier for the monomer(s) corresponding to the feature assignment. */
- readonly beg_comp_id?: Maybe<Scalars['String']>;
- /** An identifier for the leading monomer feature position. */
- readonly beg_seq_id: Scalars['Int'];
- /** An identifier for the terminal monomer feature position. */
- readonly end_seq_id?: Maybe<Scalars['Int']>;
- /** The value of the feature at the monomer position. */
- readonly value?: Maybe<Scalars['Float']>;
-};
-
-export type EmCtfCorrection = {
+ readonly pdbx_diffrn_protocol?: Maybe<Scalars['String']>;
/**
- * Any additional details about CTF correction
- *
+ * Monochromatic or Laue.
+ *
+ * Allowable values:
+ * L, M
+ *
+ */
+ readonly pdbx_monochromatic_or_laue_m_l?: Maybe<Scalars['String']>;
+ /**
+ * The radiation scattering type for this diffraction data set.
+ *
+ * Allowable values:
+ * electron, neutron, x-ray
+ *
+ */
+ readonly pdbx_scattering_type?: Maybe<Scalars['String']>;
+ /** Wavelength of radiation. */
+ readonly pdbx_wavelength?: Maybe<Scalars['String']>;
+ /** Comma separated list of wavelengths or wavelength range. */
+ readonly pdbx_wavelength_list?: Maybe<Scalars['String']>;
+ /**
+ * The nature of the radiation. This is typically a description
+ * of the X-ray wavelength in Siegbahn notation.
+ *
* Examples:
- * CTF amplitude correction was performed following 3D reconstruction
+ * CuK\a, Cu K\a~1~, Cu K-L~2,3~, white-beam
+ *
*/
- readonly details?: Maybe<Scalars['String']>;
- /** Foreign key to the EM_IMAGE_PROCESSING category */
- readonly em_image_processing_id?: Maybe<Scalars['String']>;
- /** Primary key */
- readonly id: Scalars['String'];
- /** Type of CTF correction applied */
readonly type?: Maybe<Scalars['String']>;
-};
-
-export type CoreEntityAlignmentsScores = {
- readonly query_coverage: Scalars['Int'];
- readonly query_length: Scalars['Int'];
- readonly target_coverage: Scalars['Int'];
- readonly target_length: Scalars['Int'];
-};
-
-export type RcsbChemCompContainerIdentifiers = {
/**
- * The Anatomical Therapeutic Chemical (ATC) Classification System identifiers corresponding
- * to the chemical component.
+ * This data item is a pointer to _diffrn_radiation_wavelength.id
+ * in the DIFFRN_RADIATION_WAVELENGTH category.
*/
- readonly atc_codes?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
- /** The chemical component identifier. */
- readonly comp_id: Scalars['String'];
- /** The DrugBank identifier corresponding to the chemical component. */
- readonly drugbank_id?: Maybe<Scalars['String']>;
- /** The BIRD definition identifier. */
- readonly prd_id?: Maybe<Scalars['String']>;
- /** A unique identifier for the chemical definition in this container. */
- readonly rcsb_id?: Maybe<Scalars['String']>;
- /** The list of subcomponents contained in this component. */
- readonly subcomponent_ids?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
+ readonly wavelength_id?: Maybe<Scalars['String']>;
};
-export type PdbxAuditSupport = {
- /** The country/region providing the funding support for the entry. */
- readonly country?: Maybe<Scalars['String']>;
+export type DiffrnSource = {
+ /** A description of special aspects of the radiation source used. */
+ readonly details?: Maybe<Scalars['String']>;
/**
- * The name of the organization providing funding support for the
- * entry.
- *
- * Examples:
- * National Institutes of Health, Welcome Trust, National Institutes of Health/National Institute of General Medical Sciences
+ * This data item is a pointer to _diffrn.id in the DIFFRN
+ * category.
*/
- readonly funding_organization?: Maybe<Scalars['String']>;
- /** The grant number associated with this source of support. */
- readonly grant_number?: Maybe<Scalars['String']>;
+ readonly diffrn_id: Scalars['String'];
/**
- * A unique sequential integer identifier for each source of support for this entry.
- *
+ * Synchrotron beamline.
+ *
* Examples:
- * 1, 2, 3
+ * 17-ID-1, 19-ID
+ *
*/
- readonly ordinal: Scalars['Int'];
-};
-
-export type Entry = {
+ readonly pdbx_synchrotron_beamline?: Maybe<Scalars['String']>;
/**
- * The value of _entry.id identifies the data block.
- *
- * Note that this item need not be a number; it can be any unique
- * identifier.
+ * Synchrotron site.
+ *
+ * Examples:
+ * APS, NSLS-II
+ *
*/
- readonly id: Scalars['String'];
-};
-
-export type EmSpecimen = {
+ readonly pdbx_synchrotron_site?: Maybe<Scalars['String']>;
+ /** Wavelength of radiation. */
+ readonly pdbx_wavelength?: Maybe<Scalars['String']>;
/**
- * The concentration (in milligrams per milliliter, mg/ml)
- * of the complex in the sample.
- *
+ * Comma separated list of wavelengths or wavelength range.
+ *
* Examples:
- * 1.35
+ * 0.987 or 0.987, 0.988, 1.0 or 0.99-1.5
+ *
*/
- readonly concentration?: Maybe<Scalars['Float']>;
+ readonly pdbx_wavelength_list?: Maybe<Scalars['String']>;
/**
- * A description of any additional details of the specimen preparation.
- *
+ * The general class of the radiation source.
+ *
* Examples:
- * This sample was monodisperse., Au was deposited at a 30 degree angle to 15 nm thickness., Colloidal gold particles were deposited by dipping into dilute solution., The specimen was frozen at high pressure using the bal-tec hpm 010 instrument., The embedded sample was sectioned at 100 K to 50 nm final thickness.
+ * sealed X-ray tube, nuclear reactor, spallation source, electron microscope, rotating-anode X-ray tube, synchrotron
+ *
*/
- readonly details?: Maybe<Scalars['String']>;
+ readonly source?: Maybe<Scalars['String']>;
/**
- * 'YES' indicates that the specimen has been embedded.
- *
- * Allowable values:
- * NO, YES
+ * The make, model or name of the source of radiation.
+ *
+ * Examples:
+ * NSLS beamline X8C, Rigaku RU200
+ *
*/
- readonly embedding_applied?: Maybe<Scalars['String']>;
- /** Pointer to _em_experiment.id. */
- readonly experiment_id: Scalars['String'];
+ readonly type?: Maybe<Scalars['String']>;
+};
+
+export type DrugbankContainerIdentifiers = {
+ /** The DrugBank accession code */
+ readonly drugbank_id: Scalars['String'];
+};
+
+export type DrugbankInfo = {
+ /** The DrugBank drug affected organisms. */
+ readonly affected_organisms?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
+ /** The Anatomical Therapeutic Chemical Classification System (ATC) codes. */
+ readonly atc_codes?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
+ /** DrugBank drug brand names. */
+ readonly brand_names?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
/**
- * The item _em_specimen.id uniquely identifies a specimen along with
- * its preparation methods.
+ * The DrugBank assigned Chemical Abstracts Service identifier.
+ *
+ * Examples:
+ * 56-65-5
+ *
*/
- readonly id: Scalars['String'];
+ readonly cas_number?: Maybe<Scalars['String']>;
+ /** The DrugBank drug description. */
+ readonly description?: Maybe<Scalars['String']>;
+ /** The DrugBank drug categories. */
+ readonly drug_categories?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
+ /** The DrugBank drug drug groups. */
+ readonly drug_groups?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
+ /** The DrugBank accession code */
+ readonly drugbank_id: Scalars['String'];
/**
- * 'YES' indicates that the specimen has been shadowed.
- *
- * Allowable values:
- * NO, YES
+ * The DrugBank drug indication.
+ *
+ * Examples:
+ * For nutritional supplementation, also for treating dietary shortage or imbalance
+ *
*/
- readonly shadowing_applied?: Maybe<Scalars['String']>;
+ readonly indication?: Maybe<Scalars['String']>;
/**
- * 'YES' indicates that the specimen has been stained.
- *
- * Allowable values:
- * NO, YES
+ * The DrugBank drug mechanism of actions.
+ *
+ * Examples:
+ * ATP is able to store and transport chemical energy within cells.
+ *
*/
- readonly staining_applied?: Maybe<Scalars['String']>;
+ readonly mechanism_of_action?: Maybe<Scalars['String']>;
+ /** The DrugBank drug name. */
+ readonly name?: Maybe<Scalars['String']>;
/**
- * 'YES' indicates that the specimen was vitrified by cryopreservation.
- *
- * Allowable values:
- * NO, YES
+ * The DrugBank drug pharmacology.
+ *
+ * Examples:
+ * Adenosine triphosphate (ATP) is the nucleotide known in biochemistry as the "molecular currency" of intracellular energy transfer; that is, ATP is able to store and transport chemical energy within cells. ATP also plays an important role in the synthesis of nucleic acids. The total quantity of ATP in the human body is about 0.1 mole. The energy used by human cells requires the hydrolysis of 200 to 300 moles of ATP daily. This means that each ATP molecule is recycled 2000 to 3000 times during a single day. ATP cannot be stored, hence its consumption must closely follow its synthesis.
+ *
*/
- readonly vitrification_applied?: Maybe<Scalars['String']>;
+ readonly pharmacology?: Maybe<Scalars['String']>;
+ /** DrugBank drug name synonyms. */
+ readonly synonyms?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
};
-export type PdbxChemCompDescriptor = {
- /**
- * This data item is a pointer to _chem_comp.id in the CHEM_COMP
- * category.
- */
- readonly comp_id: Scalars['String'];
+export type DrugbankTarget = {
+ /** The type of target interaction. */
+ readonly interaction_type?: Maybe<Scalars['String']>;
+ /** The target name. */
+ readonly name?: Maybe<Scalars['String']>;
/**
- * This data item contains the descriptor value for this
- * component.
+ * The value of _drugbank_target.ordinal distinguishes
+ * related examples for each chemical component.
*/
- readonly descriptor?: Maybe<Scalars['String']>;
+ readonly ordinal: Scalars['Int'];
+ /** The organism common name. */
+ readonly organism_common_name?: Maybe<Scalars['String']>;
/**
- * This data item contains the name of the program
- * or library used to compute the descriptor.
- *
+ * The reference identifier code for the target interaction reference.
+ *
* Examples:
- * OPENEYE, CACTVS, DAYLIGHT, OTHER
- */
- readonly program: Scalars['String'];
- /**
- * This data item contains the version of the program
- * or library used to compute the descriptor.
+ * Q9HD40
+ *
*/
- readonly program_version: Scalars['String'];
+ readonly reference_database_accession_code?: Maybe<Scalars['String']>;
/**
- * This data item contains the descriptor type.
- *
+ * The reference database name for the target interaction.
+ *
* Allowable values:
- * InChI, InChIKey, InChI_CHARGE, InChI_FIXEDH, InChI_ISOTOPE, InChI_MAIN, InChI_MAIN_CONNECT, InChI_MAIN_FORMULA, InChI_MAIN_HATOM, InChI_RECONNECT, InChI_STEREO, SMILES, SMILES_CANNONICAL, SMILES_CANONICAL
+ * UniProt
+ *
*/
- readonly type: Scalars['String'];
-};
-
-export type RcsbChemCompDescriptor = {
+ readonly reference_database_name?: Maybe<Scalars['String']>;
/**
- * Standard IUPAC International Chemical Identifier (InChI) descriptor for the chemical component.
- *
- * InChI, the IUPAC International Chemical Identifier,
- * by Stephen R Heller, Alan McNaught, Igor Pletnev, Stephen Stein and Dmitrii Tchekhovskoi,
- * Journal of Cheminformatics, 2015, 7:23;
- */
- readonly InChI?: Maybe<Scalars['String']>;
- /**
- * Standard IUPAC International Chemical Identifier (InChI) descriptor key
- * for the chemical component
- *
- * InChI, the IUPAC International Chemical Identifier,
- * by Stephen R Heller, Alan McNaught, Igor Pletnev, Stephen Stein and Dmitrii Tchekhovskoi,
- * Journal of Cheminformatics, 2015, 7:23
- */
- readonly InChIKey?: Maybe<Scalars['String']>;
- /**
- * Simplified molecular-input line-entry system (SMILES) descriptor for the chemical component.
- *
- * Weininger D (February 1988). "SMILES, a chemical language and information system. 1.
- * Introduction to methodology and encoding rules". Journal of Chemical Information and Modeling. 28 (1): 31-6.
- *
- * Weininger D, Weininger A, Weininger JL (May 1989).
- * "SMILES. 2. Algorithm for generation of unique SMILES notation",
- * Journal of Chemical Information and Modeling. 29 (2): 97-101.
+ * Target sequence expressed as string of one-letter amino acid codes.
+ *
+ * Examples:
+ * MAKQRSG...
+ *
*/
- readonly SMILES?: Maybe<Scalars['String']>;
+ readonly seq_one_letter_code?: Maybe<Scalars['String']>;
+ /** The actions of the target interaction. */
+ readonly target_actions?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
+};
+
+export type Em2dCrystalEntity = {
+ /** Unit-cell angle gamma in degrees. */
+ readonly angle_gamma?: Maybe<Scalars['Float']>;
+ /** Length used to sample the reciprocal lattice lines in the c-direction. */
+ readonly c_sampling_length?: Maybe<Scalars['Float']>;
+ /** Unique key for the 2d_crystal_entity category. */
+ readonly id: Scalars['String'];
+ /** pointer to _em_image_processing.id in the EM_IMAGE_PROCESSING category. */
+ readonly image_processing_id: Scalars['String'];
+ /** Unit-cell length a in Angstroms. */
+ readonly length_a?: Maybe<Scalars['Float']>;
+ /** Unit-cell length b in Angstroms. */
+ readonly length_b?: Maybe<Scalars['Float']>;
+ /** Thickness of 2D crystal */
+ readonly length_c?: Maybe<Scalars['Float']>;
/**
- * Simplified molecular-input line-entry system (SMILES) descriptor for the chemical
- * component including stereochemical features.
- *
- * Weininger D (February 1988). "SMILES, a chemical language and information system. 1.
- * Introduction to methodology and encoding rules".
- * Journal of Chemical Information and Modeling. 28 (1): 31-6.
- *
- * Weininger D, Weininger A, Weininger JL (May 1989).
- * "SMILES. 2. Algorithm for generation of unique SMILES notation".
- * Journal of Chemical Information and Modeling. 29 (2): 97-101.
+ * There are 17 plane groups classified as oblique, rectangular, square, and hexagonal.
+ * To describe the symmetry of 2D crystals of biological molecules,
+ * plane groups are expanded to equivalent noncentrosymmetric space groups.
+ * The 2D crystal plane corresponds to the 'ab' plane of the space group.
+ *
+ * Enumerated space group descriptions include the plane group number in parentheses,
+ * the H-M plane group symbol, and the plane group class.
+ *
+ * Allowable values:
+ * C 1 2, C 2 2 2, P 1, P 1 2, P 1 21, P 2, P 2 2 2, P 2 2 21, P 2 21 21, P 3, P 3 1 2, P 3 2 1, P 4, P 4 2 2, P 4 21 2, P 6, P 6 2 2
+ *
*/
- readonly SMILES_stereo?: Maybe<Scalars['String']>;
- /** The chemical component identifier. */
- readonly comp_id: Scalars['String'];
+ readonly space_group_name_H_M?: Maybe<Scalars['String']>;
};
-export type PdbxNmrEnsemble = {
+export type Em3dCrystalEntity = {
+ /** Unit-cell angle alpha in degrees. */
+ readonly angle_alpha?: Maybe<Scalars['Float']>;
+ /** Unit-cell angle beta in degrees. */
+ readonly angle_beta?: Maybe<Scalars['Float']>;
+ /** Unit-cell angle gamma in degrees. */
+ readonly angle_gamma?: Maybe<Scalars['Float']>;
+ /** Unique key for the em_3d_crystal_entity category. */
+ readonly id: Scalars['String'];
+ /** pointer to _em_image_processing.id in the EM_IMAGE_PROCESSING category. */
+ readonly image_processing_id: Scalars['String'];
+ /** Unit-cell length a in Angstroms. */
+ readonly length_a?: Maybe<Scalars['Float']>;
+ /** Unit-cell length b in Angstroms. */
+ readonly length_b?: Maybe<Scalars['Float']>;
+ /** Unit-cell length c in Angstroms. */
+ readonly length_c?: Maybe<Scalars['Float']>;
/**
- * The average number of constraint violations on a per residue basis for
- * the ensemble.
- *
+ * Space group name.
+ *
* Examples:
- * 0.25
+ * P 1, P 21 21 2, I 4, H 3
+ *
*/
- readonly average_constraint_violations_per_residue?: Maybe<Scalars['Int']>;
+ readonly space_group_name?: Maybe<Scalars['String']>;
+ /** Space group number. */
+ readonly space_group_num?: Maybe<Scalars['Int']>;
+};
+
+export type Em3dFitting = {
/**
- * The average number of constraints per residue for the ensemble
- *
+ * Any additional details regarding fitting of atomic coordinates into
+ * the 3DEM volume, including data and considerations from other
+ * methods used in computation of the model.
+ *
* Examples:
- * 30.2
+ * Initial local fitting was done using Chimera and then NMFF was used for flexible fitting.
+ *
*/
- readonly average_constraints_per_residue?: Maybe<Scalars['Int']>;
+ readonly details?: Maybe<Scalars['String']>;
/**
- * The average distance restraint violation for the ensemble.
- *
- * Examples:
- * 0.11
+ * The value of _em_3d_fitting.id must uniquely identify
+ * a fitting procedure of atomic coordinates
+ * into 3dem reconstructed map volume.
*/
- readonly average_distance_constraint_violation?: Maybe<Scalars['Float']>;
+ readonly id: Scalars['String'];
/**
- * The average torsion angle constraint violation for the ensemble.
- *
- * Examples:
- * 2.4
+ * The method used to fit atomic coordinates
+ * into the 3dem reconstructed map.
*/
- readonly average_torsion_angle_constraint_violation?: Maybe<Scalars['Float']>;
+ readonly method?: Maybe<Scalars['String']>;
+ /** The overall B (temperature factor) value for the 3d-em volume. */
+ readonly overall_b_value?: Maybe<Scalars['Float']>;
/**
- * By highlighting the appropriate choice(s), describe how the submitted
- * conformer (models) were selected.
- *
- * Examples:
- * structures with the lowest energy, structures with the least restraint violations, structures with acceptable covalent geometry, structures with favorable non-bond energy, target function, back calculated data agree with experimental NOESY spectrum, all calculated structures submitted, The submitted conformer models are the 25 structures with the lowest
- * energy., The submitted conformer models are those with the fewest number of
- * constraint violations.
+ * The refinement protocol used.
+ *
+ * Allowable values:
+ * AB INITIO MODEL, BACKBONE TRACE, FLEXIBLE FIT, OTHER, RIGID BODY FIT
+ *
*/
- readonly conformer_selection_criteria?: Maybe<Scalars['String']>;
+ readonly ref_protocol?: Maybe<Scalars['String']>;
/**
- * The total number of conformer (models) that were calculated in the final round.
- *
- * Examples:
- * 40
+ * A flag to indicate whether fitting was carried out in real
+ * or reciprocal refinement space.
+ *
+ * Allowable values:
+ * REAL, RECIPROCAL
+ *
*/
- readonly conformers_calculated_total_number?: Maybe<Scalars['Int']>;
+ readonly ref_space?: Maybe<Scalars['String']>;
/**
- * The number of conformer (models) that are submitted for the ensemble.
- *
+ * The measure used to assess quality of fit of the atomic coordinates in the
+ * 3DEM map volume.
+ *
* Examples:
- * 20
+ * Cross-correlation coefficient
+ *
*/
- readonly conformers_submitted_total_number?: Maybe<Scalars['Int']>;
+ readonly target_criteria?: Maybe<Scalars['String']>;
+};
+
+export type Em3dFittingList = {
/**
- * Describe the method used to calculate the distance constraint violation statistics,
- * i.e. are they calculated over all the distance constraints or calculated for
- * violations only?
- *
- * Examples:
- * Statistics were calculated over all of the distance constraints., Statistics were calculated for violations only
+ * The value of _em_3d_fitting_list.3d_fitting_id is a pointer
+ * to _em_3d_fitting.id in the 3d_fitting category
*/
- readonly distance_constraint_violation_method?: Maybe<Scalars['String']>;
+ readonly _3d_fitting_id: Scalars['String'];
+ /** Details about the model used in fitting. */
+ readonly details?: Maybe<Scalars['String']>;
+ /** This data item is a unique identifier. */
+ readonly id: Scalars['String'];
/**
- * The maximum distance constraint violation for the ensemble.
- *
- * Examples:
- * 0.4
+ * The ID of the biopolymer chain used for fitting, e.g., A. Please note that
+ * only one chain can be specified per instance. If all chains of a particular
+ * structure have been used for fitting, this field can be left blank.
*/
- readonly maximum_distance_constraint_violation?: Maybe<Scalars['Float']>;
+ readonly pdb_chain_id?: Maybe<Scalars['String']>;
+ /** The molecular entities represented in this fitting description. */
+ readonly pdb_chain_residue_range?: Maybe<Scalars['String']>;
/**
- * The maximum lower distance constraint violation for the ensemble.
- *
+ * The PDB code for the entry used in fitting.
+ *
* Examples:
- * 0.3
+ * PDB entry 1EHZ
+ *
*/
- readonly maximum_lower_distance_constraint_violation?: Maybe<Scalars['Float']>;
+ readonly pdb_entry_id?: Maybe<Scalars['String']>;
+};
+
+export type Em3dReconstruction = {
/**
- * The maximum torsion angle constraint violation for the ensemble.
- *
+ * The actual pixel size of projection set of images.
+ *
* Examples:
- * 4
+ * null, null
+ *
*/
- readonly maximum_torsion_angle_constraint_violation?: Maybe<Scalars['Float']>;
+ readonly actual_pixel_size?: Maybe<Scalars['Float']>;
+ /** The algorithm used project from 2D orientations to 3D map. */
+ readonly algorithm?: Maybe<Scalars['String']>;
/**
- * The maximum upper distance constraint violation for the ensemble.
- *
+ * Any additional details used in the 3d reconstruction.
+ *
* Examples:
- * 0.4
+ * a modified version of SPIDER program was used for the reconstruction
+ *
*/
- readonly maximum_upper_distance_constraint_violation?: Maybe<Scalars['Float']>;
+ readonly details?: Maybe<Scalars['String']>;
/**
- * The number of the conformer identified as most representative.
- *
- * Examples:
- * 20
+ * The value of _em_3d_reconstruction.id must
+ * uniquely identify the 3d reconstruction.
*/
- readonly representative_conformer?: Maybe<Scalars['Int']>;
+ readonly id: Scalars['String'];
+ /** Foreign key to the EM_IMAGE_PROCESSING category */
+ readonly image_processing_id: Scalars['String'];
/**
- * This item describes the method used to calculate the torsion angle constraint violation statistics.
- * i.e. are the entered values based on all torsion angle or calculated for violations only?
- *
+ * The magnification calibration method for the 3d reconstruction.
+ *
* Examples:
- * Statistics were calculated over all the torsion angle constraints., Statistics were calculated for torsion angle constraints violations only.
+ * TMV images
+ *
*/
- readonly torsion_angle_constraint_violation_method?: Maybe<Scalars['String']>;
-};
-
-export type RefineLsRestr = {
+ readonly magnification_calibration?: Maybe<Scalars['String']>;
/**
- * For the given parameter type, the root-mean-square deviation
- * between the ideal values used as restraints in the least-squares
- * refinement and the values obtained by refinement. For instance,
- * bond distances may deviate by 0.018 \%A (r.m.s.) from ideal
- * values in the current model.
+ * The algorithm method used for the 3d-reconstruction.
+ *
+ * Examples:
+ * cross-common lines, polar Fourier transform (PFT)
+ *
*/
- readonly dev_ideal?: Maybe<Scalars['Float']>;
+ readonly method?: Maybe<Scalars['String']>;
/**
- * For the given parameter type, the target root-mean-square
- * deviation between the ideal values used as restraints in the
- * least-squares refinement and the values obtained by refinement.
+ * The nominal pixel size of the projection set of images.
+ *
+ * Examples:
+ * null, null
+ *
*/
- readonly dev_ideal_target?: Maybe<Scalars['Float']>;
+ readonly nominal_pixel_size?: Maybe<Scalars['Float']>;
/**
- * The number of parameters of this type subjected to restraint in
- * least-squares refinement.
+ * This item was correspondence to two type of em dataset
+ * processing_emDataSet_singleParticle.numClassAverages
+ * processing_emDataSet_icosahedral.numClassAverages
*/
- readonly number?: Maybe<Scalars['Int']>;
+ readonly num_class_averages?: Maybe<Scalars['Int']>;
+ /** The number of 2D projections or 3D subtomograms used in the 3d reconstruction */
+ readonly num_particles?: Maybe<Scalars['Int']>;
/**
- * This data item uniquely identifies a refinement within an entry.
- * _refine_ls_restr.pdbx_refine_id can be used to distinguish the results
- * of joint refinements.
+ * type of refinement performed in order to determine map resolution
+ *
+ * Allowable values:
+ * HALF-MAPS REFINED AGAINST SAME DATA, HALF-MAPS REFINED INDEPENDENTLY, HALF-MAPS REFINED INDEPENDENTLY WITH FREQUENCY RANGE OMITTED, HALF-MAPS REFINED WITH FREQUENCY RANGE OMITTED, OTHER
+ *
*/
- readonly pdbx_refine_id: Scalars['String'];
+ readonly refinement_type?: Maybe<Scalars['String']>;
/**
- * The functional form of the restraint function used in the least-squares
- * refinement.
- *
+ * The final resolution (in Angstroms)of the 3D reconstruction.
+ *
* Examples:
- * SINUSOIDAL, HARMONIC, SEMIHARMONIC
+ * null, null
+ *
*/
- readonly pdbx_restraint_function?: Maybe<Scalars['String']>;
+ readonly resolution?: Maybe<Scalars['Float']>;
/**
- * The type of the parameter being restrained.
- * Explicit sets of data values are provided for the programs
- * PROTIN/PROLSQ (beginning with p_) and RESTRAIN (beginning with
- * RESTRAIN_). As computer programs change, these data values
- * are given as examples, not as an enumeration list. Computer
- * programs that convert a data block to a refinement table will
- * expect the exact form of the data values given here to be used.
- *
+ * The method used to determine the final resolution
+ * of the 3d reconstruction.
+ * The Fourier Shell Correlation criterion as a measure of
+ * resolution is based on the concept of splitting the (2D)
+ * data set into two halves; averaging each and comparing them
+ * using the Fourier Ring Correlation (FRC) technique.
+ *
* Examples:
- * p_bond_d, p_angle_d, p_planar_d, p_xhbond_d, p_xhangle_d, p_hydrog_d, p_special_d, p_planar, p_chiral, p_singtor_nbd, p_multtor_nbd, p_xyhbond_nbd, p_xhyhbond_nbd, p_special_tor, p_planar_tor, p_staggered_tor, p_orthonormal_tor, p_mcbond_it, p_mcangle_it, p_scbond_it, p_scangle_it, p_xhbond_it, p_xhangle_it, p_special_it, RESTRAIN_Distances < 2.12, RESTRAIN_Distances 2.12 < D < 2.625, RESTRAIN_Distances > 2.625, RESTRAIN_Peptide Planes, RESTRAIN_Ring and other planes, RESTRAIN_rms diffs for Uiso atoms at dist 1.2-1.4, RESTRAIN_rms diffs for Uiso atoms at dist 1.4-1.6, RESTRAIN_rms diffs for Uiso atoms at dist 1.8-2.0, RESTRAIN_rms diffs for Uiso atoms at dist 2.0-2.2, RESTRAIN_rms diffs for Uiso atoms at dist 2.2-2.4, RESTRAIN_rms diffs for Uiso atoms at dist >2.4
+ * FSC at 0.5 cut-off
+ *
*/
- readonly type: Scalars['String'];
+ readonly resolution_method?: Maybe<Scalars['String']>;
/**
- * The weighting value applied to this type of restraint in
- * the least-squares refinement.
+ * The type of symmetry applied to the reconstruction
+ *
+ * Allowable values:
+ * 2D CRYSTAL, 3D CRYSTAL, HELICAL, POINT
+ *
*/
- readonly weight?: Maybe<Scalars['Float']>;
+ readonly symmetry_type?: Maybe<Scalars['String']>;
};
-export type PdbxReferenceEntityList = {
- /** The component number of this entity within the molecule. */
- readonly component_id: Scalars['Int'];
- /** Additional details about this entity. */
- readonly details?: Maybe<Scalars['String']>;
- /**
- * The value of _pdbx_reference_entity_list.prd_id is a reference
- * _pdbx_reference_molecule.prd_id in the PDBX_REFERENCE_MOLECULE category.
- */
- readonly prd_id: Scalars['String'];
- /**
- * The value of _pdbx_reference_entity_list.ref_entity_id is a unique identifier
- * the a constituent entity within this reference molecule.
- */
- readonly ref_entity_id: Scalars['String'];
+export type EmCtfCorrection = {
/**
- * Defines the polymer characteristic of the entity.
- *
- * Allowable values:
- * branched, non-polymer, polymer, polymer-like
+ * Any additional details about CTF correction
+ *
+ * Examples:
+ * CTF amplitude correction was performed following 3D reconstruction
+ *
*/
+ readonly details?: Maybe<Scalars['String']>;
+ /** Foreign key to the EM_IMAGE_PROCESSING category */
+ readonly em_image_processing_id?: Maybe<Scalars['String']>;
+ /** Primary key */
+ readonly id: Scalars['String'];
+ /** Type of CTF correction applied */
readonly type?: Maybe<Scalars['String']>;
};
-export type RcsbUniprotAlignments = {
- readonly core_entity_alignments?: Maybe<ReadonlyArray<Maybe<RcsbUniprotAlignmentsCoreEntityAlignments>>>;
-};
-
-export type CoreNonpolymerEntity = {
- /** Get PDB entry that contains this non-polymer entity. */
- readonly entry?: Maybe<CoreEntry>;
- /** Get a non-polymer chemical components described in this molecular entity. */
- readonly nonpolymer_comp?: Maybe<CoreChemComp>;
- /** Get all unique non-polymer instances (chains) for this non-polymer entity. */
- readonly nonpolymer_entity_instances?: Maybe<ReadonlyArray<Maybe<CoreNonpolymerEntityInstance>>>;
- readonly pdbx_entity_nonpoly?: Maybe<PdbxEntityNonpoly>;
- /** Get a BIRD chemical components described in this molecular entity. */
- readonly prd?: Maybe<CoreChemComp>;
+export type EmDiffraction = {
+ /** TODO */
+ readonly camera_length?: Maybe<Scalars['Float']>;
+ /** Primary key */
+ readonly id: Scalars['String'];
+ /** Foreign key to the EM_IMAGING category */
+ readonly imaging_id?: Maybe<Scalars['String']>;
/**
- * A unique identifier for each object in this entity container formed by
- * an underscore separated concatenation of entry and entity identifiers.
+ * Comma-separated list of tilt angles (in degrees) used in the electron diffraction experiment.
+ *
+ * Examples:
+ * 20,40,50,55
+ *
*/
- readonly rcsb_id: Scalars['String'];
- readonly rcsb_latest_revision?: Maybe<RcsbLatestRevision>;
- readonly rcsb_nonpolymer_entity?: Maybe<RcsbNonpolymerEntity>;
- readonly rcsb_nonpolymer_entity_annotation?: Maybe<ReadonlyArray<Maybe<RcsbNonpolymerEntityAnnotation>>>;
- readonly rcsb_nonpolymer_entity_container_identifiers?: Maybe<RcsbNonpolymerEntityContainerIdentifiers>;
- readonly rcsb_nonpolymer_entity_feature?: Maybe<ReadonlyArray<Maybe<RcsbNonpolymerEntityFeature>>>;
- readonly rcsb_nonpolymer_entity_feature_summary?: Maybe<ReadonlyArray<Maybe<RcsbNonpolymerEntityFeatureSummary>>>;
- readonly rcsb_nonpolymer_entity_keywords?: Maybe<RcsbNonpolymerEntityKeywords>;
- readonly rcsb_nonpolymer_entity_name_com?: Maybe<ReadonlyArray<Maybe<RcsbNonpolymerEntityNameCom>>>;
+ readonly tilt_angle_list?: Maybe<Scalars['String']>;
};
-export type RcsbPolymerEntity = {
- /** A description of special aspects of the entity. */
- readonly details?: Maybe<Scalars['String']>;
- /** Formula mass (KDa) of the entity. */
- readonly formula_weight?: Maybe<Scalars['Float']>;
+export type EmDiffractionShell = {
+ /** Pointer to EM CRYSTALLOGRAPHY STATS */
+ readonly em_diffraction_stats_id?: Maybe<Scalars['String']>;
/**
- * A description of the polymer entity.
- *
+ * Completeness of the structure factor data within this resolution shell, in percent
+ *
* Examples:
- * Green fluorescent protein, DNA (5'-D(*GP*(CH3)CP*GP*(CH3)CP*GP*C)-3'), PROFLAVINE, PROTEIN (DEOXYRIBONUCLEASE I (E.C.3.1.21.1))
+ * null
+ *
*/
- readonly pdbx_description?: Maybe<Scalars['String']>;
+ readonly fourier_space_coverage?: Maybe<Scalars['Float']>;
/**
- * Enzyme Commission (EC) number(s)
- *
+ * High resolution limit for this shell (Angstroms)
+ *
* Examples:
- * 2.7.7.7
+ * null
+ *
*/
- readonly pdbx_ec?: Maybe<Scalars['String']>;
+ readonly high_resolution?: Maybe<Scalars['Float']>;
+ /** Unique identifier for the category em_diffraction_shell */
+ readonly id: Scalars['String'];
/**
- * Polymer entity fragment description(s).
- *
+ * Low resolution limit for this shell (Angstroms)
+ *
* Examples:
- * KLENOW FRAGMENT, REPLICASE OPERATOR HAIRPIN, C-TERMINAL DOMAIN
+ * null
+ *
*/
- readonly pdbx_fragment?: Maybe<Scalars['String']>;
+ readonly low_resolution?: Maybe<Scalars['Float']>;
/**
- * Details about any polymer entity mutation(s).
- *
+ * Multiplicity (average number of measurements) for the structure factors in this resolution shell
+ *
* Examples:
- * Y31H, DEL(298-323)
+ * null
+ *
*/
- readonly pdbx_mutation?: Maybe<Scalars['String']>;
+ readonly multiplicity?: Maybe<Scalars['Float']>;
+ /** Number of measured structure factors in this resolution shell */
+ readonly num_structure_factors?: Maybe<Scalars['Int']>;
/**
- * The number of molecules of the entity in the entry.
- *
+ * Phase residual for this resolution shell, in degrees
+ *
* Examples:
- * 1, 2, 3
+ * null
+ *
*/
- readonly pdbx_number_of_molecules?: Maybe<Scalars['Int']>;
- readonly rcsb_ec_lineage?: Maybe<ReadonlyArray<Maybe<RcsbPolymerEntityRcsbEcLineage>>>;
- readonly rcsb_enzyme_class_combined?: Maybe<ReadonlyArray<Maybe<RcsbPolymerEntityRcsbEnzymeClassCombined>>>;
- readonly rcsb_macromolecular_names_combined?: Maybe<ReadonlyArray<Maybe<RcsbPolymerEntityRcsbMacromolecularNamesCombined>>>;
+ readonly phase_residual?: Maybe<Scalars['Float']>;
+};
+
+export type EmDiffractionStats = {
/**
- * A code indicating the entity has multiple biological sources.
- *
- * Allowable values:
- * N, Y
+ * Any addition details about the structure factor measurements
+ *
+ * Examples:
+ * Phases were obtained from micrograph images of the 2D crystals
+ *
*/
- readonly rcsb_multiple_source_flag?: Maybe<Scalars['String']>;
+ readonly details?: Maybe<Scalars['String']>;
/**
- * The number of biological sources for the polymer entity. Multiple source contributions
- * may come from the same organism (taxonomy).
+ * Completeness of the structure factor data within the defined space group
+ * at the reported resolution (percent).
+ *
+ * Examples:
+ * null
+ *
*/
- readonly rcsb_source_part_count?: Maybe<Scalars['Int']>;
- /** The number of distinct source taxonomies for the polymer entity. Commonly used to identify chimeric polymers. */
- readonly rcsb_source_taxonomy_count?: Maybe<Scalars['Int']>;
+ readonly fourier_space_coverage?: Maybe<Scalars['Float']>;
/**
- * The method by which the sample for the polymer entity was produced.
- * Entities isolated directly from natural sources (tissues, soil
- * samples etc.) are expected to have further information in the
- * ENTITY_SRC_NAT category. Entities isolated from genetically
- * manipulated sources are expected to have further information in
- * the ENTITY_SRC_GEN category.
- *
- * Allowable values:
- * man, nat, syn
+ * High resolution limit of the structure factor data, in Angstroms
+ *
+ * Examples:
+ * null
+ *
*/
- readonly src_method?: Maybe<Scalars['String']>;
-};
-
-export type RcsbUniprotFeatureFeaturePositions = {
- /** An identifier for the monomer(s) corresponding to the feature assignment. */
- readonly beg_comp_id?: Maybe<Scalars['String']>;
- /** An identifier for the monomer at which this segment of the feature begins. */
- readonly beg_seq_id: Scalars['Int'];
- /** An identifier for the monomer at which this segment of the feature ends. */
- readonly end_seq_id?: Maybe<Scalars['Int']>;
- /** The value for the feature over this monomer segment. */
- readonly value?: Maybe<Scalars['Float']>;
-};
-
-export type CoreNonpolymerEntityInstance = {
- /** Get non-polymer entity for this non-polymer entity instance. */
- readonly nonpolymer_entity?: Maybe<CoreNonpolymerEntity>;
- readonly pdbx_struct_special_symmetry?: Maybe<ReadonlyArray<Maybe<PdbxStructSpecialSymmetry>>>;
+ readonly high_resolution?: Maybe<Scalars['Float']>;
+ /** Identifier for this category */
+ readonly id: Scalars['String'];
+ /** Pointer to _em_image_processing.id */
+ readonly image_processing_id?: Maybe<Scalars['String']>;
+ /** Total number of diffraction intensities measured (before averaging) */
+ readonly num_intensities_measured?: Maybe<Scalars['Int']>;
+ /** Number of structure factors obtained (merged amplitudes + phases) */
+ readonly num_structure_factors?: Maybe<Scalars['Int']>;
/**
- * A unique identifier for each object in this entity instance container formed by
- * an 'dot' (.) separated concatenation of entry and entity instance identifiers.
+ * Overall phase error in degrees
+ *
+ * Examples:
+ * null
+ *
*/
- readonly rcsb_id: Scalars['String'];
- readonly rcsb_latest_revision?: Maybe<RcsbLatestRevision>;
- readonly rcsb_nonpolymer_entity_instance_container_identifiers?: Maybe<RcsbNonpolymerEntityInstanceContainerIdentifiers>;
- readonly rcsb_nonpolymer_instance_annotation?: Maybe<ReadonlyArray<Maybe<RcsbNonpolymerInstanceAnnotation>>>;
- readonly rcsb_nonpolymer_instance_feature?: Maybe<ReadonlyArray<Maybe<RcsbNonpolymerInstanceFeature>>>;
- readonly rcsb_nonpolymer_instance_feature_summary?: Maybe<ReadonlyArray<Maybe<RcsbNonpolymerInstanceFeatureSummary>>>;
- readonly rcsb_nonpolymer_struct_conn?: Maybe<ReadonlyArray<Maybe<RcsbNonpolymerStructConn>>>;
-};
-
-export type RcsbUniprotProteinEc = {
- readonly number?: Maybe<Scalars['String']>;
- /** Historical record of the data attribute. */
- readonly provenance_code?: Maybe<Scalars['String']>;
-};
-
-export type RcsbChemCompSynonyms = {
- /** The chemical component to which this synonym applies. */
- readonly comp_id: Scalars['String'];
- /** The synonym of this particular chemical component. */
- readonly name?: Maybe<Scalars['String']>;
+ readonly overall_phase_error?: Maybe<Scalars['Float']>;
/**
- * This data item is an ordinal index for the
- * RCSB_CHEM_COMP_SYNONYMS category.
+ * Overall phase residual in degrees
+ *
+ * Examples:
+ * null
+ *
*/
- readonly ordinal: Scalars['Int'];
+ readonly overall_phase_residual?: Maybe<Scalars['Float']>;
/**
- * The provenance of this synonym.
- *
- * Allowable values:
- * ACDLabs, Author, ChEBI, ChEMBL, DrugBank, GMML, Lexichem, OpenEye OEToolkits, OpenEye/Lexichem, PDB Reference Data, PDB Reference Data (Preferred), PDB-CARE, PubChem, RESID
+ * Criteria used to reject phases
+ *
+ * Examples:
+ * Structure factors with phase errors higher than 20 degrees were omitted from refinement
+ *
*/
- readonly provenance_source?: Maybe<Scalars['String']>;
+ readonly phase_error_rejection_criteria?: Maybe<Scalars['String']>;
/**
- * This data item contains the synonym type.
- *
- * Allowable values:
- * Common Name, Condensed IUPAC Carbohydrate Symbol, IUPAC Carbohydrate Symbol, Preferred Common Name, Preferred Name, Preferred Synonym, SNFG Carbohydrate Symbol, Synonym, Systematic Name
+ * Rmerge value (percent)
+ *
+ * Examples:
+ * null
+ *
*/
- readonly type?: Maybe<Scalars['String']>;
+ readonly r_merge?: Maybe<Scalars['Float']>;
+ /**
+ * Rsym value (percent)
+ *
+ * Examples:
+ * null
+ *
+ */
+ readonly r_sym?: Maybe<Scalars['Float']>;
};
-export type PdbxDepositGroup = {
- /** A description of the contents of entries in the collection. */
- readonly group_description?: Maybe<Scalars['String']>;
- /** A unique identifier for a group of entries deposited as a collection. */
- readonly group_id: Scalars['String'];
- /** A title to describe the group of entries deposited in the collection. */
- readonly group_title?: Maybe<Scalars['String']>;
+export type EmEmbedding = {
/**
- * Text to describe a grouping of entries in multiple collections
- *
- * Allowable values:
- * changed state, ground state, undefined
+ * Staining procedure used in the specimen preparation.
+ *
+ * Examples:
+ * The crystal suspension was injected into the lens of a drop of buffer containing
+ * 1 % tannin sitting on a carbon film supported by a molybdenum grid. An equal volume
+ * of 1% glucose was then added and the solution thoroughly but gently mixed. The grid
+ * was then blotted, air dried, and frozen in LN2.
+ *
*/
- readonly group_type?: Maybe<Scalars['String']>;
+ readonly details?: Maybe<Scalars['String']>;
+ /** This data item is the primary key of the category. */
+ readonly id: Scalars['String'];
+ /**
+ * The embedding material.
+ *
+ * Examples:
+ * tannin and glucose
+ *
+ */
+ readonly material?: Maybe<Scalars['String']>;
+ /** Foreign key relationship to the EMD SPECIMEN category */
+ readonly specimen_id?: Maybe<Scalars['String']>;
};
-export type Reflns = {
+export type EmEntityAssembly = {
/**
- * The value of the overall isotropic displacement parameter
- * estimated from the slope of the Wilson plot.
+ * Additional details about the component.
+ *
+ * Examples:
+ * Fab fragment generated by proteolytic cleavage of LA2 IgG antibody.
+ *
*/
- readonly B_iso_Wilson_estimate?: Maybe<Scalars['Float']>;
+ readonly details?: Maybe<Scalars['String']>;
/**
- * A description of the method by which a subset of reflections was
- * selected for exclusion from refinement so as to be used in the
- * calculation of a 'free' R factor.
- *
- * Examples:
- * The data set was sorted with l varying most
- * rapidly and h varying least rapidly. Every
- * 10th reflection in this sorted list was
- * excluded from refinement and included in the
- * calculation of a 'free' R factor.
+ * macromolecules associated with this component, if defined
+ * as comma separated list of entity ids (integers).
*/
- readonly R_free_details?: Maybe<Scalars['String']>;
+ readonly entity_id_list?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
/**
- * Residual factor Rmerge for all reflections that satisfy the
- * resolution limits established by _reflns.d_resolution_high
- * and _reflns.d_resolution_low.
- *
- * sum~i~(sum~j~|F~j~ - <F>|)
- * Rmerge(F) = --------------------------
- * sum~i~(sum~j~<F>)
- *
- * F~j~ = the amplitude of the jth observation of reflection i
- * <F> = the mean of the amplitudes of all observations of
- * reflection i
- *
- * sum~i~ is taken over all reflections
- * sum~j~ is taken over all observations of each reflection
+ * The value of _em_entity_assembly.id identifies
+ * one component of the complex.
*/
- readonly Rmerge_F_all?: Maybe<Scalars['Float']>;
+ readonly id: Scalars['String'];
/**
- * Residual factor Rmerge for reflections that satisfy the
- * resolution limits established by _reflns.d_resolution_high
- * and _reflns.d_resolution_low and the observation limit
- * established by _reflns.observed_criterion.
- *
- * sum~i~(sum~j~|F~j~ - <F>|)
- * Rmerge(F) = --------------------------
- * sum~i~(sum~j~<F>)
- *
- * F~j~ = the amplitude of the jth observation of reflection i
- * <F> = the mean of the amplitudes of all observations of
- * reflection i
- *
- * sum~i~ is taken over all reflections
- * sum~j~ is taken over all observations of each reflection
+ * Name of this component in the observed assembly.
+ *
+ * Examples:
+ * Ternary complex of alpha-tubulin with tubulin folding cofactors TBCE and TBCB, 80S Ribosome bound to emetine, messenger RNA, initiation factor 2, GroEL, antibody Fab fragment
+ *
*/
- readonly Rmerge_F_obs?: Maybe<Scalars['Float']>;
+ readonly name?: Maybe<Scalars['String']>;
+ /** oligomeric details */
+ readonly oligomeric_details?: Maybe<Scalars['String']>;
/**
- * The smallest value for the interplanar spacings for
- * the reflection data. This is called the highest resolution.
+ * The parent of this assembly.
+ * This data item is an internal category pointer to _em_entity_assembly.id.
+ * By convention, the full assembly (top of hierarchy) is assigned parent id 0 (zero).
*/
- readonly d_resolution_high?: Maybe<Scalars['Float']>;
+ readonly parent_id?: Maybe<Scalars['Int']>;
/**
- * The largest value for the interplanar spacings for the
- * reflection data. This is called the lowest resolution.
+ * The assembly type.
+ *
+ * Allowable values:
+ * MULTIPLE SOURCES, NATURAL, RECOMBINANT, SYNTHETIC
+ *
*/
- readonly d_resolution_low?: Maybe<Scalars['Float']>;
+ readonly source?: Maybe<Scalars['String']>;
/**
- * A description of special aspects of the data-reduction
- * procedures.
- *
+ * Alternative name of the component.
+ *
* Examples:
- * Merging and scaling based on only those
- * reflections with I > sig(I).
+ * FADV-1
+ *
*/
- readonly data_reduction_details?: Maybe<Scalars['String']>;
+ readonly synonym?: Maybe<Scalars['String']>;
/**
- * The method used for data reduction.
- *
- * Note that this is not the computer program used, which is
- * described in the SOFTWARE category, but the method
- * itself.
- *
- * This data item should be used to describe significant
- * methodological options used within the data-reduction programs.
- *
- * Examples:
- * Profile fitting by method of Kabsch (1987).
- * Scaling used spherical harmonic coefficients.
+ * A description of types of components of the
+ * assembly of the biological structure.
*/
- readonly data_reduction_method?: Maybe<Scalars['String']>;
+ readonly type?: Maybe<Scalars['String']>;
+};
+
+export type EmExperiment = {
/**
- * A description of reflection data not covered by other data
- * names. This should include details of the Friedel pairs.
+ * The aggregation/assembly state of the imaged specimen.
+ *
+ * Allowable values:
+ * 2D ARRAY, 3D ARRAY, CELL, FILAMENT, HELICAL ARRAY, PARTICLE, TISSUE
+ *
*/
- readonly details?: Maybe<Scalars['String']>;
+ readonly aggregation_state?: Maybe<Scalars['String']>;
+ /** Foreign key to the EM_ENTITY_ASSEMBLY category */
+ readonly entity_assembly_id?: Maybe<Scalars['String']>;
+ /** Placeholder ID. */
+ readonly id?: Maybe<Scalars['String']>;
/**
- * Maximum value of the Miller index h for the reflection data. This
- * need not have the same value as _diffrn_reflns.limit_h_max.
+ * The reconstruction method used in the EM experiment.
+ *
+ * Allowable values:
+ * CRYSTALLOGRAPHY, HELICAL, SINGLE PARTICLE, SUBTOMOGRAM AVERAGING, TOMOGRAPHY
+ *
*/
- readonly limit_h_max?: Maybe<Scalars['Int']>;
+ readonly reconstruction_method?: Maybe<Scalars['String']>;
+};
+
+export type EmHelicalEntity = {
/**
- * Minimum value of the Miller index h for the reflection data. This
- * need not have the same value as _diffrn_reflns.limit_h_min.
+ * The angular rotation per helical subunit in degrees.
+ *
+ * Examples:
+ * null
+ *
*/
- readonly limit_h_min?: Maybe<Scalars['Int']>;
+ readonly angular_rotation_per_subunit?: Maybe<Scalars['Float']>;
/**
- * Maximum value of the Miller index k for the reflection data. This
- * need not have the same value as _diffrn_reflns.limit_k_max.
+ * The axial rise per subunit in the helical assembly.
+ *
+ * Examples:
+ * null
+ *
*/
- readonly limit_k_max?: Maybe<Scalars['Int']>;
+ readonly axial_rise_per_subunit?: Maybe<Scalars['Float']>;
/**
- * Minimum value of the Miller index k for the reflection data. This
- * need not have the same value as _diffrn_reflns.limit_k_min.
+ * Symmetry of the helical axis, either cyclic (Cn) or dihedral (Dn), where n>=1.
+ *
+ * Examples:
+ * C1, D2, C7
+ *
*/
- readonly limit_k_min?: Maybe<Scalars['Int']>;
+ readonly axial_symmetry?: Maybe<Scalars['String']>;
/**
- * Maximum value of the Miller index l for the reflection data. This
- * need not have the same value as _diffrn_reflns.limit_l_max.
+ * Any other details regarding the helical assembly
+ *
+ * Examples:
+ * Dihedral symmetry
+ *
*/
- readonly limit_l_max?: Maybe<Scalars['Int']>;
+ readonly details?: Maybe<Scalars['String']>;
/**
- * Minimum value of the Miller index l for the reflection data. This
- * need not have the same value as _diffrn_reflns.limit_l_min.
+ * The value of _em_helical_entity.id must uniquely identify
+ * a set of the filament parameters for this assembly component.
*/
- readonly limit_l_min?: Maybe<Scalars['Int']>;
+ readonly id: Scalars['String'];
/**
- * The total number of reflections in the REFLN list (not the
- * DIFFRN_REFLN list). This number may contain Friedel-equivalent
- * reflections according to the nature of the structure and the
- * procedures used. The item _reflns.details describes the
- * reflection data.
+ * The value of _em_helical_entity.reconstruction_id identifies a particular reconstruction.
+ *
+ * This data item is a pointer to _em_image_processing.id.
*/
- readonly number_all?: Maybe<Scalars['Int']>;
+ readonly image_processing_id: Scalars['String'];
+};
+
+export type EmImageRecording = {
/**
- * The number of reflections in the REFLN list (not the DIFFRN_REFLN
- * list) classified as observed (see _reflns.observed_criterion).
- * This number may contain Friedel-equivalent reflections according
- * to the nature of the structure and the procedures used.
+ * The average exposure time for each image.
+ *
+ * Examples:
+ * null
+ *
*/
- readonly number_obs?: Maybe<Scalars['Int']>;
+ readonly average_exposure_time?: Maybe<Scalars['Float']>;
/**
- * The criterion used to classify a reflection as 'observed'. This
- * criterion is usually expressed in terms of a sigma(I) or
- * sigma(F) threshold.
- *
+ * The electron dose received by the specimen per image (electrons per square angstrom).
+ *
* Examples:
- * >2sigma(I)
+ * null
+ *
*/
- readonly observed_criterion?: Maybe<Scalars['String']>;
+ readonly avg_electron_dose_per_image?: Maybe<Scalars['Float']>;
/**
- * The criterion used to classify a reflection as 'observed'
- * expressed as an upper limit for the value of F.
+ * Any additional details about image recording.
+ *
+ * Examples:
+ * Images were collected in movie-mode at 17 frames per second
+ *
*/
- readonly observed_criterion_F_max?: Maybe<Scalars['Float']>;
+ readonly details?: Maybe<Scalars['String']>;
/**
- * The criterion used to classify a reflection as 'observed'
- * expressed as a lower limit for the value of F.
+ * The detector mode used during image recording.
+ *
+ * Allowable values:
+ * COUNTING, INTEGRATING, OTHER, SUPER-RESOLUTION
+ *
*/
- readonly observed_criterion_F_min?: Maybe<Scalars['Float']>;
+ readonly detector_mode?: Maybe<Scalars['String']>;
/**
- * The criterion used to classify a reflection as 'observed'
- * expressed as an upper limit for the value of I.
+ * The detector type used for recording images.
+ * Usually film or CCD camera.
*/
- readonly observed_criterion_I_max?: Maybe<Scalars['Float']>;
+ readonly film_or_detector_model?: Maybe<Scalars['String']>;
/**
- * The criterion used to classify a reflection as 'observed'
- * expressed as a lower limit for the value of I.
+ * The item _em_image_recording.id uniquely identifies
+ * a set of recorded images.
*/
- readonly observed_criterion_I_min?: Maybe<Scalars['Float']>;
+ readonly id: Scalars['String'];
+ /** This data item the id of the microscopy settings used in the imaging. */
+ readonly imaging_id: Scalars['String'];
+ /** The number of diffraction images collected. */
+ readonly num_diffraction_images?: Maybe<Scalars['Int']>;
+ /** Number of grids in the microscopy session */
+ readonly num_grids_imaged?: Maybe<Scalars['Int']>;
+ /** The number of micrograph images collected. */
+ readonly num_real_images?: Maybe<Scalars['Int']>;
+};
+
+export type EmImaging = {
+ /** A value of accelerating voltage (in kV) used for imaging. */
+ readonly accelerating_voltage?: Maybe<Scalars['Int']>;
/**
- * The criterion used to classify a reflection as 'observed'
- * expressed as a multiple of the value of sigma(F).
+ * microscope alignment procedure
+ *
+ * Allowable values:
+ * BASIC, COMA FREE, NONE, OTHER, ZEMLIN TABLEAU
+ *
*/
- readonly observed_criterion_sigma_F?: Maybe<Scalars['Float']>;
+ readonly alignment_procedure?: Maybe<Scalars['String']>;
+ /** astigmatism */
+ readonly astigmatism?: Maybe<Scalars['String']>;
/**
- * The criterion used to classify a reflection as 'observed'
- * expressed as a multiple of the value of sigma(I).
+ * The open diameter of the c2 condenser lens,
+ * in microns.
*/
- readonly observed_criterion_sigma_I?: Maybe<Scalars['Float']>;
+ readonly c2_aperture_diameter?: Maybe<Scalars['Float']>;
/**
- * The Pearson's correlation coefficient expressed as a decimal value
- * between the average intensities from randomly selected
- * half-datasets.
- *
- * Ref: Karplus & Diederichs (2012), Science 336, 1030-33
+ * The maximum defocus value of the objective lens (in nanometers) used
+ * to obtain the recorded images.
*/
- readonly pdbx_CC_half?: Maybe<Scalars['Float']>;
+ readonly calibrated_defocus_max?: Maybe<Scalars['Float']>;
/**
- * R split measures the agreement between the sets of intensities created by merging
- * odd- and even-numbered images from the overall data.
- *
- * Ref: T. A. White, R. A. Kirian, A. V. Martin, A. Aquila, K. Nass, A. Barty
- * and H. N. Chapman (2012), J. Appl. Cryst. 45, 335-341
+ * The minimum defocus value of the objective lens (in nanometers) used
+ * to obtain the recorded images.
*/
- readonly pdbx_R_split?: Maybe<Scalars['Float']>;
+ readonly calibrated_defocus_min?: Maybe<Scalars['Float']>;
/**
- * The R value for merging intensities satisfying the observed
- * criteria in this data set.
+ * The magnification value obtained for a known standard just
+ * prior to, during or just after the imaging experiment.
*/
- readonly pdbx_Rmerge_I_obs?: Maybe<Scalars['Float']>;
+ readonly calibrated_magnification?: Maybe<Scalars['Int']>;
/**
- * The precision-indicating merging R factor value Rpim,
- * for merging all intensities in this data set.
- *
- * sum~i~ [1/(N~i~ - 1)]1/2^ sum~j~ | I~j~ - <I~i~> |
- * Rpim = --------------------------------------------------
- * sum~i~ ( sum~j~ I~j~ )
- *
- * I~j~ = the intensity of the jth observation of reflection i
- * <I~i~> = the mean of the intensities of all observations
- * of reflection i
- * N~i~ = the redundancy (the number of times reflection i
- * has been measured).
- *
- * sum~i~ is taken over all reflections
- * sum~j~ is taken over all observations of each reflection.
- *
- * Ref: Diederichs, K. & Karplus, P. A. (1997). Nature Struct.
- * Biol. 4, 269-275.
- * Weiss, M. S. & Hilgenfeld, R. (1997). J. Appl. Cryst.
- * 30, 203-205.
- * Weiss, M. S. (2001). J. Appl. Cryst. 34, 130-135.
+ * Cryogen type used to maintain the specimen stage temperature during imaging
+ * in the microscope.
+ *
+ * Allowable values:
+ * HELIUM, NITROGEN
+ *
*/
- readonly pdbx_Rpim_I_all?: Maybe<Scalars['Float']>;
+ readonly cryogen?: Maybe<Scalars['String']>;
/**
- * The redundancy-independent merging R factor value Rrim,
- * also denoted Rmeas, for merging all intensities in this
- * data set.
- *
- * sum~i~ [N~i~/(N~i~ - 1)]1/2^ sum~j~ | I~j~ - <I~i~> |
- * Rrim = ----------------------------------------------------
- * sum~i~ ( sum~j~ I~j~ )
- *
- * I~j~ = the intensity of the jth observation of reflection i
- * <I~i~> = the mean of the intensities of all observations of
- * reflection i
- * N~i~ = the redundancy (the number of times reflection i
- * has been measured).
- *
- * sum~i~ is taken over all reflections
- * sum~j~ is taken over all observations of each reflection.
- *
- * Ref: Diederichs, K. & Karplus, P. A. (1997). Nature Struct.
- * Biol. 4, 269-275.
- * Weiss, M. S. & Hilgenfeld, R. (1997). J. Appl. Cryst.
- * 30, 203-205.
- * Weiss, M. S. (2001). J. Appl. Cryst. 34, 130-135.
+ * Date (YYYY-MM-DD) of imaging experiment or the date at which
+ * a series of experiments began.
+ *
+ * Examples:
+ * 2001-05-08
+ *
*/
- readonly pdbx_Rrim_I_all?: Maybe<Scalars['Float']>;
+ readonly date?: Maybe<Scalars['Date']>;
/**
- * The R sym value as a decimal number.
- *
+ * Any additional imaging details.
+ *
* Examples:
- * 0.02
+ * Preliminary grid screening was performed manually.
+ *
*/
- readonly pdbx_Rsym_value?: Maybe<Scalars['Float']>;
- /** Overall Chi-squared statistic. */
- readonly pdbx_chi_squared?: Maybe<Scalars['Float']>;
+ readonly details?: Maybe<Scalars['String']>;
/**
- * An identifier for the diffraction data set for this set of summary statistics.
- *
- * Multiple diffraction data sets entered as a comma separated list.
+ * The camera length (in millimeters). The camera length is the
+ * product of the objective focal length and the combined magnification
+ * of the intermediate and projector lenses when the microscope is
+ * operated in the diffraction mode.
*/
- readonly pdbx_diffrn_id?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
+ readonly detector_distance?: Maybe<Scalars['Float']>;
+ /** electron beam tilt params */
+ readonly electron_beam_tilt_params?: Maybe<Scalars['String']>;
+ /** The source of electrons. The electron gun. */
+ readonly electron_source?: Maybe<Scalars['String']>;
/**
- * The ratio of the average intensity to the average uncertainty,
- * <I>/<sigma(I)>.
+ * The value of _em_imaging.id must uniquely identify
+ * each imaging experiment.
*/
- readonly pdbx_netI_over_av_sigmaI?: Maybe<Scalars['Float']>;
+ readonly id: Scalars['String'];
/**
- * The mean of the ratio of the intensities to their
- * standard uncertainties, <I/sigma(I)>.
+ * The mode of illumination.
+ *
+ * Allowable values:
+ * FLOOD BEAM, OTHER, SPOT SCAN
+ *
*/
- readonly pdbx_netI_over_sigmaI?: Maybe<Scalars['Float']>;
+ readonly illumination_mode?: Maybe<Scalars['String']>;
/**
- * Total number of measured reflections.
- *
- * Examples:
- * 23000, 140000
+ * The name of the model of microscope.
+ *
+ * Allowable values:
+ * FEI MORGAGNI, FEI POLARA 300, FEI TALOS ARCTICA, FEI TECNAI 10, FEI TECNAI 12, FEI TECNAI 20, FEI TECNAI ARCTICA, FEI TECNAI F20, FEI TECNAI F30, FEI TECNAI SPHERA, FEI TECNAI SPIRIT, FEI TITAN, FEI TITAN KRIOS, FEI/PHILIPS CM10, FEI/PHILIPS CM12, FEI/PHILIPS CM120T, FEI/PHILIPS CM200FEG, FEI/PHILIPS CM200FEG/SOPHIE, FEI/PHILIPS CM200FEG/ST, FEI/PHILIPS CM200FEG/UT, FEI/PHILIPS CM200T, FEI/PHILIPS CM300FEG/HE, FEI/PHILIPS CM300FEG/ST, FEI/PHILIPS CM300FEG/T, FEI/PHILIPS EM400, FEI/PHILIPS EM420, HITACHI EF2000, HITACHI EF3000, HITACHI H-9500SD, HITACHI H3000 UHVEM, HITACHI H7600, HITACHI HF2000, HITACHI HF3000, JEOL 1000EES, JEOL 100B, JEOL 100CX, JEOL 1010, JEOL 1200, JEOL 1200EX, JEOL 1200EXII, JEOL 1230, JEOL 1400, JEOL 2000EX, JEOL 2000EXII, JEOL 2010, JEOL 2010F, JEOL 2010HC, JEOL 2010HT, JEOL 2010UHR, JEOL 2011, JEOL 2100, JEOL 2100F, JEOL 2200FS, JEOL 2200FSC, JEOL 3000SFF, JEOL 3100FEF, JEOL 3100FFC, JEOL 3200FS, JEOL 3200FSC, JEOL 4000, JEOL 4000EX, JEOL CRYO ARM 200, JEOL CRYO ARM 300, JEOL KYOTO-3000SFF, SIEMENS SULEIKA, TFS GLACIOS, TFS KRIOS, TFS TALOS, TFS TALOS F200C, TFS TALOS L120C, TFS TUNDRA, ZEISS LEO912, ZEISS LIBRA120PLUS
+ *
*/
- readonly pdbx_number_measured_all?: Maybe<Scalars['Int']>;
- /** An ordinal identifier for this set of reflection statistics. */
- readonly pdbx_ordinal: Scalars['Int'];
- /** Overall redundancy for this data set (%). */
- readonly pdbx_redundancy?: Maybe<Scalars['Float']>;
- /** Number of reflections rejected in scaling operations. */
- readonly pdbx_scaling_rejects?: Maybe<Scalars['Int']>;
+ readonly microscope_model?: Maybe<Scalars['String']>;
/**
- * The percentage of geometrically possible reflections represented
- * by reflections that satisfy the resolution limits established
- * by _reflns.d_resolution_high and _reflns.d_resolution_low and
- * the observation limit established by
- * _reflns.observed_criterion.
+ * The mode of imaging.
+ *
+ * Allowable values:
+ * BRIGHT FIELD, DARK FIELD, DIFFRACTION, OTHER
+ *
*/
- readonly percent_possible_obs?: Maybe<Scalars['Float']>;
+ readonly mode?: Maybe<Scalars['String']>;
/**
- * The value of _reflns.phase_calculation_details describes a
- * special details about calculation of phases in _refln.phase_calc.
- *
+ * The spherical aberration coefficient (Cs) in millimeters,
+ * of the objective lens.
+ *
* Examples:
- * From model, NCS averaging, Solvent flipping, Solvent flattening, Multiple crystal averaging, Multiple phase modification, Other phase modification
+ * null
+ *
*/
- readonly phase_calculation_details?: Maybe<Scalars['String']>;
-};
-
-export type RcsbLatestRevision = {
- /** The major version number of the latest revision. */
- readonly major_revision?: Maybe<Scalars['Int']>;
- /** The minor version number of the latest revision. */
- readonly minor_revision?: Maybe<Scalars['Int']>;
- /** The release date of the latest revision item. */
- readonly revision_date?: Maybe<Scalars['Date']>;
-};
-
-export type RcsbPolymerEntityRcsbEcLineage = {
- /** Members of the enzyme classification lineage as parent classification hierarchy depth (1-N). */
- readonly depth?: Maybe<Scalars['Int']>;
- /** Members of the enzyme classification lineage as parent classification codes. */
- readonly id?: Maybe<Scalars['String']>;
- /** Members of the enzyme classification lineage as parent classification names. */
- readonly name?: Maybe<Scalars['String']>;
-};
-
-export type RcsbAssemblyInfo = {
- /** Entity identifier for the container. */
- readonly assembly_id?: Maybe<Scalars['String']>;
- /** The assembly non-hydrogen atomic coordinate count. */
- readonly atom_count?: Maybe<Scalars['Int']>;
- /** The assembly non-hydrogen branched entity atomic coordinate count. */
- readonly branched_atom_count?: Maybe<Scalars['Int']>;
- /** The number of distinct branched entities in the generated assembly. */
- readonly branched_entity_count?: Maybe<Scalars['Int']>;
+ readonly nominal_cs?: Maybe<Scalars['Float']>;
/**
- * The number of branched instances in the generated assembly data set.
- * This is the total count of branched entity instances generated in the assembly coordinate data.
+ * The maximum defocus value of the objective lens (in nanometers) used
+ * to obtain the recorded images.
*/
- readonly branched_entity_instance_count?: Maybe<Scalars['Int']>;
- /** The PDB entry accession code. */
- readonly entry_id: Scalars['String'];
+ readonly nominal_defocus_max?: Maybe<Scalars['Float']>;
/**
- * The number of modeled polymer monomers in the assembly coordinate data.
- * This is the total count of monomers with reported coordinate data for all polymer
- * entity instances in the generated assembly coordinate data.
+ * The minimum defocus value of the objective lens (in nanometers) used
+ * to obtain the recorded images.
*/
- readonly modeled_polymer_monomer_count?: Maybe<Scalars['Int']>;
+ readonly nominal_defocus_min?: Maybe<Scalars['Float']>;
+ /** The magnification indicated by the microscope readout. */
+ readonly nominal_magnification?: Maybe<Scalars['Int']>;
/**
- * Nucleic acid polymer entity type categories describing the generated assembly.
- *
- * Allowable values:
- * DNA (only), DNA/RNA (only), NA-hybrid (only), Other, RNA (only)
+ * The specimen temperature maximum (degrees Kelvin) for the duration
+ * of imaging.
*/
- readonly na_polymer_entity_types?: Maybe<Scalars['String']>;
- /** The assembly non-hydrogen non-polymer entity atomic coordinate count. */
- readonly nonpolymer_atom_count?: Maybe<Scalars['Int']>;
- /** The number of distinct non-polymer entities in the generated assembly exclusive of solvent. */
- readonly nonpolymer_entity_count?: Maybe<Scalars['Int']>;
+ readonly recording_temperature_maximum?: Maybe<Scalars['Float']>;
/**
- * The number of non-polymer instances in the generated assembly data set exclusive of solvent.
- * This is the total count of non-polymer entity instances generated in the assembly coordinate data.
+ * The specimen temperature minimum (degrees Kelvin) for the duration
+ * of imaging.
*/
- readonly nonpolymer_entity_instance_count?: Maybe<Scalars['Int']>;
- /** The assembly non-hydrogen polymer entity atomic coordinate count. */
- readonly polymer_atom_count?: Maybe<Scalars['Int']>;
+ readonly recording_temperature_minimum?: Maybe<Scalars['Float']>;
+ /** residual tilt of the electron beam */
+ readonly residual_tilt?: Maybe<Scalars['Float']>;
/**
- * Categories describing the polymer entity composition for the generated assembly.
- *
+ * The name of the model of specimen holder used during imaging.
+ *
* Allowable values:
- * DNA, DNA/RNA, NA-hybrid, NA/oligosaccharide, RNA, heteromeric protein, homomeric protein, oligosaccharide, other, other type composition, other type pair, protein/NA, protein/NA/oligosaccharide, protein/oligosaccharide
+ * FEI TITAN KRIOS AUTOGRID HOLDER, FISCHIONE 2550, FISCHIONE INSTRUMENTS DUAL AXIS TOMOGRAPHY HOLDER, GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER, GATAN 910 MULTI-SPECIMEN SINGLE TILT CRYO TRANSFER HOLDER, GATAN 914 HIGH TILT LIQUID NITROGEN CRYO TRANSFER TOMOGRAPHY HOLDER, GATAN 915 DOUBLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER, GATAN CHDT 3504 DOUBLE TILT HIGH RESOLUTION NITROGEN COOLING HOLDER, GATAN CT3500 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER, GATAN CT3500TR SINGLE TILT ROTATION LIQUID NITROGEN CRYO TRANSFER HOLDER, GATAN ELSA 698 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER, GATAN HC 3500 SINGLE TILT HEATING/NITROGEN COOLING HOLDER, GATAN HCHDT 3010 DOUBLE TILT HIGH RESOLUTION HELIUM COOLING HOLDER, GATAN HCHST 3008 SINGLE TILT HIGH RESOLUTION HELIUM COOLING HOLDER, GATAN HELIUM, GATAN LIQUID NITROGEN, GATAN UHRST 3500 SINGLE TILT ULTRA HIGH RESOLUTION NITROGEN COOLING HOLDER, GATAN ULTDT ULTRA LOW TEMPERATURE DOUBLE TILT HELIUM COOLING HOLDER, GATAN ULTST ULTRA LOW TEMPERATURE SINGLE TILT HELIUM COOLING HOLDER, HOME BUILD, JEOL, JEOL 3200FSC CRYOHOLDER, JEOL CRYOSPECPORTER, OTHER, PHILIPS ROTATION HOLDER, SIDE ENTRY, EUCENTRIC
+ *
*/
- readonly polymer_composition?: Maybe<Scalars['String']>;
- /** The number of distinct polymer entities in the generated assembly. */
- readonly polymer_entity_count?: Maybe<Scalars['Int']>;
- /** The number of distinct DNA polymer entities in the generated assembly. */
- readonly polymer_entity_count_DNA?: Maybe<Scalars['Int']>;
- /** The number of distinct RNA polymer entities in the generated assembly. */
- readonly polymer_entity_count_RNA?: Maybe<Scalars['Int']>;
- /** The number of distinct nucleic acid polymer entities (DNA or RNA) in the generated assembly. */
- readonly polymer_entity_count_nucleic_acid?: Maybe<Scalars['Int']>;
- /** The number of distinct hybrid nucleic acid polymer entities in the generated assembly. */
- readonly polymer_entity_count_nucleic_acid_hybrid?: Maybe<Scalars['Int']>;
- /** The number of distinct protein polymer entities in the generated assembly. */
- readonly polymer_entity_count_protein?: Maybe<Scalars['Int']>;
+ readonly specimen_holder_model?: Maybe<Scalars['String']>;
/**
- * The number of polymer instances in the generated assembly data set.
- * This is the total count of polymer entity instances generated in the assembly coordinate data.
+ * The type of specimen holder used during imaging.
+ *
+ * Examples:
+ * cryo
+ *
*/
- readonly polymer_entity_instance_count?: Maybe<Scalars['Int']>;
+ readonly specimen_holder_type?: Maybe<Scalars['String']>;
+ /** Foreign key to the EM_SPECIMEN category */
+ readonly specimen_id?: Maybe<Scalars['String']>;
/**
- * The number of DNA polymer instances in the generated assembly data set.
- * This is the total count of DNA polymer entity instances generated in the assembly coordinate data.
+ * The mean specimen stage temperature (degrees Kelvin) during imaging
+ * in the microscope.
*/
- readonly polymer_entity_instance_count_DNA?: Maybe<Scalars['Int']>;
+ readonly temperature?: Maybe<Scalars['Float']>;
/**
- * The number of RNA polymer instances in the generated assembly data set.
- * This is the total count of RNA polymer entity instances generated in the assembly coordinate data.
+ * The maximum angle at which the specimen was tilted to obtain
+ * recorded images.
*/
- readonly polymer_entity_instance_count_RNA?: Maybe<Scalars['Int']>;
+ readonly tilt_angle_max?: Maybe<Scalars['Float']>;
/**
- * The number of nucleic acid polymer instances in the generated assembly data set.
- * This is the total count of nucleic acid polymer entity instances generated in the assembly coordinate data.
+ * The minimum angle at which the specimen was tilted to obtain
+ * recorded images.
*/
- readonly polymer_entity_instance_count_nucleic_acid?: Maybe<Scalars['Int']>;
+ readonly tilt_angle_min?: Maybe<Scalars['Float']>;
+};
+
+export type EmParticleSelection = {
/**
- * The number of hybrid nucleic acide polymer instances in the generated assembly data set.
- * This is the total count of hybrid nucleic acid polymer entity instances generated in the assembly coordinate data.
+ * Any additional details used for selecting particles
+ *
+ * Examples:
+ * negative monitor contrast facilitated particle picking
+ *
*/
- readonly polymer_entity_instance_count_nucleic_acid_hybrid?: Maybe<Scalars['Int']>;
+ readonly details?: Maybe<Scalars['String']>;
+ /** Ordinal identifier */
+ readonly id: Scalars['String'];
/**
- * The number of protein polymer instances in the generated assembly data set.
- * This is the total count of protein polymer entity instances generated in the assembly coordinate data.
+ * The value of _em_particle_selection.image_processing_id points to
+ * the EM_IMAGE_PROCESSING category.
*/
- readonly polymer_entity_instance_count_protein?: Maybe<Scalars['Int']>;
+ readonly image_processing_id: Scalars['String'];
+ /** The number of particles selected from the projection set of images. */
+ readonly num_particles_selected?: Maybe<Scalars['Int']>;
+};
+
+export type EmSingleParticleEntity = {
+ /** Unique category label. */
+ readonly id: Scalars['Int'];
+ /** pointer to _em_image_processing.id. */
+ readonly image_processing_id: Scalars['String'];
/**
- * The number of polymer monomers in sample entity instances comprising the assembly data set.
- * This is the total count of monomers for all polymer entity instances
- * in the generated assembly coordinate data.
+ * Point symmetry symbol, either Cn, Dn, T, O, or I
+ *
+ * Examples:
+ * C1, C5, C4
+ *
*/
- readonly polymer_monomer_count?: Maybe<Scalars['Int']>;
+ readonly point_symmetry?: Maybe<Scalars['String']>;
+};
+
+export type EmSoftware = {
/**
- * Selected polymer entity type categories describing the generated assembly.
- *
+ * The purpose of the software.
+ *
* Allowable values:
- * Nucleic acid (only), Other, Protein (only), Protein/NA
+ * CLASSIFICATION, CRYSTALLOGRAPHY MERGING, CTF CORRECTION, DIFFRACTION INDEXING, FINAL EULER ASSIGNMENT, IMAGE ACQUISITION, INITIAL EULER ASSIGNMENT, LATTICE DISTORTION CORRECTION, LAYERLINE INDEXING, MASKING, MODEL FITTING, MODEL REFINEMENT, MOLECULAR REPLACEMENT, OTHER, PARTICLE SELECTION, RECONSTRUCTION, SERIES ALIGNMENT, SYMMETRY DETERMINATION, VOLUME SELECTION
+ *
*/
- readonly selected_polymer_entity_types?: Maybe<Scalars['String']>;
- /** The assembly non-hydrogen solvent atomic coordinate count. */
- readonly solvent_atom_count?: Maybe<Scalars['Int']>;
- /** The number of distinct solvent entities in the generated assembly. */
- readonly solvent_entity_count?: Maybe<Scalars['Int']>;
+ readonly category?: Maybe<Scalars['String']>;
/**
- * The number of solvent instances in the generated assembly data set.
- * This is the total count of solvent entity instances generated in the assembly coordinate data.
+ * Details about the software used.
+ *
+ * Examples:
+ * EMAN2 e2boxer.py was used to automatically select particle images.
+ *
*/
- readonly solvent_entity_instance_count?: Maybe<Scalars['Int']>;
+ readonly details?: Maybe<Scalars['String']>;
+ /** pointer to _em_3d_fitting.id in the EM_3D_FITTING category. */
+ readonly fitting_id?: Maybe<Scalars['String']>;
+ /** Unique identifier for each software description. */
+ readonly id: Scalars['String'];
+ /** pointer to _em_image_processing.id in the EM_IMAGE_PROCESSING category. */
+ readonly image_processing_id?: Maybe<Scalars['String']>;
+ /** pointer to _em_imaging.id in the EM_IMAGING category. */
+ readonly imaging_id?: Maybe<Scalars['String']>;
/**
- * The number of unmodeled polymer monomers in the assembly coordinate data. This is
- * the total count of monomers with unreported coordinate data for all polymer
- * entity instances in the generated assembly coordinate data.
+ * The name of the software package used, e.g., RELION. Depositors are strongly
+ * encouraged to provide a value in this field.
+ *
+ * Examples:
+ * EMAN, Imagic, Spider, Bsoft, UCSF-Chimera
+ *
*/
- readonly unmodeled_polymer_monomer_count?: Maybe<Scalars['Int']>;
+ readonly name?: Maybe<Scalars['String']>;
+ /**
+ * The version of the software.
+ *
+ * Examples:
+ * 9.03, 2.1
+ *
+ */
+ readonly version?: Maybe<Scalars['String']>;
};
-export type RcsbBindingAffinity = {
+export type EmSpecimen = {
/**
- * Ligand identifier.
- *
+ * The concentration (in milligrams per milliliter, mg/ml)
+ * of the complex in the sample.
+ *
* Examples:
- * 0WE, SPE, CL
+ * null
+ *
*/
- readonly comp_id: Scalars['String'];
- /** Link to external resource referencing the data. */
- readonly link: Scalars['String'];
+ readonly concentration?: Maybe<Scalars['Float']>;
/**
- * The resource name for the related binding affinity reference.
- *
- * Allowable values:
- * PDBBind, Binding MOAD, BindingDB
+ * A description of any additional details of the specimen preparation.
+ *
+ * Examples:
+ * This sample was monodisperse., Au was deposited at a 30 degree angle to 15 nm thickness., Colloidal gold particles were deposited by dipping into dilute solution., The specimen was frozen at high pressure using the bal-tec hpm 010 instrument., The embedded sample was sectioned at 100 K to 50 nm final thickness.
+ *
*/
- readonly provenance_code: Scalars['String'];
+ readonly details?: Maybe<Scalars['String']>;
/**
- * Data point provided by BindingDB. Percent identity between PDB sequence and reference sequence.
- *
- * Examples:
- * null, null, null
+ * 'YES' indicates that the specimen has been embedded.
+ *
+ * Allowable values:
+ * NO, YES
+ *
*/
- readonly reference_sequence_identity?: Maybe<Scalars['Int']>;
+ readonly embedding_applied?: Maybe<Scalars['String']>;
+ /** Pointer to _em_experiment.id. */
+ readonly experiment_id: Scalars['String'];
/**
- * Binding affinity symbol indicating approximate or precise strength of the binding.
- *
- * Examples:
- * ~, =, >, <, >=, <=
+ * The item _em_specimen.id uniquely identifies a specimen along with
+ * its preparation methods.
*/
- readonly symbol?: Maybe<Scalars['String']>;
+ readonly id: Scalars['String'];
/**
- * Binding affinity measurement given in one of the following types: The concentration constants: IC50: the concentration of ligand that reduces enzyme activity by 50%; EC50: the concentration of compound that generates a half-maximal response; The binding constant: Kd: dissociation constant; Ka: association constant; Ki: enzyme inhibition constant; The thermodynamic parameters: delta G: Gibbs free energy of binding (for association reaction); delta H: change in enthalpy associated with a chemical reaction; delta S: change in entropy associated with a chemical reaction.
- *
+ * 'YES' indicates that the specimen has been shadowed.
+ *
* Allowable values:
- * IC50, EC50, Kd, Ka, Ki, ΔG, ΔH, -TΔS
+ * NO, YES
+ *
*/
- readonly type: Scalars['String'];
+ readonly shadowing_applied?: Maybe<Scalars['String']>;
/**
- * Binding affinity unit. Dissociation constant Kd is normally in molar units (or millimolar , micromolar, nanomolar, etc). Association constant Ka is normally expressed in inverse molar units (e.g. M-1).
- *
- * Examples:
- * nM, kJ/mol
+ * 'YES' indicates that the specimen has been stained.
+ *
+ * Allowable values:
+ * NO, YES
+ *
*/
- readonly unit: Scalars['String'];
- /** Binding affinity value between a ligand and its target molecule. */
- readonly value: Scalars['Float'];
-};
-
-export type RcsbBranchedEntityFeatureSummary = {
- /** The feature count. */
- readonly count?: Maybe<Scalars['Int']>;
- /** The fractional feature coverage relative to the full branched entity. */
- readonly coverage?: Maybe<Scalars['Float']>;
- /** The maximum feature length. */
- readonly maximum_length?: Maybe<Scalars['Int']>;
- /** The maximum feature value. */
- readonly maximum_value?: Maybe<Scalars['Float']>;
- /** The minimum feature length. */
- readonly minimum_length?: Maybe<Scalars['Int']>;
- /** The minimum feature value. */
- readonly minimum_value?: Maybe<Scalars['Float']>;
+ readonly staining_applied?: Maybe<Scalars['String']>;
/**
- * Type or category of the feature.
- *
+ * 'YES' indicates that the specimen was vitrified by cryopreservation.
+ *
* Allowable values:
- * mutation
+ * NO, YES
+ *
*/
- readonly type?: Maybe<Scalars['String']>;
+ readonly vitrification_applied?: Maybe<Scalars['String']>;
};
-export type EmEntityAssembly = {
+export type EmStaining = {
/**
- * Additional details about the component.
- *
+ * Staining procedure used in the specimen preparation.
+ *
* Examples:
- * Fab fragment generated by proteolytic cleavage of LA2 IgG antibody.
+ * Negatively stained EM specimens were prepared using a carbon-sandwich technique
+ * and uranyl-formate stain.
+ *
*/
readonly details?: Maybe<Scalars['String']>;
- /**
- * macromolecules associated with this component, if defined
- * as comma separated list of entity ids (integers).
- */
- readonly entity_id_list?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
- /**
- * The value of _em_entity_assembly.id identifies
- * one component of the complex.
- */
+ /** This data item is the primary key of the category. */
readonly id: Scalars['String'];
/**
- * Name of this component in the observed assembly.
- *
+ * The staining material.
+ *
* Examples:
- * Ternary complex of alpha-tubulin with tubulin folding cofactors TBCE and TBCB, 80S Ribosome bound to emetine, messenger RNA, initiation factor 2, GroEL, antibody Fab fragment
+ * Uranyl Acetate
+ *
*/
- readonly name?: Maybe<Scalars['String']>;
- /** oligomeric details */
- readonly oligomeric_details?: Maybe<Scalars['String']>;
+ readonly material?: Maybe<Scalars['String']>;
+ /** Foreign key relationship to the EMD SPECIMEN category */
+ readonly specimen_id?: Maybe<Scalars['String']>;
/**
- * The parent of this assembly.
- * This data item is an internal category pointer to _em_entity_assembly.id.
- * By convention, the full assembly (top of hierarchy) is assigned parent id 0 (zero).
+ * type of staining
+ *
+ * Allowable values:
+ * NEGATIVE, NONE, POSITIVE
+ *
*/
- readonly parent_id?: Maybe<Scalars['Int']>;
+ readonly type?: Maybe<Scalars['String']>;
+};
+
+export type EmVitrification = {
+ /** The temperature (in degrees Kelvin) of the sample just prior to vitrification. */
+ readonly chamber_temperature?: Maybe<Scalars['Float']>;
/**
- * The assembly type.
- *
+ * This is the name of the cryogen.
+ *
* Allowable values:
- * MULTIPLE SOURCES, NATURAL, RECOMBINANT
+ * ETHANE, ETHANE-PROPANE, FREON 12, FREON 22, HELIUM, METHANE, NITROGEN, OTHER, PROPANE
+ *
*/
- readonly source?: Maybe<Scalars['String']>;
+ readonly cryogen_name?: Maybe<Scalars['String']>;
/**
- * Alternative name of the component.
- *
+ * Any additional details relating to vitrification.
+ *
* Examples:
- * FADV-1
+ * Vitrification carried out in argon atmosphere.
+ *
*/
- readonly synonym?: Maybe<Scalars['String']>;
+ readonly details?: Maybe<Scalars['String']>;
+ /** The humidity (%) in the vicinity of the vitrification process. */
+ readonly humidity?: Maybe<Scalars['Float']>;
/**
- * A description of types of components of the
- * assembly of the biological structure.
+ * The value of _em_vitrification.id must uniquely identify
+ * the vitrification procedure.
*/
- readonly type?: Maybe<Scalars['String']>;
-};
-
-export type RcsbUniprotProteinSourceOrganism = {
- /** Historical record of the data attribute. */
- readonly provenance_code: Scalars['String'];
- /** The scientific name of the organism in which a protein occurs. */
- readonly scientific_name: Scalars['String'];
- /** NCBI Taxonomy identifier for the organism in which a protein occurs. */
- readonly taxonomy_id?: Maybe<Scalars['Int']>;
-};
-
-export type CoreDrugbank = {
- readonly drugbank_container_identifiers?: Maybe<DrugbankContainerIdentifiers>;
- readonly drugbank_info?: Maybe<DrugbankInfo>;
- readonly drugbank_target?: Maybe<ReadonlyArray<Maybe<DrugbankTarget>>>;
-};
-
-export type PdbxAuditRevisionGroup = {
+ readonly id: Scalars['String'];
/**
- * The type of file that the pdbx_audit_revision_history record refers to.
- *
+ * The type of instrument used in the vitrification process.
+ *
* Allowable values:
- * Chemical component, NMR restraints, NMR shifts, Structure factors, Structure model
+ * EMS-002 RAPID IMMERSION FREEZER, FEI VITROBOT MARK I, FEI VITROBOT MARK II, FEI VITROBOT MARK III, FEI VITROBOT MARK IV, GATAN CRYOPLUNGE 3, HOMEMADE PLUNGER, LEICA EM CPC, LEICA EM GP, LEICA KF80, LEICA PLUNGER, REICHERT-JUNG PLUNGER, SPOTITON, ZEISS PLUNGE FREEZER CRYOBOX
+ *
*/
- readonly data_content_type: Scalars['String'];
+ readonly instrument?: Maybe<Scalars['String']>;
/**
- * The collection of categories updated with this revision.
- *
- * Allowable values:
- * Advisory, Atomic model, Author supporting evidence, Data collection, Data processing, Database references, Derived calculations, Experimental data, Experimental preparation, Initial release, Non-polymer description, Other, Polymer sequence, Refinement description, Source and taxonomy, Structure summary, Version format compliance
+ * The procedure for vitrification.
+ *
+ * Examples:
+ * plunge freezing
+ *
*/
- readonly group?: Maybe<Scalars['String']>;
+ readonly method?: Maybe<Scalars['String']>;
+ /** This data item is a pointer to _em_specimen.id */
+ readonly specimen_id: Scalars['String'];
/**
- * A unique identifier for the pdbx_audit_revision_group record.
- *
- * Examples:
- * 1
+ * The vitrification temperature (in degrees Kelvin), e.g.,
+ * temperature of the plunge instrument cryogen bath.
*/
- readonly ordinal: Scalars['Int'];
+ readonly temp?: Maybe<Scalars['Float']>;
/**
- * A pointer to _pdbx_audit_revision_history.ordinal
- *
+ * The length of time after an event effecting the sample that
+ * vitrification was induced and a description of the event.
+ *
* Examples:
- * 1
+ * plunge 30 msec after spraying with effector
+ *
*/
- readonly revision_ordinal: Scalars['Int'];
+ readonly time_resolved_state?: Maybe<Scalars['String']>;
};
-export type RcsbChemCompAnnotation = {
- /** An identifier for the annotation. */
- readonly annotation_id?: Maybe<Scalars['String']>;
- readonly annotation_lineage?: Maybe<ReadonlyArray<Maybe<RcsbChemCompAnnotationAnnotationLineage>>>;
- /** Identifies the version of the annotation assignment. */
- readonly assignment_version?: Maybe<Scalars['String']>;
- /** A description for the annotation. */
- readonly description?: Maybe<Scalars['String']>;
- /** A name for the annotation. */
- readonly name?: Maybe<Scalars['String']>;
- /**
- * Code identifying the individual, organization or program that
- * assigned the annotation.
- */
- readonly provenance_source?: Maybe<Scalars['String']>;
+export type EntityPoly = {
/**
- * A type or category of the annotation.
- *
+ * A flag to indicate whether the polymer contains at least
+ * one monomer-to-monomer link different from that implied by
+ * _entity_poly.type.
+ *
* Allowable values:
- * ATC, Carbohydrate Anomer, Carbohydrate Isomer, Carbohydrate Primary Carbonyl Group, Carbohydrate Ring, Generating Enzyme, Modification Type, PSI-MOD
+ * n, no, y, yes
+ *
*/
- readonly type?: Maybe<Scalars['String']>;
-};
-
-export type ExptlCrystalGrow = {
+ readonly nstd_linkage?: Maybe<Scalars['String']>;
/**
- * This data item is a pointer to _exptl_crystal.id in the
- * EXPTL_CRYSTAL category.
+ * A flag to indicate whether the polymer contains at least
+ * one monomer that is not considered standard.
+ *
+ * Allowable values:
+ * n, no, y, yes
+ *
*/
- readonly crystal_id: Scalars['String'];
+ readonly nstd_monomer?: Maybe<Scalars['String']>;
/**
- * A description of special aspects of the crystal growth.
- *
- * Examples:
- * Solution 2 was prepared as a well solution and
- * mixed. A droplet containing 2 \ml of solution
- * 1 was delivered onto a cover slip; 2 \ml of
- * solution 2 was added to the droplet without
- * mixing., Crystal plates were originally stored at room
- * temperature for 1 week but no nucleation
- * occurred. They were then transferred to 4
- * degrees C, at which temperature well formed
- * single crystals grew in 2 days., The dependence on pH for successful crystal
- * growth is very sharp. At pH 7.4 only showers
- * of tiny crystals grew, at pH 7.5 well formed
- * single crystals grew, at pH 7.6 no
- * crystallization occurred at all.
+ * Sequence of protein or nucleic acid polymer in standard one-letter
+ * codes of amino acids or nucleotides. Non-standard amino
+ * acids/nucleotides are represented by their Chemical
+ * Component Dictionary (CCD) codes in
+ * parenthesis. Deoxynucleotides are represented by the
+ * specially-assigned 2-letter CCD codes in parenthesis,
+ * with 'D' prefix added to their ribonucleotide
+ * counterparts. For hybrid polymer, each residue is
+ * represented by the code of its individual type. A
+ * cyclic polymer is represented in linear sequence from
+ * the chosen start to end.
+ *
+ * A for Alanine or Adenosine-5'-monophosphate
+ * C for Cysteine or Cytidine-5'-monophosphate
+ * D for Aspartic acid
+ * E for Glutamic acid
+ * F for Phenylalanine
+ * G for Glycine or Guanosine-5'-monophosphate
+ * H for Histidine
+ * I for Isoleucine or Inosinic Acid
+ * L for Leucine
+ * K for Lysine
+ * M for Methionine
+ * N for Asparagine or Unknown ribonucleotide
+ * O for Pyrrolysine
+ * P for Proline
+ * Q for Glutamine
+ * R for Arginine
+ * S for Serine
+ * T for Threonine
+ * U for Selenocysteine or Uridine-5'-monophosphate
+ * V for Valine
+ * W for Tryptophan
+ * Y for Tyrosine
+ * (DA) for 2'-deoxyadenosine-5'-monophosphate
+ * (DC) for 2'-deoxycytidine-5'-monophosphate
+ * (DG) for 2'-deoxyguanosine-5'-monophosphate
+ * (DT) for Thymidine-5'-monophosphate
+ * (MSE) for Selenomethionine
+ * (SEP) for Phosphoserine
+ * (PTO) for Phosphothreonine
+ * (PTR) for Phosphotyrosine
+ * (PCA) for Pyroglutamic acid
+ * (UNK) for Unknown amino acid
+ * (ACE) for Acetylation cap
+ * (NH2) for Amidation cap
+ *
+ * Examples:
+ * HHHH(MSE)AKQRSG or AUCGGAAU, (MSE)SHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGAAFNVEFD
+ *
*/
- readonly details?: Maybe<Scalars['String']>;
+ readonly pdbx_seq_one_letter_code?: Maybe<Scalars['String']>;
/**
- * The method used to grow the crystals.
- *
+ * Canonical sequence of protein or nucleic acid polymer in standard
+ * one-letter codes of amino acids or nucleotides,
+ * corresponding to the sequence in
+ * _entity_poly.pdbx_seq_one_letter_code. Non-standard
+ * amino acids/nucleotides are represented by the codes of
+ * their parents if parent is specified in
+ * _chem_comp.mon_nstd_parent_comp_id, or by letter 'X' if
+ * parent is not specified. Deoxynucleotides are
+ * represented by their canonical one-letter codes of A,
+ * C, G, or T.
+ *
* Examples:
- * MICROBATCH, VAPOR DIFFUSION, HANGING DROP
+ * MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGAAFNVEFD
+ *
*/
- readonly method?: Maybe<Scalars['String']>;
+ readonly pdbx_seq_one_letter_code_can?: Maybe<Scalars['String']>;
/**
- * The pH at which the crystal was grown. If more than one pH was
- * employed during the crystallization process, the final pH should
- * be noted here and the protocol involving multiple pH values
- * should be described in _exptl_crystal_grow.details.
- *
+ * The PDB strand/chain id(s) corresponding to this polymer entity.
+ *
* Examples:
- * 7.4, 7.6, 4.3
+ * A,B, A, B, A,B,C
+ *
*/
- readonly pH?: Maybe<Scalars['Float']>;
+ readonly pdbx_strand_id?: Maybe<Scalars['String']>;
/**
- * Text description of crystal growth procedure.
- *
+ * For Structural Genomics entries, the sequence's target identifier registered at the TargetTrack database.
+ *
* Examples:
- * PEG 4000, potassium phosphate, magnesium chloride, cacodylate
+ * JCSG-11211, 356560
+ *
*/
- readonly pdbx_details?: Maybe<Scalars['String']>;
+ readonly pdbx_target_identifier?: Maybe<Scalars['String']>;
/**
- * The range of pH values at which the crystal was grown. Used when
- * a point estimate of pH is not appropriate.
- *
- * Examples:
- * 5.6 - 6.4
+ * Number of regions in the sample sequence identified as expression tags, linkers, or
+ * cloning artifacts.
*/
- readonly pdbx_pH_range?: Maybe<Scalars['String']>;
+ readonly rcsb_artifact_monomer_count?: Maybe<Scalars['Int']>;
+ /** Number of monomer conflicts relative to the reference sequence. */
+ readonly rcsb_conflict_count?: Maybe<Scalars['Int']>;
+ /** Number of monomer deletions relative to the reference sequence. */
+ readonly rcsb_deletion_count?: Maybe<Scalars['Int']>;
/**
- * The temperature in kelvins at which the crystal was grown.
- * If more than one temperature was employed during the
- * crystallization process, the final temperature should be noted
- * here and the protocol involving multiple temperatures should be
- * described in _exptl_crystal_grow.details.
+ * A coarse-grained polymer entity type.
+ *
+ * Allowable values:
+ * DNA, NA-hybrid, Other, Protein, RNA
+ *
*/
- readonly temp?: Maybe<Scalars['Float']>;
+ readonly rcsb_entity_polymer_type?: Maybe<Scalars['String']>;
+ /** Number of monomer insertions relative to the reference sequence. */
+ readonly rcsb_insertion_count?: Maybe<Scalars['Int']>;
+ /** Number of engineered mutations engineered in the sample sequence. */
+ readonly rcsb_mutation_count?: Maybe<Scalars['Int']>;
+ /** Number of non-standard monomers in the sample sequence. */
+ readonly rcsb_non_std_monomer_count?: Maybe<Scalars['Int']>;
+ /** Unique list of non-standard monomer chemical component identifiers in the sample sequence. */
+ readonly rcsb_non_std_monomers?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
+ /** For polymer BIRD molecules the BIRD identifier for the entity. */
+ readonly rcsb_prd_id?: Maybe<Scalars['String']>;
+ /** The monomer length of the sample sequence. */
+ readonly rcsb_sample_sequence_length?: Maybe<Scalars['Int']>;
/**
- * A description of special aspects of temperature control during
- * crystal growth.
+ * The type of the polymer.
+ *
+ * Allowable values:
+ * cyclic-pseudo-peptide, other, peptide nucleic acid, polydeoxyribonucleotide, polydeoxyribonucleotide/polyribonucleotide hybrid, polypeptide(D), polypeptide(L), polyribonucleotide
+ *
*/
- readonly temp_details?: Maybe<Scalars['String']>;
+ readonly type?: Maybe<Scalars['String']>;
};
-export type CoreBranchedEntityInstance = {
- /** Get branched entity for this branched entity instance. */
- readonly branched_entity?: Maybe<CoreBranchedEntity>;
- readonly pdbx_struct_special_symmetry?: Maybe<ReadonlyArray<Maybe<PdbxStructSpecialSymmetry>>>;
- readonly rcsb_branched_entity_instance_container_identifiers?: Maybe<RcsbBranchedEntityInstanceContainerIdentifiers>;
- readonly rcsb_branched_instance_annotation?: Maybe<ReadonlyArray<Maybe<RcsbBranchedInstanceAnnotation>>>;
- readonly rcsb_branched_instance_feature?: Maybe<ReadonlyArray<Maybe<RcsbBranchedInstanceFeature>>>;
- readonly rcsb_branched_instance_feature_summary?: Maybe<ReadonlyArray<Maybe<RcsbBranchedInstanceFeatureSummary>>>;
- readonly rcsb_branched_struct_conn?: Maybe<ReadonlyArray<Maybe<RcsbBranchedStructConn>>>;
+export type EntitySrcGen = {
/**
- * A unique identifier for each object in this entity instance container formed by
- * an 'dot' (.) separated concatenation of entry and entity instance identifiers.
+ * A unique identifier for the expression system. This
+ * should be extracted from a local list of expression
+ * systems.
*/
- readonly rcsb_id: Scalars['String'];
- readonly rcsb_latest_revision?: Maybe<RcsbLatestRevision>;
-};
-
-export type RcsbBranchedEntity = {
- /** A description of special aspects of the branched entity. */
- readonly details?: Maybe<Scalars['String']>;
- /** Formula mass (KDa) of the branched entity. */
- readonly formula_weight?: Maybe<Scalars['Float']>;
- /** A description of the branched entity. */
- readonly pdbx_description?: Maybe<Scalars['String']>;
+ readonly expression_system_id?: Maybe<Scalars['String']>;
/**
- * The number of molecules of the branched entity in the entry.
- *
+ * The common name of the natural organism from which the gene was
+ * obtained.
+ *
* Examples:
- * 1, 2, 3
+ * man, yeast, bacteria
+ *
*/
- readonly pdbx_number_of_molecules?: Maybe<Scalars['Int']>;
-};
-
-export type RcsbPolymerEntityAlignAlignedRegions = {
- /** An identifier for the monomer in the entity sequence at which this segment of the alignment begins. */
- readonly entity_beg_seq_id?: Maybe<Scalars['Int']>;
- /** An length of the this segment of the alignment. */
- readonly length?: Maybe<Scalars['Int']>;
- /** An identifier for the monomer in the reference sequence at which this segment of the alignment begins. */
- readonly ref_beg_seq_id?: Maybe<Scalars['Int']>;
-};
-
-export type RcsbUniprotAlignmentsCoreEntityAlignments = {
- /** Aligned region */
- readonly aligned_regions?: Maybe<ReadonlyArray<Maybe<CoreEntityAlignmentsAlignedRegions>>>;
- /** core_entity identifiers */
- readonly core_entity_identifiers?: Maybe<CoreEntityAlignmentsCoreEntityIdentifiers>;
- /** Alignment scores */
- readonly scores?: Maybe<CoreEntityAlignmentsScores>;
-};
-
-export type RcsbNonpolymerEntityInstanceContainerIdentifiers = {
- /** Instance identifier for this container. */
- readonly asym_id: Scalars['String'];
- /** Author instance identifier for this container. */
- readonly auth_asym_id?: Maybe<Scalars['String']>;
- /** Residue number for non-polymer entity instance. */
- readonly auth_seq_id?: Maybe<Scalars['String']>;
- /** Component identifier for non-polymer entity instance. */
- readonly comp_id?: Maybe<Scalars['String']>;
- /** Entity identifier for the container. */
- readonly entity_id?: Maybe<Scalars['String']>;
- /** Entry identifier for the container. */
- readonly entry_id: Scalars['String'];
+ readonly gene_src_common_name?: Maybe<Scalars['String']>;
/**
- * A unique identifier for each object in this entity instance container formed by
- * an 'dot' (.) separated concatenation of entry and entity instance identifiers.
+ * A description of special aspects of the natural organism from
+ * which the gene was obtained.
*/
- readonly rcsb_id?: Maybe<Scalars['String']>;
-};
-
-export type PdbxReferenceMoleculeDetails = {
+ readonly gene_src_details?: Maybe<Scalars['String']>;
/**
- * The value of _pdbx_reference_molecule_details.family_prd_id is a reference to
- * _pdbx_reference_molecule_list.family_prd_id' in category PDBX_REFERENCE_MOLECULE_FAMILY.
+ * The genus of the natural organism from which the gene was
+ * obtained.
+ *
+ * Examples:
+ * Homo, Saccharomyces, Escherichia
+ *
*/
- readonly family_prd_id: Scalars['String'];
+ readonly gene_src_genus?: Maybe<Scalars['String']>;
/**
- * The value of _pdbx_reference_molecule_details.ordinal is an ordinal that
- * distinguishes each descriptive text for this entity.
+ * The species of the natural organism from which the gene was
+ * obtained.
+ *
+ * Examples:
+ * sapiens, cerevisiae, coli
+ *
*/
- readonly ordinal: Scalars['Int'];
- /** A data source of this information (e.g. PubMed, Merck Index) */
- readonly source?: Maybe<Scalars['String']>;
- /** A identifier within the data source for this information. */
- readonly source_id?: Maybe<Scalars['String']>;
- /** The text of the description of special aspects of the entity. */
- readonly text?: Maybe<Scalars['String']>;
-};
-
-export type PdbxReferenceMoleculeSynonyms = {
+ readonly gene_src_species?: Maybe<Scalars['String']>;
/**
- * The value of _pdbx_reference_molecule_synonyms.family_prd_id is a reference to
- * _pdbx_reference_molecule_list.family_prd_id in category PDBX_REFERENCE_MOLECULE_FAMILY_LIST.
+ * The strain of the natural organism from which the gene was
+ * obtained, if relevant.
+ *
+ * Examples:
+ * DH5a, BMH 71-18
+ *
*/
- readonly family_prd_id: Scalars['String'];
+ readonly gene_src_strain?: Maybe<Scalars['String']>;
/**
- * A synonym name for the entity.
- *
+ * The tissue of the natural organism from which the gene was
+ * obtained.
+ *
* Examples:
- * thiostrepton
+ * heart, liver, eye lens
+ *
*/
- readonly name?: Maybe<Scalars['String']>;
+ readonly gene_src_tissue?: Maybe<Scalars['String']>;
/**
- * The value of _pdbx_reference_molecule_synonyms.ordinal is an ordinal
- * to distinguish synonyms for this entity.
+ * The subcellular fraction of the tissue of the natural organism
+ * from which the gene was obtained.
+ *
+ * Examples:
+ * mitochondria, nucleus, membrane
+ *
*/
- readonly ordinal: Scalars['Int'];
+ readonly gene_src_tissue_fraction?: Maybe<Scalars['String']>;
/**
- * The value of _pdbx_reference_molecule_synonyms.prd_id is a reference
- * _pdbx_reference_molecule.prd_id in the PDBX_REFERENCE_MOLECULE category.
+ * The common name of the organism that served as host for the
+ * production of the entity. Where full details of the protein
+ * production are available it would be expected that this item
+ * be derived from _entity_src_gen_express.host_org_common_name
+ * or via _entity_src_gen_express.host_org_tax_id
+ *
+ * Examples:
+ * yeast, bacteria
+ *
*/
- readonly prd_id: Scalars['String'];
+ readonly host_org_common_name?: Maybe<Scalars['String']>;
/**
- * The source of this synonym name for the entity.
- *
+ * A description of special aspects of the organism that served as
+ * host for the production of the entity. Where full details of
+ * the protein production are available it would be expected that
+ * this item would derived from _entity_src_gen_express.host_org_details
+ */
+ readonly host_org_details?: Maybe<Scalars['String']>;
+ /**
+ * The genus of the organism that served as host for the production
+ * of the entity.
+ *
* Examples:
- * CAS
+ * Saccharomyces, Escherichia
+ *
*/
- readonly source?: Maybe<Scalars['String']>;
-};
-
-export type RcsbPolymerInstanceFeatureSummary = {
- /** The feature count. */
- readonly count?: Maybe<Scalars['Int']>;
- /** The fractional feature coverage relative to the full entity sequence. */
- readonly coverage?: Maybe<Scalars['Float']>;
- /** The maximum feature length. */
- readonly maximum_length?: Maybe<Scalars['Int']>;
- /** The maximum feature value. */
- readonly maximum_value?: Maybe<Scalars['Float']>;
- /** The minimum feature length. */
- readonly minimum_length?: Maybe<Scalars['Int']>;
- /** The minimum feature value. */
- readonly minimum_value?: Maybe<Scalars['Float']>;
+ readonly host_org_genus?: Maybe<Scalars['String']>;
/**
- * Type or category of the feature.
- *
+ * The species of the organism that served as host for the
+ * production of the entity.
+ *
+ * Examples:
+ * cerevisiae, coli
+ *
+ */
+ readonly host_org_species?: Maybe<Scalars['String']>;
+ /**
+ * This data item identifies cases in which an alternative source
+ * modeled.
+ *
* Allowable values:
- * ANGLE_OUTLIER, BINDING_SITE, BOND_OUTLIER, CATH, CIS-PEPTIDE, HELIX_P, MOGUL_ANGLE_OUTLIER, MOGUL_BOND_OUTLIER, RAMACHANDRAN_OUTLIER, ROTAMER_OUTLIER, RSRCC_OUTLIER, RSRZ_OUTLIER, SCOP, SHEET, UNASSIGNED_SEC_STRUCT, UNOBSERVED_ATOM_XYZ, UNOBSERVED_RESIDUE_XYZ, ZERO_OCCUPANCY_ATOM_XYZ, ZERO_OCCUPANCY_RESIDUE_XYZ
+ * model, sample
+ *
*/
- readonly type?: Maybe<Scalars['String']>;
-};
-
-export type CoreEntry = {
- /** Get all assemblies for this PDB entry. */
- readonly assemblies?: Maybe<ReadonlyArray<Maybe<CoreAssembly>>>;
- readonly audit_author?: Maybe<ReadonlyArray<Maybe<AuditAuthor>>>;
- /** Get all branched entities for this PDB entry. */
- readonly branched_entities?: Maybe<ReadonlyArray<Maybe<CoreBranchedEntity>>>;
- readonly cell?: Maybe<Cell>;
- readonly citation?: Maybe<ReadonlyArray<Maybe<Citation>>>;
- readonly diffrn?: Maybe<ReadonlyArray<Maybe<Diffrn>>>;
- readonly diffrn_detector?: Maybe<ReadonlyArray<Maybe<DiffrnDetector>>>;
- readonly diffrn_radiation?: Maybe<ReadonlyArray<Maybe<DiffrnRadiation>>>;
- readonly diffrn_source?: Maybe<ReadonlyArray<Maybe<DiffrnSource>>>;
- readonly em_2d_crystal_entity?: Maybe<ReadonlyArray<Maybe<Em2dCrystalEntity>>>;
- readonly em_3d_crystal_entity?: Maybe<ReadonlyArray<Maybe<Em3dCrystalEntity>>>;
- readonly em_3d_fitting?: Maybe<ReadonlyArray<Maybe<Em3dFitting>>>;
- readonly em_3d_fitting_list?: Maybe<ReadonlyArray<Maybe<Em3dFittingList>>>;
- readonly em_3d_reconstruction?: Maybe<ReadonlyArray<Maybe<Em3dReconstruction>>>;
- readonly em_ctf_correction?: Maybe<ReadonlyArray<Maybe<EmCtfCorrection>>>;
- readonly em_diffraction?: Maybe<ReadonlyArray<Maybe<EmDiffraction>>>;
- readonly em_diffraction_shell?: Maybe<ReadonlyArray<Maybe<EmDiffractionShell>>>;
- readonly em_diffraction_stats?: Maybe<ReadonlyArray<Maybe<EmDiffractionStats>>>;
- readonly em_embedding?: Maybe<ReadonlyArray<Maybe<EmEmbedding>>>;
- readonly em_entity_assembly?: Maybe<ReadonlyArray<Maybe<EmEntityAssembly>>>;
- readonly em_experiment?: Maybe<EmExperiment>;
- readonly em_helical_entity?: Maybe<ReadonlyArray<Maybe<EmHelicalEntity>>>;
- readonly em_image_recording?: Maybe<ReadonlyArray<Maybe<EmImageRecording>>>;
- readonly em_imaging?: Maybe<ReadonlyArray<Maybe<EmImaging>>>;
- readonly em_particle_selection?: Maybe<ReadonlyArray<Maybe<EmParticleSelection>>>;
- readonly em_single_particle_entity?: Maybe<ReadonlyArray<Maybe<EmSingleParticleEntity>>>;
- readonly em_software?: Maybe<ReadonlyArray<Maybe<EmSoftware>>>;
- readonly em_specimen?: Maybe<ReadonlyArray<Maybe<EmSpecimen>>>;
- readonly em_staining?: Maybe<ReadonlyArray<Maybe<EmStaining>>>;
- readonly em_vitrification?: Maybe<ReadonlyArray<Maybe<EmVitrification>>>;
- readonly entry?: Maybe<Entry>;
- readonly exptl?: Maybe<ReadonlyArray<Maybe<Exptl>>>;
- readonly exptl_crystal?: Maybe<ReadonlyArray<Maybe<ExptlCrystal>>>;
- readonly exptl_crystal_grow?: Maybe<ReadonlyArray<Maybe<ExptlCrystalGrow>>>;
- /** Get all non-polymer (non-solvent) entities for this PDB entry. */
- readonly nonpolymer_entities?: Maybe<ReadonlyArray<Maybe<CoreNonpolymerEntity>>>;
- readonly pdbx_SG_project?: Maybe<ReadonlyArray<Maybe<PdbxSgProject>>>;
- readonly pdbx_audit_revision_category?: Maybe<ReadonlyArray<Maybe<PdbxAuditRevisionCategory>>>;
- readonly pdbx_audit_revision_details?: Maybe<ReadonlyArray<Maybe<PdbxAuditRevisionDetails>>>;
- readonly pdbx_audit_revision_group?: Maybe<ReadonlyArray<Maybe<PdbxAuditRevisionGroup>>>;
- readonly pdbx_audit_revision_history?: Maybe<ReadonlyArray<Maybe<PdbxAuditRevisionHistory>>>;
- readonly pdbx_audit_revision_item?: Maybe<ReadonlyArray<Maybe<PdbxAuditRevisionItem>>>;
- readonly pdbx_audit_support?: Maybe<ReadonlyArray<Maybe<PdbxAuditSupport>>>;
- readonly pdbx_database_PDB_obs_spr?: Maybe<ReadonlyArray<Maybe<PdbxDatabasePdbObsSpr>>>;
- readonly pdbx_database_related?: Maybe<ReadonlyArray<Maybe<PdbxDatabaseRelated>>>;
- readonly pdbx_database_status?: Maybe<PdbxDatabaseStatus>;
- readonly pdbx_deposit_group?: Maybe<ReadonlyArray<Maybe<PdbxDepositGroup>>>;
- readonly pdbx_molecule_features?: Maybe<ReadonlyArray<Maybe<PdbxMoleculeFeatures>>>;
- readonly pdbx_nmr_details?: Maybe<PdbxNmrDetails>;
- readonly pdbx_nmr_ensemble?: Maybe<PdbxNmrEnsemble>;
- readonly pdbx_nmr_exptl?: Maybe<ReadonlyArray<Maybe<PdbxNmrExptl>>>;
- readonly pdbx_nmr_exptl_sample_conditions?: Maybe<ReadonlyArray<Maybe<PdbxNmrExptlSampleConditions>>>;
- readonly pdbx_nmr_refine?: Maybe<ReadonlyArray<Maybe<PdbxNmrRefine>>>;
- readonly pdbx_nmr_representative?: Maybe<PdbxNmrRepresentative>;
- readonly pdbx_nmr_sample_details?: Maybe<ReadonlyArray<Maybe<PdbxNmrSampleDetails>>>;
- readonly pdbx_nmr_software?: Maybe<ReadonlyArray<Maybe<PdbxNmrSoftware>>>;
- readonly pdbx_nmr_spectrometer?: Maybe<ReadonlyArray<Maybe<PdbxNmrSpectrometer>>>;
- readonly pdbx_serial_crystallography_data_reduction?: Maybe<ReadonlyArray<Maybe<PdbxSerialCrystallographyDataReduction>>>;
- readonly pdbx_serial_crystallography_measurement?: Maybe<ReadonlyArray<Maybe<PdbxSerialCrystallographyMeasurement>>>;
- readonly pdbx_serial_crystallography_sample_delivery?: Maybe<ReadonlyArray<Maybe<PdbxSerialCrystallographySampleDelivery>>>;
- readonly pdbx_serial_crystallography_sample_delivery_fixed_target?: Maybe<ReadonlyArray<Maybe<PdbxSerialCrystallographySampleDeliveryFixedTarget>>>;
- readonly pdbx_serial_crystallography_sample_delivery_injection?: Maybe<ReadonlyArray<Maybe<PdbxSerialCrystallographySampleDeliveryInjection>>>;
- readonly pdbx_soln_scatter?: Maybe<ReadonlyArray<Maybe<PdbxSolnScatter>>>;
- readonly pdbx_soln_scatter_model?: Maybe<ReadonlyArray<Maybe<PdbxSolnScatterModel>>>;
- readonly pdbx_vrpt_summary?: Maybe<PdbxVrptSummary>;
- /** Get all polymer entities for this PDB entry. */
- readonly polymer_entities?: Maybe<ReadonlyArray<Maybe<CorePolymerEntity>>>;
- /** Get literature information from PubMed database. */
- readonly pubmed?: Maybe<CorePubmed>;
- readonly rcsb_accession_info?: Maybe<RcsbAccessionInfo>;
- /** The list of content types associated with this entry. */
- readonly rcsb_associated_holdings?: Maybe<CurrentEntry>;
- readonly rcsb_binding_affinity?: Maybe<ReadonlyArray<Maybe<RcsbBindingAffinity>>>;
- readonly rcsb_entry_container_identifiers: RcsbEntryContainerIdentifiers;
- readonly rcsb_entry_info: RcsbEntryInfo;
- readonly rcsb_external_references?: Maybe<ReadonlyArray<Maybe<RcsbExternalReferences>>>;
- /** A unique identifier for each object in this entry container. */
- readonly rcsb_id: Scalars['String'];
- readonly rcsb_primary_citation?: Maybe<RcsbPrimaryCitation>;
- readonly refine?: Maybe<ReadonlyArray<Maybe<Refine>>>;
- readonly refine_analyze?: Maybe<ReadonlyArray<Maybe<RefineAnalyze>>>;
- readonly refine_hist?: Maybe<ReadonlyArray<Maybe<RefineHist>>>;
- readonly refine_ls_restr?: Maybe<ReadonlyArray<Maybe<RefineLsRestr>>>;
- readonly reflns?: Maybe<ReadonlyArray<Maybe<Reflns>>>;
- readonly reflns_shell?: Maybe<ReadonlyArray<Maybe<ReflnsShell>>>;
- readonly software?: Maybe<ReadonlyArray<Maybe<Software>>>;
- readonly struct?: Maybe<Struct>;
- readonly struct_keywords?: Maybe<StructKeywords>;
- readonly symmetry?: Maybe<Symmetry>;
-};
-
-export type ReflnsShell = {
- /**
- * Residual factor Rmerge for all reflections that satisfy the
- * resolution limits established by _reflns_shell.d_res_high and
- * _reflns_shell.d_res_low.
- *
- * sum~i~(sum~j~|F~j~ - <F>|)
- * Rmerge(F) = --------------------------
- * sum~i~(sum~j~<F>)
- *
- * F~j~ = the amplitude of the jth observation of reflection i
- * <F> = the mean of the amplitudes of all observations of
- * reflection i
- *
- * sum~i~ is taken over all reflections
- * sum~j~ is taken over all observations of each reflection
- */
- readonly Rmerge_F_all?: Maybe<Scalars['Float']>;
+ readonly pdbx_alt_source_flag?: Maybe<Scalars['String']>;
/**
- * Residual factor Rmerge for reflections that satisfy the
- * resolution limits established by _reflns_shell.d_res_high and
- * _reflns_shell.d_res_low and the observation criterion
- * established by _reflns.observed_criterion.
- *
- * sum~i~(sum~j~|F~j~ - <F>|)
- * Rmerge(F) = --------------------------
- * sum~i~(sum~j~<F>)
- *
- * F~j~ = the amplitude of the jth observation of reflection i
- * <F> = the mean of the amplitudes of all observations of
- * reflection i
- *
- * sum~i~ is taken over all reflections
- * sum~j~ is taken over all observations of each reflection
+ * The beginning polymer sequence position for the polymer section corresponding
+ * to this source.
+ *
+ * A reference to the sequence position in the entity_poly category.
*/
- readonly Rmerge_F_obs?: Maybe<Scalars['Float']>;
+ readonly pdbx_beg_seq_num?: Maybe<Scalars['Int']>;
+ /** Information on the source which is not given elsewhere. */
+ readonly pdbx_description?: Maybe<Scalars['String']>;
/**
- * The value of Rmerge(I) for all reflections in a given shell.
- *
- * sum~i~(sum~j~|I~j~ - <I>|)
- * Rmerge(I) = --------------------------
- * sum~i~(sum~j~<I>)
- *
- * I~j~ = the intensity of the jth observation of reflection i
- * <I> = the mean of the intensities of all observations of
- * reflection i
- *
- * sum~i~ is taken over all reflections
- * sum~j~ is taken over all observations of each reflection
+ * The ending polymer sequence position for the polymer section corresponding
+ * to this source.
+ *
+ * A reference to the sequence position in the entity_poly category.
*/
- readonly Rmerge_I_all?: Maybe<Scalars['Float']>;
+ readonly pdbx_end_seq_num?: Maybe<Scalars['Int']>;
/**
- * The value of Rmerge(I) for reflections classified as 'observed'
- * (see _reflns.observed_criterion) in a given shell.
- *
- * sum~i~(sum~j~|I~j~ - <I>|)
- * Rmerge(I) = --------------------------
- * sum~i~(sum~j~<I>)
- *
- * I~j~ = the intensity of the jth observation of reflection i
- * <I> = the mean of the intensities of all observations of
- * reflection i
- *
- * sum~i~ is taken over all reflections
- * sum~j~ is taken over all observations of each reflection
+ * American Type Culture Collection tissue culture number.
+ *
+ * Examples:
+ * 6051
+ *
*/
- readonly Rmerge_I_obs?: Maybe<Scalars['Float']>;
+ readonly pdbx_gene_src_atcc?: Maybe<Scalars['String']>;
/**
- * The smallest value in angstroms for the interplanar spacings
- * for the reflections in this shell. This is called the highest
- * resolution.
+ * Cell type.
+ *
+ * Examples:
+ * ENDOTHELIAL
+ *
*/
- readonly d_res_high?: Maybe<Scalars['Float']>;
+ readonly pdbx_gene_src_cell?: Maybe<Scalars['String']>;
/**
- * The highest value in angstroms for the interplanar spacings
- * for the reflections in this shell. This is called the lowest
- * resolution.
+ * The specific line of cells.
+ *
+ * Examples:
+ * HELA CELLS
+ *
*/
- readonly d_res_low?: Maybe<Scalars['Float']>;
+ readonly pdbx_gene_src_cell_line?: Maybe<Scalars['String']>;
/**
- * The ratio of the mean of the intensities of all reflections
- * in this shell to the mean of the standard uncertainties of the
- * intensities of all reflections in this shell.
+ * Identifies the location inside (or outside) the cell.
+ *
+ * Examples:
+ * CYTOPLASM, NUCLEUS
+ *
*/
- readonly meanI_over_sigI_all?: Maybe<Scalars['Float']>;
+ readonly pdbx_gene_src_cellular_location?: Maybe<Scalars['String']>;
/**
- * The ratio of the mean of the intensities of the reflections
- * classified as 'observed' (see _reflns.observed_criterion) in
- * this shell to the mean of the standard uncertainties of the
- * intensities of the 'observed' reflections in this
- * shell.
+ * A domain or fragment of the molecule.
+ *
+ * Examples:
+ * CYTOPLASM, NUCLEUS
+ *
*/
- readonly meanI_over_sigI_obs?: Maybe<Scalars['Float']>;
+ readonly pdbx_gene_src_fragment?: Maybe<Scalars['String']>;
+ /** Identifies the gene. */
+ readonly pdbx_gene_src_gene?: Maybe<Scalars['String']>;
/**
- * The ratio of the mean of the intensities of all reflections
- * in this shell to the mean of the standard uncertainties of the
- * intensities of all reflections in this shell.
+ * NCBI Taxonomy identifier for the gene source organism.
+ *
+ * Reference:
+ *
+ * Wheeler DL, Chappey C, Lash AE, Leipe DD, Madden TL, Schuler GD,
+ * Tatusova TA, Rapp BA (2000). Database resources of the National
+ * Center for Biotechnology Information. Nucleic Acids Res 2000 Jan
+ * 1;28(1):10-4
+ *
+ * Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Rapp BA,
+ * Wheeler DL (2000). GenBank. Nucleic Acids Res 2000 Jan 1;28(1):15-18.
*/
- readonly meanI_over_uI_all?: Maybe<Scalars['Float']>;
+ readonly pdbx_gene_src_ncbi_taxonomy_id?: Maybe<Scalars['String']>;
/**
- * The total number of reflections measured for this
- * shell.
+ * Organized group of tissues that carries on a specialized function.
+ *
+ * Examples:
+ * KIDNEY, LIVER, PANCREAS
+ *
*/
- readonly number_measured_all?: Maybe<Scalars['Int']>;
+ readonly pdbx_gene_src_organ?: Maybe<Scalars['String']>;
/**
- * The number of reflections classified as 'observed'
- * (see _reflns.observed_criterion) for this
- * shell.
+ * Organized structure within cell.
+ *
+ * Examples:
+ * MITOCHONDRIA
+ *
*/
- readonly number_measured_obs?: Maybe<Scalars['Int']>;
+ readonly pdbx_gene_src_organelle?: Maybe<Scalars['String']>;
/**
- * The number of unique reflections it is possible to measure in
- * this shell.
+ * Scientific name of the organism.
+ *
+ * Examples:
+ * Homo sapiens, Saccharomyces Cerevisiae
+ *
*/
- readonly number_possible?: Maybe<Scalars['Int']>;
+ readonly pdbx_gene_src_scientific_name?: Maybe<Scalars['String']>;
/**
- * The total number of measured reflections which are symmetry-
- * unique after merging for this shell.
+ * Identifies the variant.
+ *
+ * Examples:
+ * DELTAH1DELTATRP
+ *
*/
- readonly number_unique_all?: Maybe<Scalars['Int']>;
+ readonly pdbx_gene_src_variant?: Maybe<Scalars['String']>;
/**
- * The total number of measured reflections classified as 'observed'
- * (see _reflns.observed_criterion) which are symmetry-unique
- * after merging for this shell.
+ * Americal Tissue Culture Collection of the expression system. Where
+ * full details of the protein production are available it would
+ * be expected that this item would be derived from
+ * _entity_src_gen_express.host_org_culture_collection
*/
- readonly number_unique_obs?: Maybe<Scalars['Int']>;
+ readonly pdbx_host_org_atcc?: Maybe<Scalars['String']>;
/**
- * The Pearson's correlation coefficient expressed as a decimal value
- * between the average intensities from randomly selected
- * half-datasets within the resolution shell.
- *
- * Ref: Karplus & Diederichs (2012), Science 336, 1030-33
+ * Cell type from which the gene is derived. Where
+ * entity.target_id is provided this should be derived from
+ * details of the target.
+ *
+ * Examples:
+ * ENDOTHELIAL
+ *
*/
- readonly pdbx_CC_half?: Maybe<Scalars['Float']>;
+ readonly pdbx_host_org_cell?: Maybe<Scalars['String']>;
/**
- * R split measures the agreement between the sets of intensities created by merging
- * odd- and even-numbered images from the data within the resolution shell.
- *
- * Ref: T. A. White, R. A. Kirian, A. V. Martin, A. Aquila, K. Nass,
- * A. Barty and H. N. Chapman (2012), J. Appl. Cryst. 45, 335-341
+ * A specific line of cells used as the expression system. Where
+ * full details of the protein production are available it would
+ * be expected that this item would be derived from
+ * entity_src_gen_express.host_org_cell_line
+ *
+ * Examples:
+ * HELA
+ *
*/
- readonly pdbx_R_split?: Maybe<Scalars['Float']>;
+ readonly pdbx_host_org_cell_line?: Maybe<Scalars['String']>;
/**
- * The precision-indicating merging R factor value Rpim,
- * for merging all intensities in a given shell.
- *
- * sum~i~ [1/(N~i~ - 1)]1/2^ sum~j~ | I~j~ - <I~i~> |
- * Rpim = --------------------------------------------------
- * sum~i~ ( sum~j~ I~j~ )
- *
- * I~j~ = the intensity of the jth observation of reflection i
- * <I~i~> = the mean of the intensities of all observations of
- * reflection i
- * N~i~ = the redundancy (the number of times reflection i
- * has been measured).
- *
- * sum~i~ is taken over all reflections
- * sum~j~ is taken over all observations of each reflection.
- *
- * Ref: Diederichs, K. & Karplus, P. A. (1997). Nature Struct.
- * Biol. 4, 269-275.
- * Weiss, M. S. & Hilgenfeld, R. (1997). J. Appl. Cryst.
- * 30, 203-205.
- * Weiss, M. S. (2001). J. Appl. Cryst. 34, 130-135.
+ * Identifies the location inside (or outside) the cell which
+ * expressed the molecule.
+ *
+ * Examples:
+ * CYTOPLASM, NUCLEUS
+ *
*/
- readonly pdbx_Rpim_I_all?: Maybe<Scalars['Float']>;
+ readonly pdbx_host_org_cellular_location?: Maybe<Scalars['String']>;
/**
- * The redundancy-independent merging R factor value Rrim,
- * also denoted Rmeas, for merging all intensities in a
- * given shell.
- *
- * sum~i~ [N~i~ /( N~i~ - 1)]1/2^ sum~j~ | I~j~ - <I~i~> |
- * Rrim = --------------------------------------------------------
- * sum~i~ ( sum~j~ I~j~ )
- *
- * I~j~ = the intensity of the jth observation of reflection i
- * <I~i~> = the mean of the intensities of all observations of
- * reflection i
- * N~i~ = the redundancy (the number of times reflection i
- * has been measured).
- *
- * sum~i~ is taken over all reflections
- * sum~j~ is taken over all observations of each reflection.
- *
- * Ref: Diederichs, K. & Karplus, P. A. (1997). Nature Struct.
- * Biol. 4, 269-275.
- * Weiss, M. S. & Hilgenfeld, R. (1997). J. Appl. Cryst.
- * 30, 203-205.
- * Weiss, M. S. (2001). J. Appl. Cryst. 34, 130-135.
+ * Culture collection of the expression system. Where
+ * full details of the protein production are available it would
+ * be expected that this item would be derived somehwere, but
+ * exactly where is not clear.
*/
- readonly pdbx_Rrim_I_all?: Maybe<Scalars['Float']>;
- /** R sym value in percent. */
- readonly pdbx_Rsym_value?: Maybe<Scalars['Float']>;
- /** Chi-squared statistic for this resolution shell. */
- readonly pdbx_chi_squared?: Maybe<Scalars['Float']>;
+ readonly pdbx_host_org_culture_collection?: Maybe<Scalars['String']>;
/**
- * An identifier for the diffraction data set corresponding to this resolution shell.
- *
- * Multiple diffraction data sets specified as a comma separated list.
+ * Specific gene which expressed the molecule.
+ *
+ * Examples:
+ * HIV-1 POL, GLNS7, U1A (2-98, Y31H, Q36R)
+ *
*/
- readonly pdbx_diffrn_id?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
+ readonly pdbx_host_org_gene?: Maybe<Scalars['String']>;
/**
- * The mean of the ratio of the intensities to their
- * standard uncertainties of all reflections in the
- * resolution shell.
- *
- * _reflns_shell.pdbx_netI_over_sigmaI_all = <I/sigma(I)>
+ * NCBI Taxonomy identifier for the expression system organism.
+ *
+ * Reference:
+ *
+ * Wheeler DL, Chappey C, Lash AE, Leipe DD, Madden TL, Schuler GD,
+ * Tatusova TA, Rapp BA (2000). Database resources of the National
+ * Center for Biotechnology Information. Nucleic Acids Res 2000 Jan
+ * 1;28(1):10-4
+ *
+ * Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Rapp BA,
+ * Wheeler DL (2000). GenBank. Nucleic Acids Res 2000 Jan 1;28(1):15-18.
*/
- readonly pdbx_netI_over_sigmaI_all?: Maybe<Scalars['Float']>;
+ readonly pdbx_host_org_ncbi_taxonomy_id?: Maybe<Scalars['String']>;
/**
- * The mean of the ratio of the intensities to their
- * standard uncertainties of observed reflections
- * (see _reflns.observed_criterion) in the resolution shell.
- *
- * _reflns_shell.pdbx_netI_over_sigmaI_obs = <I/sigma(I)>
+ * Specific organ which expressed the molecule.
+ *
+ * Examples:
+ * KIDNEY
+ *
*/
- readonly pdbx_netI_over_sigmaI_obs?: Maybe<Scalars['Float']>;
- /** An ordinal identifier for this resolution shell. */
- readonly pdbx_ordinal: Scalars['Int'];
- /** Redundancy for the current shell. */
- readonly pdbx_redundancy?: Maybe<Scalars['Float']>;
+ readonly pdbx_host_org_organ?: Maybe<Scalars['String']>;
/**
- * The number of rejected reflections in the resolution
- * shell. Reflections may be rejected from scaling
- * by setting the observation criterion,
- * _reflns.observed_criterion.
+ * Specific organelle which expressed the molecule.
+ *
+ * Examples:
+ * MITOCHONDRIA
+ *
*/
- readonly pdbx_rejects?: Maybe<Scalars['Int']>;
+ readonly pdbx_host_org_organelle?: Maybe<Scalars['String']>;
/**
- * The percentage of geometrically possible reflections represented
- * by all reflections measured for this shell.
+ * The scientific name of the organism that served as host for the
+ * production of the entity. Where full details of the protein
+ * production are available it would be expected that this item
+ * would be derived from _entity_src_gen_express.host_org_scientific_name
+ * or via _entity_src_gen_express.host_org_tax_id
+ *
+ * Examples:
+ * ESCHERICHIA COLI, SACCHAROMYCES CEREVISIAE
+ *
*/
- readonly percent_possible_all?: Maybe<Scalars['Float']>;
+ readonly pdbx_host_org_scientific_name?: Maybe<Scalars['String']>;
/**
- * The percentage of geometrically possible reflections represented
- * by reflections classified as 'observed' (see
- * _reflns.observed_criterion) for this shell.
+ * The strain of the organism in which the entity was
+ * expressed.
+ *
+ * Examples:
+ * AR120
+ *
*/
- readonly percent_possible_obs?: Maybe<Scalars['Float']>;
-};
-
-export type RcsbPubmedMeshDescriptorsLineage = {
- /** Hierarchy depth. */
- readonly depth?: Maybe<Scalars['Int']>;
- /** Identifier for MeSH classification term. */
- readonly id?: Maybe<Scalars['String']>;
- /** MeSH classification term. */
- readonly name?: Maybe<Scalars['String']>;
-};
-
-export type RcsbNonpolymerInstanceFeatureFeatureValue = {
- /** The chemical component identifier for the instance of the feature value. */
- readonly comp_id?: Maybe<Scalars['String']>;
- /** Specific details about the feature. */
- readonly details?: Maybe<Scalars['String']>;
- /** The reference value of the feature. */
- readonly reference?: Maybe<Scalars['Float']>;
- /** The reported value of the feature. */
- readonly reported?: Maybe<Scalars['Float']>;
- /** The estimated uncertainty of the reported feature value. */
- readonly uncertainty_estimate?: Maybe<Scalars['Float']>;
+ readonly pdbx_host_org_strain?: Maybe<Scalars['String']>;
/**
- * The type of estimated uncertainty for the reported feature value.
- *
+ * The specific tissue which expressed the molecule. Where full details
+ * of the protein production are available it would be expected that this
+ * item would be derived from _entity_src_gen_express.host_org_tissue
+ *
+ * Examples:
+ * heart, liver, eye lens
+ *
+ */
+ readonly pdbx_host_org_tissue?: Maybe<Scalars['String']>;
+ /**
+ * The fraction of the tissue which expressed the
+ * molecule.
+ *
+ * Examples:
+ * mitochondria, nucleus, membrane
+ *
+ */
+ readonly pdbx_host_org_tissue_fraction?: Maybe<Scalars['String']>;
+ /**
+ * Variant of the organism used as the expression system. Where
+ * full details of the protein production are available it would
+ * be expected that this item be derived from
+ * entity_src_gen_express.host_org_variant or via
+ * _entity_src_gen_express.host_org_tax_id
+ *
+ * Examples:
+ * TRP-LAC, LAMBDA DE3
+ *
+ */
+ readonly pdbx_host_org_variant?: Maybe<Scalars['String']>;
+ /**
+ * Identifies the vector used. Where full details of the protein
+ * production are available it would be expected that this item
+ * would be derived from _entity_src_gen_clone.vector_name.
+ *
+ * Examples:
+ * PBIT36, PET15B, PUC18
+ *
+ */
+ readonly pdbx_host_org_vector?: Maybe<Scalars['String']>;
+ /**
+ * Identifies the type of vector used (plasmid, virus, or cosmid).
+ * Where full details of the protein production are available it
+ * would be expected that this item would be derived from
+ * _entity_src_gen_express.vector_type.
+ *
+ * Examples:
+ * COSMID, PLASMID
+ *
+ */
+ readonly pdbx_host_org_vector_type?: Maybe<Scalars['String']>;
+ /**
+ * This data item povides additional information about the sequence type.
+ *
* Allowable values:
- * Z-Score
+ * Biological sequence, C-terminal tag, Linker, N-terminal tag
+ *
*/
- readonly uncertainty_estimate_type?: Maybe<Scalars['String']>;
-};
-
-export type RcsbPolymerEntityNameCom = {
+ readonly pdbx_seq_type?: Maybe<Scalars['String']>;
+ /** This data item is an ordinal identifier for entity_src_gen data records. */
+ readonly pdbx_src_id: Scalars['Int'];
/**
- * A common name for the polymer entity.
- *
+ * A description of special aspects of the plasmid that produced the
+ * entity in the host organism. Where full details of the protein
+ * production are available it would be expected that this item
+ * would be derived from _pdbx_construct.details of the construct
+ * pointed to from _entity_src_gen_express.plasmid_id.
+ */
+ readonly plasmid_details?: Maybe<Scalars['String']>;
+ /**
+ * The name of the plasmid that produced the entity in the host
+ * organism. Where full details of the protein production are available
+ * it would be expected that this item would be derived from
+ * _pdbx_construct.name of the construct pointed to from
+ * _entity_src_gen_express.plasmid_id.
+ *
* Examples:
- * HIV protease monomer, hemoglobin alpha chain
+ * pET3C, pT123sab
+ *
*/
- readonly name: Scalars['String'];
-};
-
-export type RcsbBranchedEntityKeywords = {
- /** Keywords describing this branched entity. */
- readonly text?: Maybe<Scalars['String']>;
-};
-
-export type EmSingleParticleEntity = {
- /** Unique category label. */
- readonly id: Scalars['Int'];
- /** pointer to _em_image_processing.id. */
- readonly image_processing_id: Scalars['String'];
- /** Point symmetry symbol, either Cn, Dn, T, O, or I */
- readonly point_symmetry?: Maybe<Scalars['String']>;
+ readonly plasmid_name?: Maybe<Scalars['String']>;
};
-export type RcsbEntryInfo = {
- /** The number of assemblies defined for this entry including the deposited assembly. */
- readonly assembly_count?: Maybe<Scalars['Int']>;
- /** The number of distinct branched entities in the structure entry. */
- readonly branched_entity_count?: Maybe<Scalars['Int']>;
- /** The maximum molecular mass (KDa) of a branched entity in the deposited structure entry. */
- readonly branched_molecular_weight_maximum?: Maybe<Scalars['Float']>;
- /** The minimum molecular mass (KDa) of a branched entity in the deposited structure entry. */
- readonly branched_molecular_weight_minimum?: Maybe<Scalars['Float']>;
- /** The number of cis-peptide linkages per deposited structure model. */
- readonly cis_peptide_count?: Maybe<Scalars['Int']>;
- /** The number of heavy atom coordinates records per deposited structure model. */
- readonly deposited_atom_count?: Maybe<Scalars['Int']>;
- /** The number of model structures deposited. */
- readonly deposited_model_count?: Maybe<Scalars['Int']>;
+export type EntitySrcNat = {
/**
- * The number of modeled polymer monomers in the deposited coordinate data.
- * This is the total count of monomers with reported coordinate data for all polymer
- * entity instances in the deposited coordinate data.
+ * The common name of the organism from which the entity
+ * was isolated.
+ *
+ * Examples:
+ * man, yeast, bacteria
+ *
*/
- readonly deposited_modeled_polymer_monomer_count?: Maybe<Scalars['Int']>;
+ readonly common_name?: Maybe<Scalars['String']>;
/**
- * The number of non-polymer instances in the deposited data set.
- * This is the total count of non-polymer entity instances reported
- * per deposited structure model.
+ * A description of special aspects of the organism from which the
+ * entity was isolated.
*/
- readonly deposited_nonpolymer_entity_instance_count?: Maybe<Scalars['Int']>;
+ readonly details?: Maybe<Scalars['String']>;
/**
- * The number of polymer instances in the deposited data set.
- * This is the total count of polymer entity instances reported
- * per deposited structure model.
+ * The genus of the organism from which the entity was isolated.
+ *
+ * Examples:
+ * Homo, Saccharomyces, Escherichia
+ *
*/
- readonly deposited_polymer_entity_instance_count?: Maybe<Scalars['Int']>;
+ readonly genus?: Maybe<Scalars['String']>;
/**
- * The number of polymer monomers in sample entity instances in the deposited data set.
- * This is the total count of monomers for all polymer entity instances reported
- * per deposited structure model.
+ * This data item identifies cases in which an alternative source
+ * modeled.
+ *
+ * Allowable values:
+ * model, sample
+ *
*/
- readonly deposited_polymer_monomer_count?: Maybe<Scalars['Int']>;
- /** The number of heavy solvent atom coordinates records per deposited structure model. */
- readonly deposited_solvent_atom_count?: Maybe<Scalars['Int']>;
+ readonly pdbx_alt_source_flag?: Maybe<Scalars['String']>;
/**
- * The number of unmodeled polymer monomers in the deposited coordinate data. This is
- * the total count of monomers with unreported coordinate data for all polymer
- * entity instances per deposited structure model.
+ * Americal Tissue Culture Collection number.
+ *
+ * Examples:
+ * 6051
+ *
*/
- readonly deposited_unmodeled_polymer_monomer_count?: Maybe<Scalars['Int']>;
- /** The maximum radiation wavelength in angstroms. */
- readonly diffrn_radiation_wavelength_maximum?: Maybe<Scalars['Float']>;
- /** The minimum radiation wavelength in angstroms. */
- readonly diffrn_radiation_wavelength_minimum?: Maybe<Scalars['Float']>;
- readonly diffrn_resolution_high?: Maybe<RcsbEntryInfoDiffrnResolutionHigh>;
- /** The number of disulfide bonds per deposited structure model. */
- readonly disulfide_bond_count?: Maybe<Scalars['Int']>;
- /** The number of distinct polymer, non-polymer, branched molecular, and solvent entities per deposited structure model. */
- readonly entity_count?: Maybe<Scalars['Int']>;
+ readonly pdbx_atcc?: Maybe<Scalars['String']>;
/**
- * The category of experimental method(s) used to determine the structure entry.
- *
- * Allowable values:
- * EM, Multiple methods, NMR, Neutron, Other, X-ray
+ * The beginning polymer sequence position for the polymer section corresponding
+ * to this source.
+ *
+ * A reference to the sequence position in the entity_poly category.
*/
- readonly experimental_method?: Maybe<Scalars['String']>;
- /** The number of experimental methods contributing data to the structure determination. */
- readonly experimental_method_count?: Maybe<Scalars['Int']>;
- /** The number of intermolecular covalent bonds. */
- readonly inter_mol_covalent_bond_count?: Maybe<Scalars['Int']>;
- /** The number of intermolecular metalic bonds. */
- readonly inter_mol_metalic_bond_count?: Maybe<Scalars['Int']>;
- /** The molecular mass (KDa) of polymer and non-polymer entities (exclusive of solvent) in the deposited structure entry. */
- readonly molecular_weight?: Maybe<Scalars['Float']>;
+ readonly pdbx_beg_seq_num?: Maybe<Scalars['Int']>;
/**
- * Nucleic acid polymer entity type categories describing the entry.
- *
- * Allowable values:
- * DNA (only), DNA/RNA (only), NA-hybrid (only), Other, RNA (only)
+ * A particular cell type.
+ *
+ * Examples:
+ * BHK-21
+ *
*/
- readonly na_polymer_entity_types?: Maybe<Scalars['String']>;
- /** Bound nonpolymer components in this entry. */
- readonly nonpolymer_bound_components?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
- /** The number of distinct non-polymer entities in the structure entry exclusive of solvent. */
- readonly nonpolymer_entity_count?: Maybe<Scalars['Int']>;
- /** The maximum molecular mass (KDa) of a non-polymer entity in the deposited structure entry. */
- readonly nonpolymer_molecular_weight_maximum?: Maybe<Scalars['Float']>;
- /** The minimum molecular mass (KDa) of a non-polymer entity in the deposited structure entry. */
- readonly nonpolymer_molecular_weight_minimum?: Maybe<Scalars['Float']>;
+ readonly pdbx_cell?: Maybe<Scalars['String']>;
/**
- * Categories describing the polymer entity composition for the entry.
- *
- * Allowable values:
- * DNA, DNA/RNA, NA-hybrid, NA/oligosaccharide, RNA, heteromeric protein, homomeric protein, oligosaccharide, other, other type composition, other type pair, protein/NA, protein/NA/oligosaccharide, protein/oligosaccharide
+ * The specific line of cells.
+ *
+ * Examples:
+ * HELA
+ *
*/
- readonly polymer_composition?: Maybe<Scalars['String']>;
- /** The number of distinct polymer entities in the structure entry. */
- readonly polymer_entity_count?: Maybe<Scalars['Int']>;
- /** The number of distinct DNA polymer entities. */
- readonly polymer_entity_count_DNA?: Maybe<Scalars['Int']>;
- /** The number of distinct RNA polymer entities. */
- readonly polymer_entity_count_RNA?: Maybe<Scalars['Int']>;
- /** The number of distinct nucleic acid polymer entities (DNA or RNA). */
- readonly polymer_entity_count_nucleic_acid?: Maybe<Scalars['Int']>;
- /** The number of distinct hybrid nucleic acid polymer entities. */
- readonly polymer_entity_count_nucleic_acid_hybrid?: Maybe<Scalars['Int']>;
- /** The number of distinct protein polymer entities. */
- readonly polymer_entity_count_protein?: Maybe<Scalars['Int']>;
- /** The number of distinct taxonomies represented among the polymer entities in the entry. */
- readonly polymer_entity_taxonomy_count?: Maybe<Scalars['Int']>;
- /** The maximum molecular mass (KDa) of a polymer entity in the deposited structure entry. */
- readonly polymer_molecular_weight_maximum?: Maybe<Scalars['Float']>;
- /** The minimum molecular mass (KDa) of a polymer entity in the deposited structure entry. */
- readonly polymer_molecular_weight_minimum?: Maybe<Scalars['Float']>;
- /** The maximum monomer count of a polymer entity per deposited structure model. */
- readonly polymer_monomer_count_maximum?: Maybe<Scalars['Int']>;
- /** The minimum monomer count of a polymer entity per deposited structure model. */
- readonly polymer_monomer_count_minimum?: Maybe<Scalars['Int']>;
- /** Combined estimates of experimental resolution contributing to the refined structural model. */
- readonly resolution_combined?: Maybe<ReadonlyArray<Maybe<Scalars['Float']>>>;
+ readonly pdbx_cell_line?: Maybe<Scalars['String']>;
+ /** Identifies the location inside (or outside) the cell. */
+ readonly pdbx_cellular_location?: Maybe<Scalars['String']>;
/**
- * Selected polymer entity type categories describing the entry.
- *
- * Allowable values:
- * Nucleic acid (only), Other, Protein (only), Protein/NA
+ * The ending polymer sequence position for the polymer section corresponding
+ * to this source.
+ *
+ * A reference to the sequence position in the entity_poly category.
*/
- readonly selected_polymer_entity_types?: Maybe<Scalars['String']>;
- /** Combined list of software programs names reported in connection with the production of this entry. */
- readonly software_programs_combined?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
- /** The number of distinct solvent entities per deposited structure model. */
- readonly solvent_entity_count?: Maybe<Scalars['Int']>;
-};
-
-export type PdbxChemCompFeature = {
+ readonly pdbx_end_seq_num?: Maybe<Scalars['Int']>;
+ /** A domain or fragment of the molecule. */
+ readonly pdbx_fragment?: Maybe<Scalars['String']>;
/**
- * The component identifier for this feature.
- *
- * Examples:
- * ABC, ATP
+ * NCBI Taxonomy identifier for the source organism.
+ *
+ * Reference:
+ *
+ * Wheeler DL, Chappey C, Lash AE, Leipe DD, Madden TL, Schuler GD,
+ * Tatusova TA, Rapp BA (2000). Database resources of the National
+ * Center for Biotechnology Information. Nucleic Acids Res 2000 Jan
+ * 1;28(1):10-4
+ *
+ * Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Rapp BA,
+ * Wheeler DL (2000). GenBank. Nucleic Acids Res 2000 Jan 1;28(1):15-18.
*/
- readonly comp_id: Scalars['String'];
+ readonly pdbx_ncbi_taxonomy_id?: Maybe<Scalars['String']>;
/**
- * The information source for the component feature.
- *
+ * Organized group of tissues that carries on a specialized function.
+ *
* Examples:
- * PDB, CHEBI, DRUGBANK, PUBCHEM
+ * KIDNEY
+ *
*/
- readonly source: Scalars['String'];
+ readonly pdbx_organ?: Maybe<Scalars['String']>;
/**
- * The component feature type.
- *
- * Allowable values:
- * CARBOHYDRATE ANOMER, CARBOHYDRATE ISOMER, CARBOHYDRATE PRIMARY CARBONYL GROUP, CARBOHYDRATE RING
+ * Organized structure within cell.
+ *
+ * Examples:
+ * MITOCHONDRIA
+ *
*/
- readonly type: Scalars['String'];
- /** The component feature value. */
- readonly value: Scalars['String'];
-};
-
-export type RcsbChemCompTarget = {
+ readonly pdbx_organelle?: Maybe<Scalars['String']>;
/**
- * The value of _rcsb_chem_comp_target.comp_id is a reference to
- * a chemical component definition.
+ * Scientific name of the organism of the natural source.
+ *
+ * Examples:
+ * Bos taurus, BOS TAURUS, SUS SCROFA, ASPERGILLUS ORYZAE
+ *
*/
- readonly comp_id: Scalars['String'];
- /** The type of target interaction. */
- readonly interaction_type?: Maybe<Scalars['String']>;
- /** The target name. */
- readonly name?: Maybe<Scalars['String']>;
+ readonly pdbx_organism_scientific?: Maybe<Scalars['String']>;
/**
- * The value of _rcsb_chem_comp_target.ordinal distinguishes
- * related examples for each chemical component.
+ * Details about the plasmid.
+ *
+ * Examples:
+ * PLC28 DERIVATIVE
+ *
*/
- readonly ordinal: Scalars['Int'];
+ readonly pdbx_plasmid_details?: Maybe<Scalars['String']>;
/**
- * A code indicating the provenance of the target interaction assignment
- *
- * Allowable values:
- * DrugBank, PDB Primary Data
+ * The plasmid containing the gene.
+ *
+ * Examples:
+ * pB322
+ *
*/
- readonly provenance_source?: Maybe<Scalars['String']>;
+ readonly pdbx_plasmid_name?: Maybe<Scalars['String']>;
/**
- * The reference identifier code for the target interaction reference.
- *
+ * Identifies the secretion from which the molecule was isolated.
+ *
* Examples:
- * Q9HD40
+ * saliva, urine, venom
+ *
*/
- readonly reference_database_accession_code?: Maybe<Scalars['String']>;
+ readonly pdbx_secretion?: Maybe<Scalars['String']>;
+ /** This data item is an ordinal identifier for entity_src_nat data records. */
+ readonly pdbx_src_id: Scalars['Int'];
+ /** Identifies the variant. */
+ readonly pdbx_variant?: Maybe<Scalars['String']>;
/**
- * The reference database name for the target interaction.
- *
- * Allowable values:
- * UniProt
+ * The species of the organism from which the entity was isolated.
+ *
+ * Examples:
+ * sapiens, cerevisiae, coli
+ *
*/
- readonly reference_database_name?: Maybe<Scalars['String']>;
- /** The actions of the target interaction. */
- readonly target_actions?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
-};
-
-export type RcsbMembraneLineage = {
- /** Hierarchy depth. */
- readonly depth?: Maybe<Scalars['Int']>;
- /** Identifier for membrane classification term (system generated for internal purposes identifier). */
- readonly id?: Maybe<Scalars['String']>;
- /** Membrane protein classification term. */
- readonly name?: Maybe<Scalars['String']>;
-};
-
-export type RcsbBranchedStructConnConnectTarget = {
+ readonly species?: Maybe<Scalars['String']>;
/**
- * A component of the identifier for the target of the structure
- * connection.
- *
- * This data item is a pointer to _atom_site.auth_asym_id in the
- * ATOM_SITE category.
+ * The strain of the organism from which the entity was isolated.
+ *
+ * Examples:
+ * DH5a, BMH 71-18
+ *
*/
- readonly auth_asym_id?: Maybe<Scalars['String']>;
+ readonly strain?: Maybe<Scalars['String']>;
/**
- * A component of the identifier for the target of the structure
- * connection.
- *
- * This data item is a pointer to _atom_site.auth_seq_id in the
- * ATOM_SITE category.
+ * The tissue of the organism from which the entity was isolated.
+ *
+ * Examples:
+ * heart, liver, eye lens
+ *
*/
- readonly auth_seq_id?: Maybe<Scalars['String']>;
+ readonly tissue?: Maybe<Scalars['String']>;
/**
- * A component of the identifier for the target of the structure
- * connection.
- *
- * This data item is a pointer to _atom_site.label_alt_id in the
- * ATOM_SITE category.
+ * The subcellular fraction of the tissue of the organism from
+ * which the entity was isolated.
+ *
+ * Examples:
+ * mitochondria, nucleus, membrane
+ *
*/
- readonly label_alt_id?: Maybe<Scalars['String']>;
+ readonly tissue_fraction?: Maybe<Scalars['String']>;
+};
+
+export type Entry = {
/**
- * A component of the identifier for the target of the structure
- * connection.
- *
- * This data item is a pointer to _atom_site.label_asym_id in the
- * ATOM_SITE category.
+ * The value of _entry.id identifies the data block.
+ *
+ * Note that this item need not be a number; it can be any unique
+ * identifier.
*/
- readonly label_asym_id: Scalars['String'];
+ readonly id: Scalars['String'];
+};
+
+export type Exptl = {
/**
- * A component of the identifier for the target of the structure
- * connection.
- *
- * This data item is a pointer to _atom_site.label_atom_id in the
- * ATOM_SITE category.
+ * The total number of crystals used in the measurement of
+ * intensities.
*/
- readonly label_atom_id?: Maybe<Scalars['String']>;
+ readonly crystals_number?: Maybe<Scalars['Int']>;
/**
- * A component of the identifier for the target of the structure
- * connection.
- *
- * This data item is a pointer to _atom_site.label_comp_id in the
- * ATOM_SITE category.
+ * Any special information about the experimental work prior to the
+ * intensity measurement. See also _exptl_crystal.preparation.
*/
- readonly label_comp_id: Scalars['String'];
+ readonly details?: Maybe<Scalars['String']>;
/**
- * A component of the identifier for the target of the structure
- * connection.
- *
- * This data item is a pointer to _atom_site.connect_target_label_seq_id in the
- * ATOM_SITE category.
+ * The method used in the experiment.
+ *
+ * Allowable values:
+ * ELECTRON CRYSTALLOGRAPHY, ELECTRON MICROSCOPY, EPR, FIBER DIFFRACTION, FLUORESCENCE TRANSFER, INFRARED SPECTROSCOPY, NEUTRON DIFFRACTION, POWDER DIFFRACTION, SOLID-STATE NMR, SOLUTION NMR, SOLUTION SCATTERING, THEORETICAL MODEL, X-RAY DIFFRACTION
+ *
*/
- readonly label_seq_id?: Maybe<Scalars['Int']>;
+ readonly method: Scalars['String'];
/**
- * Describes the symmetry operation that should be applied to the
- * atom set specified by _rcsb_branched_struct_conn.label* to generate the
- * target of the structure connection.
- *
+ * A description of special aspects of the experimental method.
+ *
* Examples:
- * 1_555, 7_645
+ * 29 structures, minimized average structure
+ *
*/
- readonly symmetry?: Maybe<Scalars['String']>;
+ readonly method_details?: Maybe<Scalars['String']>;
};
-export type PdbxNmrRefine = {
+export type ExptlCrystal = {
/**
- * Additional details about the NMR refinement.
- *
+ * The colour of the crystal.
+ *
* Examples:
- * Additional comments about the NMR refinement can be placed here, e.g.
- * the structures are based on a total of 3344 restraints, 3167 are NOE-derived
- * distance constraints, 68 dihedral angle restraints,109 distance restraints
- * from hydrogen bonds.
+ * dark green
+ *
*/
- readonly details?: Maybe<Scalars['String']>;
+ readonly colour?: Maybe<Scalars['String']>;
/**
- * The method used to determine the structure.
- *
+ * The density of the crystal, expressed as the ratio of the
+ * volume of the asymmetric unit to the molecular mass of a
+ * monomer of the structure, in units of angstroms^3^ per dalton.
+ *
+ * Ref: Matthews, B. W. (1968). J. Mol. Biol. 33, 491-497.
+ *
* Examples:
- * simulated annealing, distance geometry
- * simulated annealing
- * molecular dynamics
- * matrix relaxation
- * torsion angle dynamics
+ * null
+ *
*/
- readonly method?: Maybe<Scalars['String']>;
- /** Pointer to _software.ordinal */
- readonly software_ordinal: Scalars['Int'];
-};
-
-export type RcsbUniprotProtein = {
- /** Enzyme Commission (EC) number(s). */
- readonly ec?: Maybe<ReadonlyArray<Maybe<RcsbUniprotProteinEc>>>;
- readonly function?: Maybe<RcsbUniprotProteinFunction>;
- /** The name(s) of the gene(s) that code for the protein sequence(s) described in the entry. */
- readonly gene?: Maybe<ReadonlyArray<Maybe<RcsbUniprotProteinGene>>>;
- readonly name?: Maybe<RcsbUniprotProteinName>;
- /** Protein sequence data for canonical protein sequence. */
- readonly sequence?: Maybe<Scalars['String']>;
- /** Taxonomy information on the organism that is the source of the protein sequence. */
- readonly source_organism?: Maybe<RcsbUniprotProteinSourceOrganism>;
-};
-
-export type ClustersMembers = {
- /** Internal chain ID used in mmCIF files to uniquely identify structural elements in the asymmetric unit. */
- readonly asym_id: Scalars['String'];
- readonly pdbx_struct_oper_list_ids?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
-};
-
-export type RcsbPolymerEntityContainerIdentifiersReferenceSequenceIdentifiers = {
- /** Reference database accession code */
- readonly database_accession?: Maybe<Scalars['String']>;
- /** Reference database identifier for the sequence isoform */
- readonly database_isoform?: Maybe<Scalars['String']>;
+ readonly density_Matthews?: Maybe<Scalars['Float']>;
/**
- * Reference database name
- *
- * Allowable values:
- * EMBL, GenBank, NDB, NORINE, PDB, PIR, PRF, RefSeq, UniProt
+ * Density values measured using standard chemical and physical
+ * methods. The units are megagrams per cubic metre (grams per
+ * cubic centimetre).
*/
- readonly database_name?: Maybe<Scalars['String']>;
+ readonly density_meas?: Maybe<Scalars['Float']>;
/**
- * Source of the reference database assignment
- *
- * Allowable values:
- * PDB, RCSB, SIFTS
+ * Density value P calculated from the crystal cell and contents,
+ * expressed as per cent solvent.
+ *
+ * P = 1 - (1.23 N MMass) / V
+ *
+ * N = the number of molecules in the unit cell
+ * MMass = the molecular mass of each molecule (gm/mole)
+ * V = the volume of the unit cell (A^3^)
+ * 1.23 = a conversion factor evaluated as:
+ *
+ * (0.74 cm^3^/g) (10^24^ A^3^/cm^3^)
+ * --------------------------------------
+ * (6.02*10^23^) molecules/mole
+ *
+ * where 0.74 is an assumed value for the partial specific
+ * volume of the molecule
*/
- readonly provenance_source?: Maybe<Scalars['String']>;
-};
-
-export type RcsbEntityHostOrganism = {
+ readonly density_percent_sol?: Maybe<Scalars['Float']>;
/**
- * The beginning polymer sequence position for the polymer section corresponding
- * to this host organism.
- *
- * A reference to the sequence position in the entity_poly category.
+ * A description of the quality and habit of the crystal.
+ * The crystal dimensions should not normally be reported here;
+ * use instead the specific items in the EXPTL_CRYSTAL category
+ * relating to size for the gross dimensions of the crystal and
+ * data items in the EXPTL_CRYSTAL_FACE category to describe the
+ * relationship between individual faces.
*/
- readonly beg_seq_num?: Maybe<Scalars['Int']>;
- /** The common name of the host organism */
- readonly common_name?: Maybe<Scalars['String']>;
+ readonly description?: Maybe<Scalars['String']>;
/**
- * The ending polymer sequence position for the polymer section corresponding
- * to this host organism.
- *
- * A reference to the sequence position in the entity_poly category.
+ * The value of _exptl_crystal.id must uniquely identify a record in
+ * the EXPTL_CRYSTAL list.
+ *
+ * Note that this item need not be a number; it can be any unique
+ * identifier.
*/
- readonly end_seq_num?: Maybe<Scalars['Int']>;
+ readonly id: Scalars['String'];
/**
- * Common names associated with this taxonomy code obtained from NCBI Taxonomy Database.
- *
- * These names correspond to the taxonomy identifier assigned by the PDB depositor.
- *
- * References:
- *
- * Sayers EW, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V,
- * Church DM, DiCuccio M, Edgar R, Federhen S, Feolo M, Geer LY,
- * Helmberg W, Kapustin Y, Landsman D, Lipman DJ, Madden TL, Maglott DR,
- * Miller V, Mizrachi I, Ostell J, Pruitt KD, Schuler GD, Sequeira E,
- * Sherry ST, Shumway M, Sirotkin K, Souvorov A, Starchenko G,
- * Tatusova TA, Wagner L, Yaschenko E, Ye J (2009). Database resources
- * of the National Center for Biotechnology Information. Nucleic Acids
- * Res. 2009 Jan;37(Database issue):D5-15. Epub 2008 Oct 21.
- *
- * Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW (2009).
- * GenBank. Nucleic Acids Res. 2009 Jan;37(Database issue):D26-31.
- * Epub 2008 Oct 21.
+ * The of the distribution of mis-orientation angles specified in degrees
+ * of all the unit cells in the crystal. Lower mosaicity indicates better
+ * ordered crystals.
*/
- readonly ncbi_common_names?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
+ readonly pdbx_mosaicity?: Maybe<Scalars['Float']>;
+ /** The uncertainty in the mosaicity estimate for the crystal. */
+ readonly pdbx_mosaicity_esd?: Maybe<Scalars['Float']>;
/**
- * The parent scientific name in the NCBI taxonomy hierarchy (depth=1) associated with this taxonomy code.
- *
- * References:
- *
- * Sayers EW, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V,
- * Church DM, DiCuccio M, Edgar R, Federhen S, Feolo M, Geer LY,
- * Helmberg W, Kapustin Y, Landsman D, Lipman DJ, Madden TL, Maglott DR,
- * Miller V, Mizrachi I, Ostell J, Pruitt KD, Schuler GD, Sequeira E,
- * Sherry ST, Shumway M, Sirotkin K, Souvorov A, Starchenko G,
- * Tatusova TA, Wagner L, Yaschenko E, Ye J (2009). Database resources
- * of the National Center for Biotechnology Information. Nucleic Acids
- * Res. 2009 Jan;37(Database issue):D5-15. Epub 2008 Oct 21.
- *
- * Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW (2009).
- * GenBank. Nucleic Acids Res. 2009 Jan;37(Database issue):D26-31.
- * Epub 2008 Oct 21.
+ * Details of crystal growth and preparation of the crystal (e.g.
+ * mounting) prior to the intensity measurements.
+ *
+ * Examples:
+ * mounted in an argon-filled quartz capillary
+ *
*/
- readonly ncbi_parent_scientific_name?: Maybe<Scalars['String']>;
+ readonly preparation?: Maybe<Scalars['String']>;
+};
+
+export type ExptlCrystalGrow = {
/**
- * The scientific name associated with this taxonomy code aggregated by the NCBI Taxonomy Database.
- *
- * This name corresponds to the taxonomy identifier assigned by the PDB depositor.
- *
- *
- * References:
- *
- * Sayers EW, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V,
- * Church DM, DiCuccio M, Edgar R, Federhen S, Feolo M, Geer LY,
- * Helmberg W, Kapustin Y, Landsman D, Lipman DJ, Madden TL, Maglott DR,
- * Miller V, Mizrachi I, Ostell J, Pruitt KD, Schuler GD, Sequeira E,
- * Sherry ST, Shumway M, Sirotkin K, Souvorov A, Starchenko G,
- * Tatusova TA, Wagner L, Yaschenko E, Ye J (2009). Database resources
- * of the National Center for Biotechnology Information. Nucleic Acids
- * Res. 2009 Jan;37(Database issue):D5-15. Epub 2008 Oct 21.
- *
- * Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW (2009).
- * GenBank. Nucleic Acids Res. 2009 Jan;37(Database issue):D26-31.
- * Epub 2008 Oct 21.
+ * This data item is a pointer to _exptl_crystal.id in the
+ * EXPTL_CRYSTAL category.
*/
- readonly ncbi_scientific_name?: Maybe<Scalars['String']>;
+ readonly crystal_id: Scalars['String'];
/**
- * NCBI Taxonomy identifier for the host organism.
- *
- *
- * Reference:
- *
- * Wheeler DL, Chappey C, Lash AE, Leipe DD, Madden TL, Schuler GD,
- * Tatusova TA, Rapp BA (2000). Database resources of the National
- * Center for Biotechnology Information. Nucleic Acids Res 2000 Jan
- * 1;28(1):10-4
- *
- * Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Rapp BA,
- * Wheeler DL (2000). GenBank. Nucleic Acids Res 2000 Jan 1;28(1):15-18.
+ * A description of special aspects of the crystal growth.
+ *
+ * Examples:
+ * Solution 2 was prepared as a well solution and
+ * mixed. A droplet containing 2 \ml of solution
+ * 1 was delivered onto a cover slip; 2 \ml of
+ * solution 2 was added to the droplet without
+ * mixing., Crystal plates were originally stored at room
+ * temperature for 1 week but no nucleation
+ * occurred. They were then transferred to 4
+ * degrees C, at which temperature well formed
+ * single crystals grew in 2 days., The dependence on pH for successful crystal
+ * growth is very sharp. At pH 7.4 only showers
+ * of tiny crystals grew, at pH 7.5 well formed
+ * single crystals grew, at pH 7.6 no
+ * crystallization occurred at all.
+ *
*/
- readonly ncbi_taxonomy_id?: Maybe<Scalars['Int']>;
- /** An identifier for an entity segment. */
- readonly pdbx_src_id: Scalars['String'];
+ readonly details?: Maybe<Scalars['String']>;
/**
- * A code indicating the provenance of the host organism.
- *
- * Allowable values:
- * PDB Primary Data
+ * The method used to grow the crystals.
+ *
+ * Examples:
+ * MICROBATCH, VAPOR DIFFUSION, HANGING DROP
+ *
*/
- readonly provenance_source?: Maybe<Scalars['String']>;
- /** The scientific name of the host organism */
- readonly scientific_name?: Maybe<Scalars['String']>;
- readonly taxonomy_lineage?: Maybe<ReadonlyArray<Maybe<RcsbEntityHostOrganismTaxonomyLineage>>>;
-};
-
-export type RcsbPolymerEntityAnnotationAnnotationLineage = {
- /** Members of the annotation lineage as parent lineage depth (1-N) */
- readonly depth?: Maybe<Scalars['Int']>;
- /** Members of the annotation lineage as parent class identifiers. */
- readonly id?: Maybe<Scalars['String']>;
- /** Members of the annotation lineage as parent class names. */
- readonly name?: Maybe<Scalars['String']>;
-};
-
-export type PdbxNmrDetails = {
+ readonly method?: Maybe<Scalars['String']>;
/**
- * Additional details describing the NMR experiment.
- *
+ * The pH at which the crystal was grown. If more than one pH was
+ * employed during the crystallization process, the final pH should
+ * be noted here and the protocol involving multiple pH values
+ * should be described in _exptl_crystal_grow.details.
+ *
* Examples:
- * This structure was determined using standard 2D homonuclear techniques., The structure was determined using triple-resonance NMR spectroscopy.
+ * null, null, null
+ *
*/
- readonly text?: Maybe<Scalars['String']>;
-};
-
-export type PdbxReferenceEntitySequence = {
+ readonly pH?: Maybe<Scalars['Float']>;
/**
- * A flag to indicate a non-ribosomal entity.
- *
- * Allowable values:
- * N, Y
+ * Text description of crystal growth procedure.
+ *
+ * Examples:
+ * PEG 4000, potassium phosphate, magnesium chloride, cacodylate
+ *
*/
- readonly NRP_flag?: Maybe<Scalars['String']>;
- /** The one-letter-code sequence for this entity. Non-standard monomers are represented as 'X'. */
- readonly one_letter_codes?: Maybe<Scalars['String']>;
+ readonly pdbx_details?: Maybe<Scalars['String']>;
/**
- * The value of _pdbx_reference_entity_sequence.prd_id is a reference
- * _pdbx_reference_entity_list.prd_id in the PDBX_REFERENCE_ENTITY_LIST category.
+ * The range of pH values at which the crystal was grown. Used when
+ * a point estimate of pH is not appropriate.
+ *
+ * Examples:
+ * 5.6 - 6.4
+ *
*/
- readonly prd_id: Scalars['String'];
+ readonly pdbx_pH_range?: Maybe<Scalars['String']>;
/**
- * The value of _pdbx_reference_entity_sequence.ref_entity_id is a reference
- * to _pdbx_reference_entity_list.ref_entity_id in PDBX_REFERENCE_ENTITY_LIST category.
+ * The temperature in kelvins at which the crystal was grown.
+ * If more than one temperature was employed during the
+ * crystallization process, the final temperature should be noted
+ * here and the protocol involving multiple temperatures should be
+ * described in _exptl_crystal_grow.details.
*/
- readonly ref_entity_id: Scalars['String'];
+ readonly temp?: Maybe<Scalars['Float']>;
/**
- * The monomer type for the sequence.
- *
- * Allowable values:
- * peptide-like, saccharide
+ * A description of special aspects of temperature control during
+ * crystal growth.
*/
+ readonly temp_details?: Maybe<Scalars['String']>;
+};
+
+export type GeneName = {
+ /** Allowable values: PRIMARY, SYNONYM, ORDERED_LOCUS, ORF. */
readonly type?: Maybe<Scalars['String']>;
+ readonly value?: Maybe<Scalars['String']>;
};
-export type RcsbNonpolymerEntityFeature = {
- /** Identifies the version of the feature assignment. */
- readonly assignment_version?: Maybe<Scalars['String']>;
- /** Non-polymer(ligand) chemical component identifier for the entity. */
- readonly comp_id?: Maybe<Scalars['String']>;
- /** A description for the feature. */
- readonly description?: Maybe<Scalars['String']>;
- /** An identifier for the feature. */
- readonly feature_id?: Maybe<Scalars['String']>;
- /** A name for the feature. */
- readonly name?: Maybe<Scalars['String']>;
+export type PdbxAuditRevisionCategory = {
/**
- * Code identifying the individual, organization or program that
- * assigned the feature.
+ * The category updated in the pdbx_audit_revision_category record.
+ *
+ * Examples:
+ * audit_author, citation
+ *
*/
- readonly provenance_source?: Maybe<Scalars['String']>;
+ readonly category?: Maybe<Scalars['String']>;
/**
- * A type or category of the feature.
- *
+ * The type of file that the pdbx_audit_revision_history record refers to.
+ *
* Allowable values:
- * SUBJECT_OF_INVESTIGATION
+ * Chemical component, NMR restraints, NMR shifts, Structure factors, Structure model
+ *
*/
- readonly type?: Maybe<Scalars['String']>;
- /** The feature value. */
- readonly value?: Maybe<Scalars['Float']>;
+ readonly data_content_type: Scalars['String'];
+ /** A unique identifier for the pdbx_audit_revision_category record. */
+ readonly ordinal: Scalars['Int'];
+ /** A pointer to _pdbx_audit_revision_history.ordinal */
+ readonly revision_ordinal: Scalars['Int'];
};
-export type PdbxReferenceMoleculeFeatures = {
- /**
- * The value of _pdbx_reference_molecule_features.family_prd_id is a reference to
- * _pdbx_reference_molecule_list.family_prd_id in category PDBX_REFERENCE_MOLECULE_FAMILY_LIST.
- */
- readonly family_prd_id: Scalars['String'];
+export type PdbxAuditRevisionDetails = {
/**
- * The value of _pdbx_reference_molecule_features.ordinal distinguishes
- * each feature for this entity.
+ * The type of file that the pdbx_audit_revision_history record refers to.
+ *
+ * Allowable values:
+ * Chemical component, NMR restraints, NMR shifts, Structure factors, Structure model
+ *
*/
+ readonly data_content_type: Scalars['String'];
+ /** Additional details describing the revision. */
+ readonly description?: Maybe<Scalars['String']>;
+ /** Further details describing the revision. */
+ readonly details?: Maybe<Scalars['String']>;
+ /** A unique identifier for the pdbx_audit_revision_details record. */
readonly ordinal: Scalars['Int'];
/**
- * The value of _pdbx_reference_molecule_features.prd_id is a reference
- * _pdbx_reference_molecule.prd_id in the PDBX_REFERENCE_MOLECULE category.
- */
- readonly prd_id: Scalars['String'];
+ * The provider of the revision.
+ *
+ * Allowable values:
+ * author, repository
+ *
+ */
+ readonly provider?: Maybe<Scalars['String']>;
+ /** A pointer to _pdbx_audit_revision_history.ordinal */
+ readonly revision_ordinal: Scalars['Int'];
/**
- * The information source for the component feature.
- *
- * Examples:
- * PDB, CHEBI, DRUGBANK, PUBCHEM
+ * A type classification of the revision
+ *
+ * Allowable values:
+ * Coordinate replacement, Initial release, Obsolete, Remediation
+ *
*/
- readonly source?: Maybe<Scalars['String']>;
+ readonly type?: Maybe<Scalars['String']>;
+};
+
+export type PdbxAuditRevisionGroup = {
/**
- * The value of _pdbx_reference_molecule_features.source_ordinal provides
- * the priority order of features from a particular source or database.
+ * The type of file that the pdbx_audit_revision_history record refers to.
+ *
+ * Allowable values:
+ * Chemical component, NMR restraints, NMR shifts, Structure factors, Structure model
+ *
*/
- readonly source_ordinal?: Maybe<Scalars['Int']>;
+ readonly data_content_type: Scalars['String'];
/**
- * The entity feature type.
- *
- * Examples:
- * FUNCTION, ENZYME INHIBITED, STRUCTURE IMAGE URL
+ * The collection of categories updated with this revision.
+ *
+ * Allowable values:
+ * Advisory, Atomic model, Author supporting evidence, Data collection, Data processing, Database references, Derived calculations, Experimental data, Experimental preparation, Initial release, Non-polymer description, Other, Polymer sequence, Refinement description, Source and taxonomy, Structure summary, Version format compliance
+ *
*/
- readonly type?: Maybe<Scalars['String']>;
- /** The entity feature value. */
- readonly value?: Maybe<Scalars['String']>;
+ readonly group?: Maybe<Scalars['String']>;
+ /** A unique identifier for the pdbx_audit_revision_group record. */
+ readonly ordinal: Scalars['Int'];
+ /** A pointer to _pdbx_audit_revision_history.ordinal */
+ readonly revision_ordinal: Scalars['Int'];
};
-export type AuditAuthor = {
+export type PdbxAuditRevisionHistory = {
/**
- * The Open Researcher and Contributor ID (ORCID).
- *
- * Examples:
- * 0000-0002-6681-547X
+ * The type of file that the pdbx_audit_revision_history record refers to.
+ *
+ * Allowable values:
+ * Chemical component, NMR restraints, NMR shifts, Structure factors, Structure model
+ *
*/
- readonly identifier_ORCID?: Maybe<Scalars['String']>;
+ readonly data_content_type: Scalars['String'];
+ /** The major version number of deposition release. */
+ readonly major_revision?: Maybe<Scalars['Int']>;
+ /** The minor version number of deposition release. */
+ readonly minor_revision?: Maybe<Scalars['Int']>;
+ /** A unique identifier for the pdbx_audit_revision_history record. */
+ readonly ordinal: Scalars['Int'];
/**
- * The name of an author of this data block. If there are multiple
- * authors, _audit_author.name is looped with _audit_author.address.
- * The family name(s), followed by a comma and including any
- * dynastic components, precedes the first name(s) or initial(s).
- *
+ * The release date of the revision
+ *
* Examples:
- * Jones, T.J., Bleary, Percival R., O'Neil, F.K., Van den Bossche, G., Yang, D.-L., Simonov, Yu.A
+ * 2017-03-08
+ *
*/
- readonly name?: Maybe<Scalars['String']>;
+ readonly revision_date?: Maybe<Scalars['Date']>;
+};
+
+export type PdbxAuditRevisionItem = {
/**
- * This data item defines the order of the author's name in the
- * list of audit authors.
- *
+ * The type of file that the pdbx_audit_revision_history record refers to.
+ *
+ * Allowable values:
+ * Chemical component, NMR restraints, NMR shifts, Structure factors, Structure model
+ *
+ */
+ readonly data_content_type: Scalars['String'];
+ /**
+ * A high level explanation the author has provided for submitting a revision.
+ *
* Examples:
- * 1, 2, 3
+ * _atom_site.type_symbol
+ *
*/
- readonly pdbx_ordinal: Scalars['Int'];
+ readonly item?: Maybe<Scalars['String']>;
+ /** A unique identifier for the pdbx_audit_revision_item record. */
+ readonly ordinal: Scalars['Int'];
+ /** A pointer to _pdbx_audit_revision_history.ordinal */
+ readonly revision_ordinal: Scalars['Int'];
};
-export type RcsbPolymerEntityAnnotation = {
- /** An identifier for the annotation. */
- readonly annotation_id?: Maybe<Scalars['String']>;
- readonly annotation_lineage?: Maybe<ReadonlyArray<Maybe<RcsbPolymerEntityAnnotationAnnotationLineage>>>;
- /** Identifies the version of the annotation assignment. */
- readonly assignment_version?: Maybe<Scalars['String']>;
- /** A description for the annotation. */
- readonly description?: Maybe<Scalars['String']>;
- /** A name for the annotation. */
- readonly name?: Maybe<Scalars['String']>;
+export type PdbxAuditSupport = {
/**
- * Code identifying the individual, organization or program that
- * assigned the annotation.
+ * The country/region providing the funding support for the entry.
+ * Funding information is optionally provided for entries after June 2016.
*/
- readonly provenance_source?: Maybe<Scalars['String']>;
+ readonly country?: Maybe<Scalars['String']>;
/**
- * A type or category of the annotation.
- *
- * Allowable values:
- * GO, InterPro, Pfam
+ * The name of the organization providing funding support for the
+ * entry. Funding information is optionally provided for entries
+ * after June 2016.
+ *
+ * Examples:
+ * National Institutes of Health, Wellcome Trust, National Institutes of Health/National Institute of General Medical Sciences
+ *
*/
- readonly type?: Maybe<Scalars['String']>;
+ readonly funding_organization?: Maybe<Scalars['String']>;
+ /** The grant number associated with this source of support. */
+ readonly grant_number?: Maybe<Scalars['String']>;
+ /** A unique sequential integer identifier for each source of support for this entry. */
+ readonly ordinal: Scalars['Int'];
};
-export type RefineAnalyze = {
- /**
- * The estimated coordinate error obtained from the plot of
- * the R value versus sin(theta)/lambda for the reflections
- * treated as a test set during refinement.
- *
- * Ref: Luzzati, V. (1952). Traitement statistique des erreurs
- * dans la determination des structures cristallines. Acta
- * Cryst. 5, 802-810.
- */
- readonly Luzzati_coordinate_error_free?: Maybe<Scalars['Float']>;
+export type PdbxChemCompAudit = {
/**
- * The estimated coordinate error obtained from the plot of
- * the R value versus sin(theta)/lambda for reflections classified
- * as observed.
- *
- * Ref: Luzzati, V. (1952). Traitement statistique des erreurs
- * dans la determination des structures cristallines. Acta
- * Cryst. 5, 802-810.
+ * The action associated with this audit record.
+ *
+ * Allowable values:
+ * Create component, Initial release, Modify aromatic_flag, Modify atom id, Modify charge, Modify component atom id, Modify component comp_id, Modify coordinates, Modify descriptor, Modify formal charge, Modify formula, Modify identifier, Modify internal type, Modify leaving atom flag, Modify linking type, Modify model coordinates code, Modify name, Modify one letter code, Modify parent residue, Modify processing site, Modify subcomponent list, Modify synonyms, Modify value order, Obsolete component, Other modification
+ *
*/
- readonly Luzzati_coordinate_error_obs?: Maybe<Scalars['Float']>;
+ readonly action_type?: Maybe<Scalars['String']>;
/**
- * The value of the low-resolution cutoff used in constructing the
- * Luzzati plot for reflections treated as a test set during
- * refinement.
- *
- * Ref: Luzzati, V. (1952). Traitement statistique des erreurs
- * dans la determination des structures cristallines. Acta
- * Cryst. 5, 802-810.
+ * This data item is a pointer to _chem_comp.id in the CHEM_COMP
+ * category.
*/
- readonly Luzzati_d_res_low_free?: Maybe<Scalars['Float']>;
+ readonly comp_id?: Maybe<Scalars['String']>;
+ /** The date associated with this audit record. */
+ readonly date?: Maybe<Scalars['Date']>;
/**
- * The value of the low-resolution cutoff used in
- * constructing the Luzzati plot for reflections classified as
- * observed.
- *
- * Ref: Luzzati, V. (1952). Traitement statistique des erreurs
- * dans la determination des structures cristallines. Acta
- * Cryst. 5, 802-810.
+ * Additional details decribing this change.
+ *
+ * Examples:
+ * Added C14 as a leaving atom.
+ *
*/
- readonly Luzzati_d_res_low_obs?: Maybe<Scalars['Float']>;
+ readonly details?: Maybe<Scalars['String']>;
/**
- * The value of sigma~a~ used in constructing the Luzzati plot for
- * the reflections treated as a test set during refinement.
- * Details of the estimation of sigma~a~ can be specified
- * in _refine_analyze.Luzzati_sigma_a_free_details.
- *
- * Ref: Luzzati, V. (1952). Traitement statistique des erreurs
- * dans la determination des structures cristallines. Acta
- * Cryst. 5, 802-810.
+ * This data item is an ordinal index for the
+ * PDBX_CHEM_COMP_AUDIT category.
*/
- readonly Luzzati_sigma_a_free?: Maybe<Scalars['Float']>;
+ readonly ordinal: Scalars['Int'];
+};
+
+export type PdbxChemCompDescriptor = {
/**
- * The value of sigma~a~ used in constructing the Luzzati plot for
- * reflections classified as observed. Details of the
- * estimation of sigma~a~ can be specified in
- * _refine_analyze.Luzzati_sigma_a_obs_details.
- *
- * Ref: Luzzati, V. (1952). Traitement statistique des erreurs
- * dans la determination des structures cristallines. Acta
- * Cryst. 5, 802-810.
+ * This data item is a pointer to _chem_comp.id in the CHEM_COMP
+ * category.
*/
- readonly Luzzati_sigma_a_obs?: Maybe<Scalars['Float']>;
+ readonly comp_id: Scalars['String'];
/**
- * The number of discretely disordered residues in the refined
- * model.
+ * This data item contains the descriptor value for this
+ * component.
*/
- readonly number_disordered_residues?: Maybe<Scalars['Float']>;
+ readonly descriptor?: Maybe<Scalars['String']>;
/**
- * The sum of the occupancies of the hydrogen atoms in the refined
- * model.
+ * This data item contains the name of the program
+ * or library used to compute the descriptor.
+ *
+ * Examples:
+ * OPENEYE, CACTVS, DAYLIGHT, OTHER
+ *
*/
- readonly occupancy_sum_hydrogen?: Maybe<Scalars['Float']>;
+ readonly program: Scalars['String'];
/**
- * The sum of the occupancies of the non-hydrogen atoms in the
- * refined model.
+ * This data item contains the version of the program
+ * or library used to compute the descriptor.
*/
- readonly occupancy_sum_non_hydrogen?: Maybe<Scalars['Float']>;
- /** record the high resolution for calculating Luzzati statistics. */
- readonly pdbx_Luzzati_d_res_high_obs?: Maybe<Scalars['Float']>;
+ readonly program_version: Scalars['String'];
/**
- * This data item uniquely identifies a refinement within an entry.
- * _refine_analyze.pdbx_refine_id can be used to distinguish the results
- * of joint refinements.
+ * This data item contains the descriptor type.
+ *
+ * Allowable values:
+ * InChI, InChIKey, InChI_CHARGE, InChI_FIXEDH, InChI_ISOTOPE, InChI_MAIN, InChI_MAIN_CONNECT, InChI_MAIN_FORMULA, InChI_MAIN_HATOM, InChI_RECONNECT, InChI_STEREO, SMILES, SMILES_CANNONICAL, SMILES_CANONICAL
+ *
*/
- readonly pdbx_refine_id: Scalars['String'];
+ readonly type: Scalars['String'];
};
-export type RcsbBranchedInstanceFeature = {
- /** Identifies the version of the feature assignment. */
- readonly assignment_version?: Maybe<Scalars['String']>;
- /** A description for the feature. */
- readonly description?: Maybe<Scalars['String']>;
- /** An identifier for the feature. */
- readonly feature_id?: Maybe<Scalars['String']>;
- readonly feature_positions?: Maybe<ReadonlyArray<Maybe<RcsbBranchedInstanceFeatureFeaturePositions>>>;
- readonly feature_value?: Maybe<ReadonlyArray<Maybe<RcsbBranchedInstanceFeatureFeatureValue>>>;
- /** A name for the feature. */
- readonly name?: Maybe<Scalars['String']>;
- /** Ordinal identifier for this category */
- readonly ordinal: Scalars['Int'];
+export type PdbxChemCompFeature = {
/**
- * Code identifying the individual, organization or program that
- * assigned the feature.
+ * The component identifier for this feature.
+ *
+ * Examples:
+ * ABC, ATP
+ *
*/
- readonly provenance_source?: Maybe<Scalars['String']>;
+ readonly comp_id: Scalars['String'];
/**
- * Code residue coordinate system for the assigned feature.
- *
- * Allowable values:
- * PDB entity, PDB entry
+ * The information source for the component feature.
+ *
+ * Examples:
+ * PDB, CHEBI, DRUGBANK, PUBCHEM
+ *
*/
- readonly reference_scheme?: Maybe<Scalars['String']>;
+ readonly source: Scalars['String'];
/**
- * A type or category of the feature.
- *
+ * The component feature type.
+ *
* Allowable values:
- * BINDING_SITE, CATH, MOGUL_ANGLE_OUTLIER, MOGUL_BOND_OUTLIER, RSRCC_OUTLIER, RSRZ_OUTLIER, SCOP, UNOBSERVED_ATOM_XYZ, UNOBSERVED_RESIDUE_XYZ, ZERO_OCCUPANCY_ATOM_XYZ, ZERO_OCCUPANCY_RESIDUE_XYZ
+ * CARBOHYDRATE ANOMER, CARBOHYDRATE ISOMER, CARBOHYDRATE PRIMARY CARBONYL GROUP, CARBOHYDRATE RING
+ *
*/
- readonly type?: Maybe<Scalars['String']>;
-};
-
-export type PdbxEntityNonpoly = {
- /** This data item is a pointer to _chem_comp.id in the CHEM_COMP category. */
- readonly comp_id?: Maybe<Scalars['String']>;
- /** This data item is a pointer to _entity.id in the ENTITY category. */
- readonly entity_id: Scalars['String'];
- /** A name for the non-polymer entity */
- readonly name?: Maybe<Scalars['String']>;
- /** For non-polymer BIRD molecules the BIRD identifier for the entity. */
- readonly rcsb_prd_id?: Maybe<Scalars['String']>;
+ readonly type: Scalars['String'];
+ /** The component feature value. */
+ readonly value: Scalars['String'];
};
-export type PdbxDatabaseStatus = {
+export type PdbxChemCompIdentifier = {
/**
- * This code indicates whether the entry belongs to
- * Structural Genomics Project.
- *
- * Allowable values:
- * N, Y
+ * This data item is a pointer to _chem_comp.id in the CHEM_COMP
+ * category.
*/
- readonly SG_entry?: Maybe<Scalars['String']>;
+ readonly comp_id: Scalars['String'];
/**
- * The site where the file was deposited.
- *
+ * This data item contains the identifier value for this
+ * component.
+ */
+ readonly identifier?: Maybe<Scalars['String']>;
+ /**
+ * This data item contains the name of the program
+ * or library used to compute the identifier.
+ *
+ * Examples:
+ * OPENEYE, DAYLIGHT, ACD, AUTONOM, PUBCHEM_CID, PUBCHEM_SID, OTHER, NONE
+ *
+ */
+ readonly program: Scalars['String'];
+ /**
+ * This data item contains the version of the program
+ * or library used to compute the identifier.
+ */
+ readonly program_version: Scalars['String'];
+ /**
+ * This data item contains the identifier type.
+ *
+ * Allowable values:
+ * CAS REGISTRY NUMBER, COMMON NAME, CONDENSED IUPAC CARB SYMBOL, CONDENSED IUPAC CARBOHYDRATE SYMBOL, IUPAC CARB SYMBOL, IUPAC CARBOHYDRATE SYMBOL, MDL Identifier, PUBCHEM Identifier, SNFG CARB SYMBOL, SNFG CARBOHYDRATE SYMBOL, SYNONYM, SYSTEMATIC NAME
+ *
+ */
+ readonly type: Scalars['String'];
+};
+
+export type PdbxDatabasePdbObsSpr = {
+ /**
+ * The date of replacement.
+ *
+ * Examples:
+ * 1997-03-30
+ *
+ */
+ readonly date?: Maybe<Scalars['Date']>;
+ /** Details related to the replaced or replacing entry. */
+ readonly details?: Maybe<Scalars['String']>;
+ /**
+ * Identifier for the type of obsolete entry to be added to this entry.
+ *
+ * Allowable values:
+ * OBSLTE, SPRSDE
+ *
+ */
+ readonly id?: Maybe<Scalars['String']>;
+ /**
+ * The new PDB identifier for the replaced entry.
+ *
+ * Examples:
+ * 2ABC
+ *
+ */
+ readonly pdb_id: Scalars['String'];
+ /**
+ * The PDB identifier for the replaced (OLD) entry/entries.
+ *
+ * Examples:
+ * 3ABC
+ *
+ */
+ readonly replace_pdb_id: Scalars['String'];
+};
+
+export type PdbxDatabaseRelated = {
+ /**
+ * The identifying content type of the related entry.
+ *
+ * Allowable values:
+ * associated EM volume, associated NMR restraints, associated SAS data, associated structure factors, complete structure, derivative structure, ensemble, minimized average structure, native structure, other, other EM volume, protein target sequence and/or protocol data, re-refinement, representative structure, split, unspecified
+ *
+ */
+ readonly content_type: Scalars['String'];
+ /**
+ * The identifying code in the related database.
+ *
+ * Examples:
+ * 1ABC, BDL001
+ *
+ */
+ readonly db_id: Scalars['String'];
+ /**
+ * The name of the database containing the related entry.
+ *
+ * Examples:
+ * PDB - Protein Databank
+ * NDB - Nucleic Acid Database
+ * BMRB - BioMagResBank
+ * EMDB - Electron Microscopy Database
+ * BMCD - Biological Macromolecule Crystallization Database
+ * TargetTrack - Target Registration and Protocol Database
+ * SASBDB - Small Angle Scattering Biological Data Bank
+ *
+ */
+ readonly db_name: Scalars['String'];
+ /**
+ * A description of the related entry.
+ *
+ * Examples:
+ * 1ABC contains the same protein complexed with Netropsin.
+ *
+ */
+ readonly details?: Maybe<Scalars['String']>;
+};
+
+export type PdbxDatabaseStatus = {
+ /**
+ * This code indicates whether the entry belongs to
+ * Structural Genomics Project.
+ *
+ * Allowable values:
+ * N, Y
+ *
+ */
+ readonly SG_entry?: Maybe<Scalars['String']>;
+ /**
+ * The site where the file was deposited.
+ *
* Allowable values:
* BMRB, BNL, NDB, PDBC, PDBE, PDBJ, RCSB
+ *
*/
readonly deposit_site?: Maybe<Scalars['String']>;
/**
* The methods development category in which this
* entry has been placed.
- *
+ *
* Allowable values:
* CAPRI, CASD-NMR, CASP, D3R, FoldIt, GPCR Dock, RNA-Puzzles
+ *
*/
readonly methods_development_category?: Maybe<Scalars['String']>;
/**
* A flag indicating that the entry is compatible with the PDB format.
- *
+ *
* A value of 'N' indicates that the no PDB format data file is
* corresponding to this entry is available in the PDB archive.
- *
+ *
* Allowable values:
* N, Y
+ *
*/
readonly pdb_format_compatible?: Maybe<Scalars['String']>;
/**
* The site where the file was deposited.
- *
+ *
* Allowable values:
* BNL, NDB, PDBC, PDBE, PDBJ, RCSB
+ *
*/
readonly process_site?: Maybe<Scalars['String']>;
/**
* The date of initial deposition. (The first message for
* deposition has been received.)
- *
+ *
* Examples:
* 1983-02-21
+ *
*/
readonly recvd_initial_deposition_date?: Maybe<Scalars['Date']>;
/**
* Code for status of file.
- *
+ *
* Allowable values:
* AUCO, AUTH, BIB, DEL, HOLD, HPUB, OBS, POLC, PROC, REFI, REL, REPL, REV, RMVD, TRSF, UPD, WAIT, WDRN
+ *
*/
readonly status_code?: Maybe<Scalars['String']>;
/**
* Code for status of chemical shift data file.
- *
+ *
* Allowable values:
- * AUTH, HOLD, HPUB, OBS, POLC, PROC, REL, REPL, RMVD, WAIT, WDRN
+ * AUCO, AUTH, HOLD, HPUB, OBS, POLC, PROC, REL, REPL, RMVD, WAIT, WDRN
+ *
*/
readonly status_code_cs?: Maybe<Scalars['String']>;
/**
* Code for status of NMR constraints file.
- *
+ *
* Allowable values:
- * AUTH, HOLD, HPUB, OBS, POLC, PROC, REL, REPL, RMVD, WAIT, WDRN
+ * AUCO, AUTH, HOLD, HPUB, OBS, POLC, PROC, REL, REPL, RMVD, WAIT, WDRN
+ *
*/
readonly status_code_mr?: Maybe<Scalars['String']>;
/**
* Code for status of structure factor file.
- *
+ *
* Allowable values:
* AUTH, HOLD, HPUB, OBS, POLC, PROC, REL, REPL, RMVD, WAIT, WDRN
+ *
*/
readonly status_code_sf?: Maybe<Scalars['String']>;
};
+export type PdbxDepositGroup = {
+ /** A description of the contents of entries in the collection. */
+ readonly group_description?: Maybe<Scalars['String']>;
+ /**
+ * A unique identifier for a group of entries deposited as a collection.
+ *
+ * Examples:
+ * G_1002119, G_1002043
+ *
+ */
+ readonly group_id: Scalars['String'];
+ /** A title to describe the group of entries deposited in the collection. */
+ readonly group_title?: Maybe<Scalars['String']>;
+ /**
+ * Text to describe a grouping of entries in multiple collections
+ *
+ * Allowable values:
+ * changed state, ground state, undefined
+ *
+ */
+ readonly group_type?: Maybe<Scalars['String']>;
+};
+
+export type PdbxEntityBranch = {
+ /** Number of constituent chemical components in the branched entity. */
+ readonly rcsb_branched_component_count?: Maybe<Scalars['Int']>;
+ /**
+ * The type of this branched oligosaccharide.
+ *
+ * Allowable values:
+ * oligosaccharide
+ *
+ */
+ readonly type?: Maybe<Scalars['String']>;
+};
+
export type PdbxEntityBranchDescriptor = {
/**
- * This data item contains the descriptor value for this
+ * This data item contains the descriptor value for this
* entity.
*/
readonly descriptor?: Maybe<Scalars['String']>;
/**
* This data item contains the name of the program
* or library used to compute the descriptor.
- *
+ *
* Examples:
* PDB-CARE, OTHER, GEMS
+ *
*/
readonly program?: Maybe<Scalars['String']>;
/**
@@ -3600,755 +3691,814 @@ export type PdbxEntityBranchDescriptor = {
readonly program_version?: Maybe<Scalars['String']>;
/**
* This data item contains the descriptor type.
- *
+ *
* Allowable values:
* Glycam Condensed Core Sequence, Glycam Condensed Sequence, LINUCS, WURCS
+ *
*/
readonly type?: Maybe<Scalars['String']>;
};
-export type Em2dCrystalEntity = {
- /** Unit-cell angle gamma in degrees. */
- readonly angle_gamma?: Maybe<Scalars['Float']>;
- /** Length used to sample the reciprocal lattice lines in the c-direction. */
- readonly c_sampling_length?: Maybe<Scalars['Float']>;
- /** Unique key for the 2d_crystal_entity category. */
- readonly id: Scalars['String'];
- /** pointer to _em_image_processing.id in the EM_IMAGE_PROCESSING category. */
- readonly image_processing_id: Scalars['String'];
- /** Unit-cell length a in Angstroms. */
- readonly length_a?: Maybe<Scalars['Float']>;
- /** Unit-cell length b in Angstroms. */
- readonly length_b?: Maybe<Scalars['Float']>;
- /** Thickness of 2D crystal */
- readonly length_c?: Maybe<Scalars['Float']>;
- /**
- * There are 17 plane groups classified as oblique, rectangular, square, and hexagonal.
- * To describe the symmetry of 2D crystals of biological molecules,
- * plane groups are expanded to equivalent noncentrosymmetric space groups.
- * The 2D crystal plane corresponds to the 'ab' plane of the space group.
- *
- * Enumerated space group descriptions include the plane group number in parentheses,
- * the H-M plane group symbol, and the plane group class.
- *
- * Allowable values:
- * C 1 2, C 2 2 2, P 1, P 1 2, P 1 21, P 2, P 2 2 2, P 2 2 21, P 2 21 21, P 3, P 3 1 2, P 3 2 1, P 4, P 4 2 2, P 4 21 2, P 6, P 6 2 2
- */
- readonly space_group_name_H_M?: Maybe<Scalars['String']>;
-};
-
-export type RcsbNonpolymerEntityAnnotation = {
- /** An identifier for the annotation. */
- readonly annotation_id?: Maybe<Scalars['String']>;
- readonly annotation_lineage?: Maybe<ReadonlyArray<Maybe<RcsbNonpolymerEntityAnnotationAnnotationLineage>>>;
- /** Identifies the version of the annotation assignment. */
- readonly assignment_version?: Maybe<Scalars['String']>;
- /** Non-polymer(ligand) chemical component identifier for the entity. */
+export type PdbxEntityNonpoly = {
+ /** This data item is a pointer to _chem_comp.id in the CHEM_COMP category. */
readonly comp_id?: Maybe<Scalars['String']>;
- /** A description for the annotation. */
- readonly description?: Maybe<Scalars['String']>;
- /** A name for the annotation. */
+ /** This data item is a pointer to _entity.id in the ENTITY category. */
+ readonly entity_id: Scalars['String'];
+ /** A name for the non-polymer entity */
readonly name?: Maybe<Scalars['String']>;
- /**
- * Code identifying the individual, organization or program that
- * assigned the annotation.
- */
- readonly provenance_source?: Maybe<Scalars['String']>;
- /**
- * A type or category of the annotation.
- *
- * Allowable values:
- * SUBJECT_OF_INVESTIGATION
- */
- readonly type?: Maybe<Scalars['String']>;
+ /** For non-polymer BIRD molecules the BIRD identifier for the entity. */
+ readonly rcsb_prd_id?: Maybe<Scalars['String']>;
};
-export type RcsbNonpolymerInstanceFeature = {
- /** Identifies the version of the feature assignment. */
- readonly assignment_version?: Maybe<Scalars['String']>;
- /** Component identifier for non-polymer entity instance. */
- readonly comp_id?: Maybe<Scalars['String']>;
- /** A description for the feature. */
- readonly description?: Maybe<Scalars['String']>;
- /** An identifier for the feature. */
- readonly feature_id?: Maybe<Scalars['String']>;
- readonly feature_value?: Maybe<ReadonlyArray<Maybe<RcsbNonpolymerInstanceFeatureFeatureValue>>>;
- /** A name for the feature. */
- readonly name?: Maybe<Scalars['String']>;
- /** Ordinal identifier for this category */
- readonly ordinal: Scalars['Int'];
+export type PdbxEntitySrcSyn = {
/**
- * Code identifying the individual, organization or program that
- * assigned the feature.
+ * A description of special aspects of the source for the
+ * synthetic entity.
+ *
+ * Examples:
+ * This sequence occurs naturally in humans.
+ *
*/
- readonly provenance_source?: Maybe<Scalars['String']>;
+ readonly details?: Maybe<Scalars['String']>;
/**
- * A type or category of the feature.
- *
- * Allowable values:
- * HAS_COVALENT_LINKAGE, HAS_METAL_COORDINATION_LINKAGE, MOGUL_ANGLE_OUTLIER, MOGUL_BOND_OUTLIER, RSRCC_OUTLIER, RSRZ_OUTLIER
+ * NCBI Taxonomy identifier of the organism from which the sequence of
+ * the synthetic entity was derived.
+ *
+ * Reference:
+ *
+ * Wheeler DL, Chappey C, Lash AE, Leipe DD, Madden TL, Schuler GD,
+ * Tatusova TA, Rapp BA (2000). Database resources of the National
+ * Center for Biotechnology Information. Nucleic Acids Res 2000 Jan
+ * 1;28(1):10-4
+ *
+ * Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Rapp BA,
+ * Wheeler DL (2000). GenBank. Nucleic Acids Res 2000 Jan 1;28(1):15-18.
*/
- readonly type?: Maybe<Scalars['String']>;
-};
-
-export type RcsbNonpolymerStructConnConnectTarget = {
+ readonly ncbi_taxonomy_id?: Maybe<Scalars['String']>;
/**
- * A component of the identifier for the target of the structure
- * connection.
- *
- * This data item is a pointer to _atom_site.auth_asym_id in the
- * ATOM_SITE category.
+ * The common name of the organism from which the sequence of
+ * the synthetic entity was derived.
+ *
+ * Examples:
+ * house mouse
+ *
*/
- readonly auth_asym_id?: Maybe<Scalars['String']>;
+ readonly organism_common_name?: Maybe<Scalars['String']>;
/**
- * A component of the identifier for the target of the structure
- * connection.
- *
- * This data item is a pointer to _atom_site.auth_seq_id in the
- * ATOM_SITE category.
+ * The scientific name of the organism from which the sequence of
+ * the synthetic entity was derived.
+ *
+ * Examples:
+ * synthetic construct, Mus musculus
+ *
*/
- readonly auth_seq_id?: Maybe<Scalars['String']>;
+ readonly organism_scientific?: Maybe<Scalars['String']>;
/**
- * A component of the identifier for the target of the structure
- * connection.
- *
- * This data item is a pointer to _atom_site.label_alt_id in the
- * ATOM_SITE category.
+ * This data item identifies cases in which an alternative source
+ * modeled.
+ *
+ * Allowable values:
+ * model, sample
+ *
*/
- readonly label_alt_id?: Maybe<Scalars['String']>;
+ readonly pdbx_alt_source_flag?: Maybe<Scalars['String']>;
/**
- * A component of the identifier for the target of the structure
- * connection.
- *
- * This data item is a pointer to _atom_site.label_asym_id in the
- * ATOM_SITE category.
+ * The beginning polymer sequence position for the polymer section corresponding
+ * to this source.
+ *
+ * A reference to the sequence position in the entity_poly category.
*/
- readonly label_asym_id: Scalars['String'];
+ readonly pdbx_beg_seq_num?: Maybe<Scalars['Int']>;
/**
- * A component of the identifier for the target of the structure
- * connection.
- *
- * This data item is a pointer to _atom_site.label_atom_id in the
- * ATOM_SITE category.
+ * The ending polymer sequence position for the polymer section corresponding
+ * to this source.
+ *
+ * A reference to the sequence position in the entity_poly category.
*/
- readonly label_atom_id?: Maybe<Scalars['String']>;
+ readonly pdbx_end_seq_num?: Maybe<Scalars['Int']>;
+ /** This data item is an ordinal identifier for pdbx_entity_src_syn data records. */
+ readonly pdbx_src_id: Scalars['Int'];
+};
+
+export type PdbxFamilyPrdAudit = {
/**
- * A component of the identifier for the target of the structure
- * connection.
- *
- * This data item is a pointer to _atom_site.label_comp_id in the
- * ATOM_SITE category.
+ * The action associated with this audit record.
+ *
+ * Allowable values:
+ * Add PRD, Create family, Initial release, Modify annotation, Modify citation, Modify family classification, Modify family name, Modify feature, Modify molecule details, Modify related structures, Modify sequence, Modify synonyms, Obsolete family, Obsolete familyt, Other modification, Remove PRD
+ *
*/
- readonly label_comp_id: Scalars['String'];
+ readonly action_type: Scalars['String'];
/**
- * A component of the identifier for the target of the structure
- * connection.
- *
- * This data item is a pointer to _atom_site.connect_target_label_seq_id in the
- * ATOM_SITE category.
+ * The initials of the annotator creating of modifying the family.
+ *
+ * Examples:
+ * JO, SJ, KB
+ *
*/
- readonly label_seq_id?: Maybe<Scalars['Int']>;
+ readonly annotator?: Maybe<Scalars['String']>;
+ /** The date associated with this audit record. */
+ readonly date: Scalars['Date'];
/**
- * Describes the symmetry operation that should be applied to the
- * atom set specified by _rcsb_nonpolymer_struct_conn.label* to generate the
- * target of the structure connection.
- *
+ * Additional details decribing this change.
+ *
* Examples:
- * 1_555, 7_645
+ * Revise molecule sequence.
+ *
*/
- readonly symmetry?: Maybe<Scalars['String']>;
-};
-
-export type CoreBranchedEntity = {
- /** Get all unique branched instances (chains) for this molecular entity. */
- readonly branched_entity_instances?: Maybe<ReadonlyArray<Maybe<CoreBranchedEntityInstance>>>;
- /** Get all unique monomers described in this branched entity. */
- readonly chem_comp_monomers?: Maybe<ReadonlyArray<Maybe<CoreChemComp>>>;
- /** Get PDB entry that contains this branched entity. */
- readonly entry?: Maybe<CoreEntry>;
- readonly pdbx_entity_branch?: Maybe<PdbxEntityBranch>;
- readonly pdbx_entity_branch_descriptor?: Maybe<ReadonlyArray<Maybe<PdbxEntityBranchDescriptor>>>;
- /** Get a BIRD chemical components described in this branched entity. */
- readonly prd?: Maybe<CoreChemComp>;
- readonly rcsb_branched_entity?: Maybe<RcsbBranchedEntity>;
- readonly rcsb_branched_entity_annotation?: Maybe<ReadonlyArray<Maybe<RcsbBranchedEntityAnnotation>>>;
- readonly rcsb_branched_entity_container_identifiers?: Maybe<RcsbBranchedEntityContainerIdentifiers>;
- readonly rcsb_branched_entity_feature?: Maybe<ReadonlyArray<Maybe<RcsbBranchedEntityFeature>>>;
- readonly rcsb_branched_entity_feature_summary?: Maybe<ReadonlyArray<Maybe<RcsbBranchedEntityFeatureSummary>>>;
- readonly rcsb_branched_entity_keywords?: Maybe<RcsbBranchedEntityKeywords>;
- readonly rcsb_branched_entity_name_com?: Maybe<RcsbBranchedEntityNameCom>;
- readonly rcsb_branched_entity_name_sys?: Maybe<ReadonlyArray<Maybe<RcsbBranchedEntityNameSys>>>;
+ readonly details?: Maybe<Scalars['String']>;
/**
- * A unique identifier for each object in this entity container formed by
- * an underscore separated concatenation of entry and entity identifiers.
+ * This data item is a pointer to _pdbx_reference_molecule_family.family_prd_id in the
+ * pdbx_reference_molecule category.
*/
- readonly rcsb_id: Scalars['String'];
- readonly rcsb_latest_revision?: Maybe<RcsbLatestRevision>;
-};
-
-export type Em3dCrystalEntity = {
- /** Unit-cell angle alpha in degrees. */
- readonly angle_alpha?: Maybe<Scalars['Float']>;
- /** Unit-cell angle beta in degrees. */
- readonly angle_beta?: Maybe<Scalars['Float']>;
- /** Unit-cell angle gamma in degrees. */
- readonly angle_gamma?: Maybe<Scalars['Float']>;
- /** Unique key for the em_3d_crystal_entity category. */
- readonly id: Scalars['String'];
- /** pointer to _em_image_processing.id in the EM_IMAGE_PROCESSING category. */
- readonly image_processing_id: Scalars['String'];
- /** Unit-cell length a in Angstroms. */
- readonly length_a?: Maybe<Scalars['Float']>;
- /** Unit-cell length b in Angstroms. */
- readonly length_b?: Maybe<Scalars['Float']>;
- /** Unit-cell length c in Angstroms. */
- readonly length_c?: Maybe<Scalars['Float']>;
+ readonly family_prd_id: Scalars['String'];
/**
- * Space group name.
- *
+ * An identifier for the wwPDB site creating or modifying the family.
+ *
* Examples:
- * P 1, P 21 21 2, I 4, H 3
+ * RCSB, PDBE, PDBJ, BMRB, PDBC
+ *
*/
- readonly space_group_name?: Maybe<Scalars['String']>;
- /** Space group number. */
- readonly space_group_num?: Maybe<Scalars['Int']>;
-};
-
-export type RcsbBranchedEntityFeatureFeaturePositions = {
- /** An identifier for the leading monomer corresponding to the feature assignment. */
- readonly beg_comp_id?: Maybe<Scalars['String']>;
- /** An identifier for the leading monomer position of the feature. */
- readonly beg_seq_id: Scalars['Int'];
- /** An identifier for the leading monomer position of the feature. */
- readonly end_seq_id?: Maybe<Scalars['Int']>;
- /** The value for the feature at this monomer. */
- readonly value?: Maybe<Scalars['Float']>;
+ readonly processing_site?: Maybe<Scalars['String']>;
};
-export type GeneName = {
+export type PdbxMoleculeFeatures = {
/**
+ * Broadly defines the function of the molecule.
+ *
* Allowable values:
- * PRIMARY, SYNONYM, ORDERED_LOCUS, ORF
- */
- readonly type?: Maybe<Scalars['String']>;
- readonly value?: Maybe<Scalars['String']>;
-};
-
-export type Citation = {
- /**
- * The International Standard Book Number (ISBN) code assigned to
- * the book cited; relevant for books or book chapters.
- */
- readonly book_id_ISBN?: Maybe<Scalars['String']>;
- /**
- * The name of the publisher of the citation; relevant
- * for books or book chapters.
- *
- * Examples:
- * John Wiley and Sons
+ * Antagonist, Anthelmintic, Antibiotic, Antibiotic, Anthelmintic, Antibiotic, Antimicrobial, Antibiotic, Antineoplastic, Anticancer, Anticoagulant, Anticoagulant, Antithrombotic, Antifungal, Antigen, Antiinflammatory, Antimicrobial, Antimicrobial, Antiparasitic, Antibiotic, Antimicrobial, Antiretroviral, Antimicrobial, Antitumor, Antineoplastic, Antiparasitic, Antiretroviral, Antithrombotic, Antitumor, Antiviral, CASPASE inhibitor, Chaperone binding, Drug delivery, Enzyme inhibitor, Glycan component, Growth factor, Immunosuppressant, Inducer, Inhibitor, Lantibiotic, Metabolism, Metal transport, Nutrient, Oxidation-reduction, Protein binding, Receptor, Substrate analog, Synthetic opioid, Thrombin inhibitor, Thrombin inhibitor, Trypsin inhibitor, Toxin, Transition state mimetic, Transport activator, Trypsin inhibitor, Unknown, Water retention
+ *
*/
- readonly book_publisher?: Maybe<Scalars['String']>;
+ readonly class?: Maybe<Scalars['String']>;
+ /** Additional details describing the molecule. */
+ readonly details?: Maybe<Scalars['String']>;
/**
- * The location of the publisher of the citation; relevant
- * for books or book chapters.
- *
+ * A name of the molecule.
+ *
* Examples:
- * London
+ * thiostrepton
+ *
*/
- readonly book_publisher_city?: Maybe<Scalars['String']>;
+ readonly name?: Maybe<Scalars['String']>;
/**
- * The title of the book in which the citation appeared; relevant
- * for books or book chapters.
+ * The value of _pdbx_molecule_features.prd_id is the accession code for this
+ * reference molecule.
*/
- readonly book_title?: Maybe<Scalars['String']>;
+ readonly prd_id: Scalars['String'];
/**
- * _citation.coordinate_linkage states whether this citation
- * is concerned with precisely the set of coordinates given in the
- * data block. If, for instance, the publication described the same
- * structure, but the coordinates had undergone further refinement
- * prior to the creation of the data block, the value of this data
- * item would be 'no'.
- *
+ * Defines the structural classification of the molecule.
+ *
* Allowable values:
- * n, no, y, yes
+ * Amino acid, Aminoglycoside, Ansamycin, Anthracycline, Anthraquinone, Chalkophore, Chalkophore, Polypeptide, Chromophore, Cyclic depsipeptide, Cyclic lipopeptide, Cyclic peptide, Glycopeptide, Heterocyclic, Imino sugar, Keto acid, Lipoglycopeptide, Lipopeptide, Macrolide, Non-polymer, Nucleoside, Oligopeptide, Oligosaccharide, Peptaibol, Peptide-like, Polycyclic, Polypeptide, Polysaccharide, Quinolone, Siderophore, Thiolactone, Thiopeptide, Unknown
+ *
*/
- readonly coordinate_linkage?: Maybe<Scalars['String']>;
+ readonly type?: Maybe<Scalars['String']>;
+};
+
+export type PdbxNmrDetails = {
/**
- * The country/region of publication; relevant for books
- * and book chapters.
+ * Additional details describing the NMR experiment.
+ *
+ * Examples:
+ * This structure was determined using standard 2D homonuclear techniques., The structure was determined using triple-resonance NMR spectroscopy.
+ *
*/
- readonly country?: Maybe<Scalars['String']>;
+ readonly text?: Maybe<Scalars['String']>;
+};
+
+export type PdbxNmrEnsemble = {
/**
- * The value of _citation.id must uniquely identify a record in the
- * CITATION list.
- *
- * The _citation.id 'primary' should be used to indicate the
- * citation that the author(s) consider to be the most pertinent to
- * the contents of the data block.
- *
- * Note that this item need not be a number; it can be any unique
- * identifier.
- *
+ * The average number of constraint violations on a per residue basis for
+ * the ensemble.
+ *
* Examples:
- * primary, 1, 2
+ * null
+ *
*/
- readonly id: Scalars['String'];
+ readonly average_constraint_violations_per_residue?: Maybe<Scalars['Int']>;
/**
- * Abbreviated name of the cited journal as given in the
- * Chemical Abstracts Service Source Index.
- *
+ * The average number of constraints per residue for the ensemble
+ *
* Examples:
- * J.Mol.Biol., J. Mol. Biol.
+ * null
+ *
*/
- readonly journal_abbrev?: Maybe<Scalars['String']>;
+ readonly average_constraints_per_residue?: Maybe<Scalars['Int']>;
/**
- * The American Society for Testing and Materials (ASTM) code
- * assigned to the journal cited (also referred to as the CODEN
- * designator of the Chemical Abstracts Service); relevant for
- * journal articles.
+ * The average distance restraint violation for the ensemble.
+ *
+ * Examples:
+ * null
+ *
*/
- readonly journal_id_ASTM?: Maybe<Scalars['String']>;
+ readonly average_distance_constraint_violation?: Maybe<Scalars['Float']>;
/**
- * The Cambridge Structural Database (CSD) code assigned to the
- * journal cited; relevant for journal articles. This is also the
- * system used at the Protein Data Bank (PDB).
- *
+ * The average torsion angle constraint violation for the ensemble.
+ *
* Examples:
- * 0070
+ * null
+ *
*/
- readonly journal_id_CSD?: Maybe<Scalars['String']>;
+ readonly average_torsion_angle_constraint_violation?: Maybe<Scalars['Float']>;
/**
- * The International Standard Serial Number (ISSN) code assigned to
- * the journal cited; relevant for journal articles.
+ * By highlighting the appropriate choice(s), describe how the submitted
+ * conformer (models) were selected.
+ *
+ * Examples:
+ * structures with the lowest energy, structures with the least restraint violations, structures with acceptable covalent geometry, structures with favorable non-bond energy, target function, back calculated data agree with experimental NOESY spectrum, all calculated structures submitted, The submitted conformer models are the 25 structures with the lowest
+ * energy., The submitted conformer models are those with the fewest number of
+ * constraint violations.
+ *
*/
- readonly journal_id_ISSN?: Maybe<Scalars['String']>;
+ readonly conformer_selection_criteria?: Maybe<Scalars['String']>;
+ /** The total number of conformer (models) that were calculated in the final round. */
+ readonly conformers_calculated_total_number?: Maybe<Scalars['Int']>;
+ /** The number of conformer (models) that are submitted for the ensemble. */
+ readonly conformers_submitted_total_number?: Maybe<Scalars['Int']>;
/**
- * Issue number of the journal cited; relevant for journal
- * articles.
- *
+ * Describe the method used to calculate the distance constraint violation statistics,
+ * i.e. are they calculated over all the distance constraints or calculated for
+ * violations only?
+ *
* Examples:
- * 2
+ * Statistics were calculated over all of the distance constraints., Statistics were calculated for violations only
+ *
*/
- readonly journal_issue?: Maybe<Scalars['String']>;
+ readonly distance_constraint_violation_method?: Maybe<Scalars['String']>;
/**
- * Volume number of the journal cited; relevant for journal
- * articles.
- *
+ * The maximum distance constraint violation for the ensemble.
+ *
* Examples:
- * 174
+ * null
+ *
*/
- readonly journal_volume?: Maybe<Scalars['String']>;
+ readonly maximum_distance_constraint_violation?: Maybe<Scalars['Float']>;
/**
- * Language in which the cited article is written.
- *
+ * The maximum lower distance constraint violation for the ensemble.
+ *
* Examples:
- * German
+ * null
+ *
*/
- readonly language?: Maybe<Scalars['String']>;
+ readonly maximum_lower_distance_constraint_violation?: Maybe<Scalars['Float']>;
+ /** The maximum torsion angle constraint violation for the ensemble. */
+ readonly maximum_torsion_angle_constraint_violation?: Maybe<Scalars['Float']>;
/**
- * The first page of the citation; relevant for journal
- * articles, books and book chapters.
+ * The maximum upper distance constraint violation for the ensemble.
+ *
+ * Examples:
+ * null
+ *
*/
- readonly page_first?: Maybe<Scalars['String']>;
+ readonly maximum_upper_distance_constraint_violation?: Maybe<Scalars['Float']>;
+ /** The number of the conformer identified as most representative. */
+ readonly representative_conformer?: Maybe<Scalars['Int']>;
/**
- * The last page of the citation; relevant for journal
- * articles, books and book chapters.
+ * This item describes the method used to calculate the torsion angle constraint violation statistics.
+ * i.e. are the entered values based on all torsion angle or calculated for violations only?
+ *
+ * Examples:
+ * Statistics were calculated over all the torsion angle constraints., Statistics were calculated for torsion angle constraints violations only.
+ *
*/
- readonly page_last?: Maybe<Scalars['String']>;
+ readonly torsion_angle_constraint_violation_method?: Maybe<Scalars['String']>;
+};
+
+export type PdbxNmrExptl = {
/**
- * Document Object Identifier used by doi.org to uniquely
- * specify bibliographic entry.
- *
+ * The number to identify the set of sample conditions.
+ *
* Examples:
- * 10.2345/S1384107697000225
+ * 1, 2, 3
+ *
*/
- readonly pdbx_database_id_DOI?: Maybe<Scalars['String']>;
+ readonly conditions_id: Scalars['String'];
/**
- * Ascession number used by PubMed to categorize a specific
- * bibliographic entry.
- *
+ * A numerical ID for each experiment.
+ *
* Examples:
- * 12627512
- */
- readonly pdbx_database_id_PubMed?: Maybe<Scalars['Int']>;
- /**
- * Names of the authors of the citation; relevant for journal
- * articles, books and book chapters. Names are separated by vertical bars.
- *
- * The family name(s), followed by a comma and including any
- * dynastic components, precedes the first name(s) or initial(s).
+ * 1, 2, 3
+ *
*/
- readonly rcsb_authors?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
+ readonly experiment_id: Scalars['String'];
/**
- * Flag to indicate a primary citation.
- *
+ * Physical state of the sample either anisotropic or isotropic.
+ *
* Allowable values:
- * N, Y
- */
- readonly rcsb_is_primary?: Maybe<Scalars['String']>;
- /**
- * Normalized journal abbreviation.
- *
- * Examples:
- * Nat Struct Mol Biol
+ * anisotropic, isotropic
+ *
*/
- readonly rcsb_journal_abbrev?: Maybe<Scalars['String']>;
+ readonly sample_state?: Maybe<Scalars['String']>;
/**
- * The title of the citation; relevant for journal articles, books
- * and book chapters.
- *
+ * The solution_id from the Experimental Sample to identify the sample
+ * that these conditions refer to.
+ *
+ * [Remember to save the entries here before returning to the
+ * Experimental Sample form]
+ *
* Examples:
- * Structure of diferric duck ovotransferrin
- * at 2.35 Angstroms resolution.
- */
- readonly title?: Maybe<Scalars['String']>;
- /**
- * Flag to indicate that this citation will not be published.
- *
- * Allowable values:
- * N, Y
+ * 1, 2, 3
+ *
*/
- readonly unpublished_flag?: Maybe<Scalars['String']>;
+ readonly solution_id: Scalars['String'];
+ /** Pointer to '_pdbx_nmr_spectrometer.spectrometer_id' */
+ readonly spectrometer_id?: Maybe<Scalars['Int']>;
/**
- * The year of the citation; relevant for journal articles, books
- * and book chapters.
- *
+ * The type of NMR experiment.
+ *
* Examples:
- * 1984
+ * 2D NOESY, 3D_15N-separated_NOESY, 3D_13C-separated_NOESY, 4D_13C-separated_NOESY, 4D_13C/15N-separated_NOESY, 3D_15N-separated_ROESY, 3D_13C-separated_ROESY, HNCA-J, HNHA, DQF-COSY, P-COSY, PE-COSY, E-COSY
+ *
*/
- readonly year?: Maybe<Scalars['Int']>;
-};
-
-export type RcsbEntitySourceOrganismTaxonomyLineage = {
- /** Members of the NCBI Taxonomy lineage as parent taxonomy lineage depth (1-N) */
- readonly depth?: Maybe<Scalars['Int']>;
- /** Members of the NCBI Taxonomy lineage as parent taxonomy idcodes. */
- readonly id?: Maybe<Scalars['String']>;
- /** Memebers of the NCBI Taxonomy lineage as parent taxonomy names. */
- readonly name?: Maybe<Scalars['String']>;
+ readonly type?: Maybe<Scalars['String']>;
};
-export type RcsbPrimaryCitation = {
+export type PdbxNmrExptlSampleConditions = {
/**
- * The International Standard Book Number (ISBN) code assigned to
- * the book cited; relevant for books or book chapters.
+ * The condition number as defined above.
+ *
+ * Examples:
+ * 1, 2, 3
+ *
*/
- readonly book_id_ISBN?: Maybe<Scalars['String']>;
+ readonly conditions_id: Scalars['String'];
/**
- * The name of the publisher of the citation; relevant
- * for books or book chapters.
- *
+ * General details describing conditions of both the sample and the environment
+ * during measurements.
+ *
* Examples:
- * John Wiley and Sons
+ * The high salinity of the sample may have contributed to overheating of the sample during experiments with long saturation periods like the TOCSY experiments.
+ *
*/
- readonly book_publisher?: Maybe<Scalars['String']>;
+ readonly details?: Maybe<Scalars['String']>;
/**
- * The location of the publisher of the citation; relevant
- * for books or book chapters.
- *
- * Examples:
- * London
+ * The ionic strength at which the NMR data were collected -in lieu of
+ * this enter the concentration and identity of the salt in the sample.
*/
- readonly book_publisher_city?: Maybe<Scalars['String']>;
+ readonly ionic_strength?: Maybe<Scalars['String']>;
/**
- * The title of the book in which the citation appeared; relevant
- * for books or book chapters.
+ * Estimate of the standard error for the value for the sample ionic strength.
+ *
+ * Examples:
+ * null
+ *
*/
- readonly book_title?: Maybe<Scalars['String']>;
+ readonly ionic_strength_err?: Maybe<Scalars['Float']>;
/**
- * _rcsb_primary_citation.coordinate_linkage states whether this citation
- * is concerned with precisely the set of coordinates given in the
- * data block. If, for instance, the publication described the same
- * structure, but the coordinates had undergone further refinement
- * prior to the creation of the data block, the value of this data
- * item would be 'no'.
- *
+ * Units for the value of the sample condition ionic strength..
+ *
* Allowable values:
- * n, no, y, yes
+ * M, Not defined, mM
+ *
*/
- readonly coordinate_linkage?: Maybe<Scalars['String']>;
+ readonly ionic_strength_units?: Maybe<Scalars['String']>;
/**
- * The country/region of publication; relevant for books
- * and book chapters.
+ * A descriptive label that uniquely identifies this set of sample conditions.
+ *
+ * Examples:
+ * conditions_1
+ *
*/
- readonly country?: Maybe<Scalars['String']>;
+ readonly label?: Maybe<Scalars['String']>;
/**
- * The value of _rcsb_primary_citation.id must uniquely identify a record in the
- * CITATION list.
- *
- * The _rcsb_primary_citation.id 'primary' should be used to indicate the
- * citation that the author(s) consider to be the most pertinent to
- * the contents of the data block.
- *
- * Note that this item need not be a number; it can be any unique
- * identifier.
- *
+ * The pH at which the NMR data were collected.
+ *
* Examples:
- * primary
+ * null, null
+ *
*/
- readonly id: Scalars['String'];
+ readonly pH?: Maybe<Scalars['String']>;
/**
- * Abbreviated name of the cited journal as given in the
- * Chemical Abstracts Service Source Index.
- *
+ * Estimate of the standard error for the value for the sample pH.
+ *
* Examples:
- * J.Mol.Biol., J. Mol. Biol.
+ * null
+ *
*/
- readonly journal_abbrev?: Maybe<Scalars['String']>;
+ readonly pH_err?: Maybe<Scalars['Float']>;
/**
- * The American Society for Testing and Materials (ASTM) code
- * assigned to the journal cited (also referred to as the CODEN
- * designator of the Chemical Abstracts Service); relevant for
- * journal articles.
+ * Units for the value of the sample condition pH.
+ *
+ * Allowable values:
+ * Not defined, pD, pH, pH*
+ *
*/
- readonly journal_id_ASTM?: Maybe<Scalars['String']>;
+ readonly pH_units?: Maybe<Scalars['String']>;
/**
- * The Cambridge Structural Database (CSD) code assigned to the
- * journal cited; relevant for journal articles. This is also the
- * system used at the Protein Data Bank (PDB).
- *
+ * The pressure at which NMR data were collected.
+ *
* Examples:
- * 0070
+ * 1, ambient, 1atm
+ *
*/
- readonly journal_id_CSD?: Maybe<Scalars['String']>;
+ readonly pressure?: Maybe<Scalars['String']>;
/**
- * The International Standard Serial Number (ISSN) code assigned to
- * the journal cited; relevant for journal articles.
+ * Estimate of the standard error for the value for the sample pressure.
+ *
+ * Examples:
+ * null
+ *
*/
- readonly journal_id_ISSN?: Maybe<Scalars['String']>;
+ readonly pressure_err?: Maybe<Scalars['Float']>;
/**
- * Issue number of the journal cited; relevant for journal
- * articles.
- *
+ * The units of pressure at which NMR data were collected.
+ *
* Examples:
- * 2
+ * Pa, atm, Torr
+ *
*/
- readonly journal_issue?: Maybe<Scalars['String']>;
+ readonly pressure_units?: Maybe<Scalars['String']>;
/**
- * Volume number of the journal cited; relevant for journal
- * articles.
- *
- * Examples:
- * 174
+ * The temperature (in Kelvin) at which NMR data were
+ * collected.
*/
- readonly journal_volume?: Maybe<Scalars['String']>;
+ readonly temperature?: Maybe<Scalars['String']>;
/**
- * Language in which the cited article is written.
- *
+ * Estimate of the standard error for the value for the sample temperature.
+ *
* Examples:
- * German
+ * null
+ *
*/
- readonly language?: Maybe<Scalars['String']>;
+ readonly temperature_err?: Maybe<Scalars['Float']>;
/**
- * The first page of the citation; relevant for journal
- * articles, books and book chapters.
+ * Units for the value of the sample condition temperature.
+ *
+ * Allowable values:
+ * C, K, Not defined
+ *
*/
- readonly page_first?: Maybe<Scalars['String']>;
+ readonly temperature_units?: Maybe<Scalars['String']>;
+};
+
+export type PdbxNmrRefine = {
/**
- * The last page of the citation; relevant for journal
- * articles, books and book chapters.
+ * Additional details about the NMR refinement.
+ *
+ * Examples:
+ * Additional comments about the NMR refinement can be placed here, e.g.
+ * the structures are based on a total of 3344 restraints, 3167 are NOE-derived
+ * distance constraints, 68 dihedral angle restraints,109 distance restraints
+ * from hydrogen bonds.
+ *
*/
- readonly page_last?: Maybe<Scalars['String']>;
+ readonly details?: Maybe<Scalars['String']>;
/**
- * Document Object Identifier used by doi.org to uniquely
- * specify bibliographic entry.
- *
+ * The method used to determine the structure.
+ *
* Examples:
- * 10.2345/S1384107697000225
+ * simulated annealing, distance geometry
+ * simulated annealing
+ * molecular dynamics
+ * matrix relaxation
+ * torsion angle dynamics
+ *
*/
- readonly pdbx_database_id_DOI?: Maybe<Scalars['String']>;
+ readonly method?: Maybe<Scalars['String']>;
+ /** Pointer to _software.ordinal */
+ readonly software_ordinal: Scalars['Int'];
+};
+
+export type PdbxNmrRepresentative = {
/**
- * Ascession number used by PubMed to categorize a specific
- * bibliographic entry.
- *
+ * If a member of the ensemble has been selected as a representative
+ * structure, identify it by its model number.
+ *
* Examples:
- * 12627512
+ * 15
+ *
*/
- readonly pdbx_database_id_PubMed?: Maybe<Scalars['Int']>;
+ readonly conformer_id?: Maybe<Scalars['String']>;
/**
- * Names of the authors of the citation; relevant for journal
- * articles, books and book chapters. Names are separated by vertical bars.
- *
- * The family name(s), followed by a comma and including any
- * dynastic components, precedes the first name(s) or initial(s).
+ * By highlighting the appropriate choice(s), describe the criteria used to
+ * select this structure as a representative structure, or if an average
+ * structure has been calculated describe how this was done.
+ *
+ * Examples:
+ * The structure closest to the average.
+ * The structure with the lowest energy was selected.
+ * The structure with the fewest number of violations was selected.
+ * A minimized average structure was calculated.
+ *
*/
- readonly rcsb_authors?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
+ readonly selection_criteria?: Maybe<Scalars['String']>;
+};
+
+export type PdbxNmrSampleDetails = {
/**
- * Normalized journal abbreviation.
- *
+ * A complete description of each NMR sample. Include the concentration
+ * and concentration units for each component (include buffers, etc.). For each
+ * component describe the isotopic composition, including the % labeling level,
+ * if known.
+ *
+ * For example:
+ * 1. Uniform (random) labeling with 15N: U-15N
+ * 2. Uniform (random) labeling with 13C, 15N at known labeling
+ * levels: U-95% 13C;U-98% 15N
+ * 3. Residue selective labeling: U-95% 15N-Thymine
+ * 4. Site specific labeling: 95% 13C-Ala18,
+ * 5. Natural abundance labeling in an otherwise uniformly labeled
+ * biomolecule is designated by NA: U-13C; NA-K,H
+ *
* Examples:
- * Nat Struct Mol Biol
+ * 2mM Ribonuclease U-15N,13C; 50mM phosphate buffer NA; 90% H2O, 10% D2O
+ *
*/
- readonly rcsb_journal_abbrev?: Maybe<Scalars['String']>;
+ readonly contents?: Maybe<Scalars['String']>;
/**
- * The title of the citation; relevant for journal articles, books
- * and book chapters.
- *
+ * Brief description of the sample providing additional information not captured by other items in the category.
+ *
* Examples:
- * Structure of diferric duck ovotransferrin
- * at 2.35 Angstroms resolution.
+ * The added glycerol was used to raise the viscosity of the solution to 1.05 poisson.
+ *
*/
- readonly title?: Maybe<Scalars['String']>;
+ readonly details?: Maybe<Scalars['String']>;
/**
- * The year of the citation; relevant for journal articles, books
- * and book chapters.
- *
+ * A value that uniquely identifies this sample from the other samples listed
+ * in the entry.
+ *
* Examples:
- * 1984
+ * 15N_sample
+ *
*/
- readonly year?: Maybe<Scalars['Int']>;
-};
-
-export type PdbxStructOperList = {
+ readonly label?: Maybe<Scalars['String']>;
/**
- * This identifier code must uniquely identify a
- * record in the PDBX_STRUCT_OPER_LIST list.
+ * The name (number) of the sample.
+ *
+ * Examples:
+ * 1, 2, 3
+ *
*/
- readonly id: Scalars['String'];
- /**
- * The [1][1] element of the 3x3 matrix component of the
- * transformation operation.
- */
- readonly matrix_1_1?: Maybe<Scalars['Float']>;
+ readonly solution_id: Scalars['String'];
/**
- * The [1][2] element of the 3x3 matrix component of the
- * transformation operation.
+ * The solvent system used for this sample.
+ *
+ * Examples:
+ * 90% H2O, 10% D2O
+ *
*/
- readonly matrix_1_2?: Maybe<Scalars['Float']>;
+ readonly solvent_system?: Maybe<Scalars['String']>;
/**
- * The [1][3] element of the 3x3 matrix component of the
- * transformation operation.
+ * A descriptive term for the sample that defines the general physical properties
+ * of the sample.
+ *
+ * Allowable values:
+ * bicelle, emulsion, fiber, fibrous protein, filamentous virus, gel solid, gel solution, liposome, lyophilized powder, membrane, micelle, oriented membrane film, polycrystalline powder, reverse micelle, single crystal, solid, solution
+ *
*/
- readonly matrix_1_3?: Maybe<Scalars['Float']>;
+ readonly type?: Maybe<Scalars['String']>;
+};
+
+export type PdbxNmrSoftware = {
/**
- * The [2][1] element of the 3x3 matrix component of the
- * transformation operation.
+ * The name of the authors of the software used in this
+ * procedure.
+ *
+ * Examples:
+ * Brunger, Guentert
+ *
*/
- readonly matrix_2_1?: Maybe<Scalars['Float']>;
+ readonly authors?: Maybe<Scalars['String']>;
/**
- * The [2][2] element of the 3x3 matrix component of the
- * transformation operation.
+ * The purpose of the software.
+ *
+ * Examples:
+ * collection, processing, data analysis, structure solution, refinement, iterative matrix relaxation
+ *
*/
- readonly matrix_2_2?: Maybe<Scalars['Float']>;
+ readonly classification?: Maybe<Scalars['String']>;
/**
- * The [2][3] element of the 3x3 matrix component of the
- * transformation operation.
+ * The name of the software used for the task.
+ *
+ * Examples:
+ * ANSIG, AURELIA, AZARA, CHARMM, CoMAND, CORMA, DIANA, DYANA, DSPACE, DISGEO, DGII, DISMAN, DINOSAUR, DISCOVER, FELIX, FT_NMR, GROMOS, IRMA, MARDIGRAS, NMRPipe, SA, UXNMR, VNMR, X-PLOR, XWINNMR
+ *
*/
- readonly matrix_2_3?: Maybe<Scalars['Float']>;
+ readonly name?: Maybe<Scalars['String']>;
+ /** An ordinal index for this category */
+ readonly ordinal: Scalars['Int'];
/**
- * The [3][1] element of the 3x3 matrix component of the
- * transformation operation.
+ * The version of the software.
+ *
+ * Examples:
+ * 940501.3, 2.1
+ *
*/
- readonly matrix_3_1?: Maybe<Scalars['Float']>;
+ readonly version?: Maybe<Scalars['String']>;
+};
+
+export type PdbxNmrSpectrometer = {
+ /** A text description of the NMR spectrometer. */
+ readonly details?: Maybe<Scalars['String']>;
+ /** The field strength in MHz of the spectrometer */
+ readonly field_strength?: Maybe<Scalars['Float']>;
/**
- * The [3][2] element of the 3x3 matrix component of the
- * transformation operation.
+ * The name of the manufacturer of the spectrometer.
+ *
+ * Examples:
+ * Varian, Bruker, JEOL, GE
+ *
*/
- readonly matrix_3_2?: Maybe<Scalars['Float']>;
+ readonly manufacturer?: Maybe<Scalars['String']>;
/**
- * The [3][3] element of the 3x3 matrix component of the
- * transformation operation.
+ * The model of the NMR spectrometer.
+ *
+ * Examples:
+ * AVANCE, AVANCE II, AVANCE III, AVANCE III HD, WH, WM, AM, AMX, DMX, DRX, MSL, OMEGA, OMEGA PSG, GX, GSX, A, AL, EC, EX, LA, ECP, VXRS, UNITY, UNITYPLUS, INOVA
+ *
*/
- readonly matrix_3_3?: Maybe<Scalars['Float']>;
+ readonly model?: Maybe<Scalars['String']>;
/**
- * A descriptive name for the transformation operation.
- *
+ * Assign a numerical ID to each instrument.
+ *
* Examples:
- * 1_555, two-fold rotation
+ * 1, 2, 3
+ *
*/
- readonly name?: Maybe<Scalars['String']>;
+ readonly spectrometer_id: Scalars['String'];
/**
- * The symmetry operation corresponding to the transformation operation.
- *
+ * Select the instrument manufacturer(s) and the model(s) of the NMR(s)
+ * used for this work.
+ *
* Examples:
- * x,y,z, x+1/2,y,-z
+ * Bruker WH, Bruker WM, Bruker AM, Bruker AMX, Bruker DMX, Bruker DRX, Bruker MSL, Bruker AVANCE, GE Omega, GE Omega PSG, JEOL GX, JEOL GSX, JEOL A, JEOL AL, JEOL EC, JEOL EX, JEOL LA, JEOL ECP, Varian VXRS, Varian UNITY, Varian UNITYplus, Varian INOVA, other
+ *
*/
- readonly symmetry_operation?: Maybe<Scalars['String']>;
+ readonly type?: Maybe<Scalars['String']>;
+};
+
+export type PdbxPrdAudit = {
/**
- * A code to indicate the type of operator.
- *
+ * The action associated with this audit record.
+ *
* Allowable values:
- * 2D crystal symmetry operation, 3D crystal symmetry operation, build 2D crystal asymmetric unit, build 3D crystal asymmetric unit, build helical asymmetric unit, build point asymmetric unit, crystal symmetry operation, helical symmetry operation, identity operation, point symmetry operation, transform to 2D crystal frame, transform to 3D crystal frame, transform to crystal frame, transform to helical frame, transform to point frame
+ * Create molecule, Initial release, Modify audit, Modify class, Modify linkage, Modify molecule name, Modify representation, Modify sequence, Modify taxonomy organism, Modify type, Obsolete molecule, Other modification
+ *
*/
- readonly type?: Maybe<Scalars['String']>;
+ readonly action_type: Scalars['String'];
/**
- * The [1] element of the three-element vector component of the
- * transformation operation.
+ * The initials of the annotator creating of modifying the molecule.
+ *
+ * Examples:
+ * JO, SJ, KB
+ *
*/
- readonly vector_1?: Maybe<Scalars['Float']>;
+ readonly annotator?: Maybe<Scalars['String']>;
+ /** The date associated with this audit record. */
+ readonly date: Scalars['Date'];
/**
- * The [2] element of the three-element vector component of the
- * transformation operation.
+ * Additional details decribing this change.
+ *
+ * Examples:
+ * Revise molecule sequence.
+ *
*/
- readonly vector_2?: Maybe<Scalars['Float']>;
+ readonly details?: Maybe<Scalars['String']>;
/**
- * The [3] element of the three-element vector component of the
- * transformation operation.
+ * This data item is a pointer to _pdbx_reference_molecule.prd_id in the
+ * pdbx_reference_molecule category.
*/
- readonly vector_3?: Maybe<Scalars['Float']>;
+ readonly prd_id: Scalars['String'];
+ /**
+ * An identifier for the wwPDB site creating or modifying the molecule.
+ *
+ * Allowable values:
+ * BMRB, PDBC, PDBJ, PDBe, RCSB
+ *
+ */
+ readonly processing_site?: Maybe<Scalars['String']>;
};
-export type StructKeywords = {
+export type PdbxReferenceEntityList = {
+ /** The component number of this entity within the molecule. */
+ readonly component_id: Scalars['Int'];
+ /** Additional details about this entity. */
+ readonly details?: Maybe<Scalars['String']>;
/**
- * Terms characterizing the macromolecular structure.
- *
- * Examples:
- * DNA, RNA, T-RNA, DNA/RNA, RIBOZYME, PROTEIN/DNA, PROTEIN/RNA, PEPTIDE NUCLEIC ACID, PEPTIDE NUCLEIC ACID/DNA, DNA-BINDING PROTEIN, RNA-BINDING PROTEIN
+ * The value of _pdbx_reference_entity_list.prd_id is a reference
+ * _pdbx_reference_molecule.prd_id in the PDBX_REFERENCE_MOLECULE category.
*/
- readonly pdbx_keywords?: Maybe<Scalars['String']>;
+ readonly prd_id: Scalars['String'];
/**
- * Keywords describing this structure.
- *
- * Examples:
- * Inhibitor, Complex, Isomerase..., serine protease, inhibited complex, high-resolution refinement
+ * The value of _pdbx_reference_entity_list.ref_entity_id is a unique identifier
+ * the a constituent entity within this reference molecule.
*/
- readonly text?: Maybe<Scalars['String']>;
-};
-
-export type RcsbUniprotProteinFunction = {
- /** General function(s) of a protein. */
- readonly details?: Maybe<Scalars['String']>;
- /** Historical record of the data attribute. */
- readonly provenance_code?: Maybe<Scalars['String']>;
+ readonly ref_entity_id: Scalars['String'];
+ /**
+ * Defines the polymer characteristic of the entity.
+ *
+ * Allowable values:
+ * branched, non-polymer, polymer, polymer-like
+ *
+ */
+ readonly type?: Maybe<Scalars['String']>;
};
-export type RcsbPubmedContainerIdentifiers = {
- /** Unique integer value assigned to each PubMed record. */
- readonly pubmed_id?: Maybe<Scalars['Int']>;
+export type PdbxReferenceEntityPoly = {
+ /** The database code for this source information */
+ readonly db_code?: Maybe<Scalars['String']>;
+ /** The database name for this source information */
+ readonly db_name?: Maybe<Scalars['String']>;
+ /**
+ * The value of _pdbx_reference_entity_poly.prd_id is a reference
+ * _pdbx_reference_entity_list.prd_id in the PDBX_REFERENCE_ENTITY_LIST category.
+ */
+ readonly prd_id: Scalars['String'];
+ /**
+ * The value of _pdbx_reference_entity_poly.ref_entity_id is a reference
+ * to _pdbx_reference_entity_list.ref_entity_id in PDBX_REFERENCE_ENTITY_LIST category.
+ */
+ readonly ref_entity_id: Scalars['String'];
+ /**
+ * The type of the polymer.
+ *
+ * Allowable values:
+ * nucleic-acid-like, oligosaccharide, peptide-like, polysaccharide-like
+ *
+ */
+ readonly type?: Maybe<Scalars['String']>;
};
-export type RcsbPolymerInstanceAnnotation = {
- /** An identifier for the annotation. */
- readonly annotation_id?: Maybe<Scalars['String']>;
- readonly annotation_lineage?: Maybe<ReadonlyArray<Maybe<RcsbPolymerInstanceAnnotationAnnotationLineage>>>;
- /** Identifies the version of the annotation assignment. */
- readonly assignment_version?: Maybe<Scalars['String']>;
- /** A description for the annotation. */
- readonly description?: Maybe<Scalars['String']>;
- /** A name for the annotation. */
- readonly name?: Maybe<Scalars['String']>;
- /** Ordinal identifier for this category */
- readonly ordinal: Scalars['Int'];
+export type PdbxReferenceEntityPolyLink = {
/**
- * Code identifying the individual, organization or program that
- * assigned the annotation.
+ * The atom identifier/name in the first of the two components making
+ * the linkage.
*/
- readonly provenance_source?: Maybe<Scalars['String']>;
+ readonly atom_id_1?: Maybe<Scalars['String']>;
/**
- * A type or category of the annotation.
- *
+ * The atom identifier/name in the second of the two components making
+ * the linkage.
+ */
+ readonly atom_id_2?: Maybe<Scalars['String']>;
+ /**
+ * The component identifier in the first of the two components making the
+ * linkage.
+ *
+ * This data item is a pointer to _pdbx_reference_entity_poly_seq.mon_id
+ * in the PDBX_REFERENCE_ENTITY_POLY_SEQ category.
+ */
+ readonly comp_id_1?: Maybe<Scalars['String']>;
+ /**
+ * The component identifier in the second of the two components making the
+ * linkage.
+ *
+ * This data item is a pointer to _pdbx_reference_entity_poly_seq.mon_id
+ * in the PDBX_REFERENCE_ENTITY_POLY_SEQ category.
+ */
+ readonly comp_id_2?: Maybe<Scalars['String']>;
+ /** The entity component identifier entity containing the linkage. */
+ readonly component_id: Scalars['Int'];
+ /**
+ * For a polymer entity, the sequence number in the first of
+ * the two components making the linkage.
+ *
+ * This data item is a pointer to _pdbx_reference_entity_poly_seq.num
+ * in the PDBX_REFERENCE_ENTITY_POLY_SEQ category.
+ */
+ readonly entity_seq_num_1?: Maybe<Scalars['Int']>;
+ /**
+ * For a polymer entity, the sequence number in the second of
+ * the two components making the linkage.
+ *
+ * This data item is a pointer to _pdbx_reference_entity_poly_seq.num
+ * in the PDBX_REFERENCE_ENTITY_POLY_SEQ category.
+ */
+ readonly entity_seq_num_2?: Maybe<Scalars['Int']>;
+ /**
+ * The value of _pdbx_reference_entity_poly_link.link_id uniquely identifies
+ * a linkage within a polymer entity.
+ */
+ readonly link_id: Scalars['Int'];
+ /**
+ * The value of _pdbx_reference_entity_poly_link.prd_id is a reference
+ * _pdbx_reference_entity_list.prd_id in the PDBX_REFERENCE_ENTITY_POLY category.
+ */
+ readonly prd_id: Scalars['String'];
+ /**
+ * The reference entity id of the polymer entity containing the linkage.
+ *
+ * This data item is a pointer to _pdbx_reference_entity_poly.ref_entity_id
+ * in the PDBX_REFERENCE_ENTITY_POLY category.
+ */
+ readonly ref_entity_id: Scalars['String'];
+ /**
+ * The bond order target for the non-standard linkage.
+ *
* Allowable values:
- * CATH, SCOP
+ * arom, delo, doub, pi, poly, quad, sing, trip
+ *
*/
- readonly type?: Maybe<Scalars['String']>;
+ readonly value_order?: Maybe<Scalars['String']>;
};
export type PdbxReferenceEntityPolySeq = {
/**
* A flag to indicate that sequence heterogeneity at this monomer position.
- *
+ *
* Allowable values:
* N, Y
+ *
*/
readonly hetero: Scalars['String'];
/** This data item is the chemical component identifier of monomer. */
@@ -4356,16 +4506,17 @@ export type PdbxReferenceEntityPolySeq = {
/**
* The value of _pdbx_reference_entity_poly_seq.num must uniquely and sequentially
* identify a record in the PDBX_REFERENCE_ENTITY_POLY_SEQ list.
- *
+ *
* This value is conforms to author numbering conventions and does not map directly
* to the numbering conventions used for _entity_poly_seq.num.
*/
readonly num: Scalars['Int'];
/**
* A flag to indicate that this monomer is observed in the instance example.
- *
+ *
* Allowable values:
* N, Y
+ *
*/
readonly observed?: Maybe<Scalars['String']>;
/** This data item is the chemical component identifier for the parent component corresponding to this monomer. */
@@ -4382,2150 +4533,2750 @@ export type PdbxReferenceEntityPolySeq = {
readonly ref_entity_id: Scalars['String'];
};
-export type RcsbEntityHostOrganismTaxonomyLineage = {
- /** Members of the NCBI Taxonomy lineage as parent taxonomy lineage depth (1-N) */
- readonly depth?: Maybe<Scalars['Int']>;
- /** Members of the NCBI Taxonomy lineage as parent taxonomy idcodes. */
- readonly id?: Maybe<Scalars['String']>;
- /** Members of the NCBI Taxonomy lineage as parent taxonomy names. */
- readonly name?: Maybe<Scalars['String']>;
-};
-
-export type CoreEntityAlignmentsAlignedRegions = {
- /** Aligned region length */
- readonly length: Scalars['Int'];
- /** Entity seqeunce start position */
- readonly query_begin: Scalars['Int'];
- /** NCBI sequence start position */
- readonly target_begin: Scalars['Int'];
-};
-
-export type RcsbUniprotKeyword = {
- /**
- * A unique keyword identifier.
- *
- * Examples:
- * KW-0275, KW-0597
- */
- readonly id?: Maybe<Scalars['String']>;
+export type PdbxReferenceEntitySequence = {
/**
- * Human-readable keyword term.
- *
- * Examples:
- * Lipid metabolism, Phosphoprotein, Fatty acid biosynthesis
+ * A flag to indicate a non-ribosomal entity.
+ *
+ * Allowable values:
+ * N, Y
+ *
*/
- readonly value?: Maybe<Scalars['String']>;
-};
-
-export type RcsbBranchedEntityNameCom = {
+ readonly NRP_flag?: Maybe<Scalars['String']>;
+ /** The one-letter-code sequence for this entity. Non-standard monomers are represented as 'X'. */
+ readonly one_letter_codes?: Maybe<Scalars['String']>;
/**
- * A common name for the branched entity.
- *
- * Examples:
- * HIV protease monomer, hemoglobin alpha chain
+ * The value of _pdbx_reference_entity_sequence.prd_id is a reference
+ * _pdbx_reference_entity_list.prd_id in the PDBX_REFERENCE_ENTITY_LIST category.
*/
- readonly name?: Maybe<Scalars['String']>;
-};
-
-export type RcsbGenomicLineage = {
- /** Classification hierarchy depth. */
- readonly depth?: Maybe<Scalars['Int']>;
+ readonly prd_id: Scalars['String'];
/**
- * ID that identify taxonomy, chromosome or gene.
- *
- * Examples:
- * 9606, 568815441, 414325
+ * The value of _pdbx_reference_entity_sequence.ref_entity_id is a reference
+ * to _pdbx_reference_entity_list.ref_entity_id in PDBX_REFERENCE_ENTITY_LIST category.
*/
- readonly id?: Maybe<Scalars['String']>;
+ readonly ref_entity_id: Scalars['String'];
/**
- * A human-readable term name.
- *
- * Examples:
- * Homo sapiens, 8, defensin beta 103A
+ * The monomer type for the sequence.
+ *
+ * Allowable values:
+ * peptide-like, saccharide
+ *
*/
- readonly name?: Maybe<Scalars['String']>;
+ readonly type?: Maybe<Scalars['String']>;
};
-export type DiffrnDetector = {
- /** A description of special aspects of the radiation detector. */
- readonly details?: Maybe<Scalars['String']>;
+export type PdbxReferenceEntitySrcNat = {
+ /** The Americal Tissue Culture Collection code for organism from which the entity was isolated. */
+ readonly atcc?: Maybe<Scalars['String']>;
+ /** The database code for this source information */
+ readonly db_code?: Maybe<Scalars['String']>;
+ /** The database name for this source information */
+ readonly db_name?: Maybe<Scalars['String']>;
/**
- * The general class of the radiation detector.
- *
+ * The value of _pdbx_reference_entity_src_nat.ordinal distinguishes
+ * source details for this entity.
+ */
+ readonly ordinal: Scalars['Int'];
+ /**
+ * The scientific name of the organism from which the entity was isolated.
+ *
* Examples:
- * photographic film, scintillation counter, CCD plate, BF~3~ counter
+ * Mus musculus
+ *
*/
- readonly detector?: Maybe<Scalars['String']>;
+ readonly organism_scientific?: Maybe<Scalars['String']>;
/**
- * This data item is a pointer to _diffrn.id in the DIFFRN
- * category.
+ * The value of _pdbx_reference_entity_src_nat.prd_id is a reference
+ * _pdbx_reference_entity_list.prd_id in the PDBX_REFERENCE_ENTITY_LIST category.
*/
- readonly diffrn_id: Scalars['String'];
+ readonly prd_id: Scalars['String'];
/**
- * The date of data collection.
- *
- * Examples:
- * 1996-12-25
+ * The value of _pdbx_reference_entity_src_nat.ref_entity_id is a reference
+ * to _pdbx_reference_entity_list.ref_entity_id in PDBX_REFERENCE_ENTITY_LIST category.
*/
- readonly pdbx_collection_date?: Maybe<Scalars['Date']>;
- /** The operating frequency of the detector (Hz) used in data collection. */
- readonly pdbx_frequency?: Maybe<Scalars['Float']>;
- /** The make, model or name of the detector device used. */
- readonly type?: Maybe<Scalars['String']>;
-};
-
-export type RcsbSchemaContainerIdentifiers = {
- /** Collection name associated with the data in the container. */
- readonly collection_name: Scalars['String'];
- /** Version string for the schema and collection. */
- readonly collection_schema_version?: Maybe<Scalars['String']>;
- /** Schema name associated with the data in the container. */
- readonly schema_name: Scalars['String'];
+ readonly ref_entity_id: Scalars['String'];
+ /** The data source for this information. */
+ readonly source?: Maybe<Scalars['String']>;
+ /** A identifier within the data source for this information. */
+ readonly source_id?: Maybe<Scalars['String']>;
+ /** The NCBI TaxId of the organism from which the entity was isolated. */
+ readonly taxid?: Maybe<Scalars['String']>;
};
-export type RcsbBranchedInstanceAnnotation = {
- /** An identifier for the annotation. */
- readonly annotation_id?: Maybe<Scalars['String']>;
- readonly annotation_lineage?: Maybe<ReadonlyArray<Maybe<RcsbBranchedInstanceAnnotationAnnotationLineage>>>;
- /** Identifies the version of the annotation assignment. */
- readonly assignment_version?: Maybe<Scalars['String']>;
- /** Chemical component identifier. */
- readonly comp_id?: Maybe<Scalars['String']>;
- /** A description for the annotation. */
- readonly description?: Maybe<Scalars['String']>;
- /** A name for the annotation. */
- readonly name?: Maybe<Scalars['String']>;
- /** Ordinal identifier for this category */
- readonly ordinal: Scalars['Int'];
+export type PdbxReferenceMolecule = {
/**
- * Code identifying the individual, organization or program that
- * assigned the annotation.
+ * For entities represented as single molecules, the identifier
+ * corresponding to the chemical definition for the molecule.
+ *
+ * Examples:
+ * 0Z3, CD9
+ *
*/
- readonly provenance_source?: Maybe<Scalars['String']>;
+ readonly chem_comp_id?: Maybe<Scalars['String']>;
/**
- * A type or category of the annotation.
- *
+ * Broadly defines the function of the entity.
+ *
* Allowable values:
- * CATH, SCOP
+ * Antagonist, Anthelmintic, Antibiotic, Antibiotic, Anthelmintic, Antibiotic, Antimicrobial, Antibiotic, Antineoplastic, Anticancer, Anticoagulant, Anticoagulant, Antithrombotic, Antifungal, Antigen, Antiinflammatory, Antimicrobial, Antimicrobial, Antiparasitic, Antibiotic, Antimicrobial, Antiretroviral, Antimicrobial, Antitumor, Antineoplastic, Antiparasitic, Antiretroviral, Antithrombotic, Antitumor, Antiviral, CASPASE inhibitor, Chaperone binding, Drug delivery, Enzyme inhibitor, Glycan component, Growth factor, Immunosuppressant, Inducer, Inhibitor, Lantibiotic, Metabolism, Metal transport, Nutrient, Oxidation-reduction, Protein binding, Receptor, Substrate analog, Synthetic opioid, Thrombin inhibitor, Thrombin inhibitor, Trypsin inhibitor, Toxin, Transition state mimetic, Transport activator, Trypsin inhibitor, Unknown, Water retention
+ *
*/
- readonly type?: Maybe<Scalars['String']>;
-};
-
-export type CorePfam = {
- /** Accession number of Pfam entry. */
- readonly rcsb_id: Scalars['String'];
+ readonly class?: Maybe<Scalars['String']>;
+ /** Evidence for the assignment of _pdbx_reference_molecule.class */
+ readonly class_evidence_code?: Maybe<Scalars['String']>;
+ /** Special details about this molecule. */
+ readonly compound_details?: Maybe<Scalars['String']>;
+ /** Description of this molecule. */
+ readonly description?: Maybe<Scalars['String']>;
/**
- * The unique accession code of protein families and domains in the Pfam database.
- *
+ * The formula for the reference entity. Formulae are written
+ * according to the rules:
+ *
+ * 1. Only recognised element symbols may be used.
+ *
+ * 2. Each element symbol is followed by a 'count' number. A count
+ * of '1' may be omitted.
+ *
+ * 3. A space or parenthesis must separate each element symbol and
+ * its count, but in general parentheses are not used.
+ *
+ * 4. The order of elements depends on whether or not carbon is
+ * present. If carbon is present, the order should be: C, then
+ * H, then the other elements in alphabetical order of their
+ * symbol. If carbon is not present, the elements are listed
+ * purely in alphabetic order of their symbol. This is the
+ * 'Hill' system used by Chemical Abstracts.
+ *
* Examples:
- * PF00621, PF00637, PF00656
+ * C18 H19 N7 O8 S
+ *
*/
- readonly rcsb_pfam_accession: Scalars['String'];
- /** Details of the Pfam clan to which the entity belongs. */
- readonly rcsb_pfam_clan_id?: Maybe<Scalars['String']>;
- /** Textual description of the family. */
- readonly rcsb_pfam_comment?: Maybe<Scalars['String']>;
- readonly rcsb_pfam_container_identifiers: RcsbPfamContainerIdentifiers;
+ readonly formula?: Maybe<Scalars['String']>;
+ /** Formula mass in daltons of the entity. */
+ readonly formula_weight?: Maybe<Scalars['Float']>;
/**
- * A human-readable name of protein families and domains.
- *
+ * A name of the entity.
+ *
* Examples:
- * Lectin like domain, Cell division control protein 24, OB domain 2, Protein of unknown function (DUF722)
+ * thiostrepton
+ *
*/
- readonly rcsb_pfam_description?: Maybe<Scalars['String']>;
+ readonly name?: Maybe<Scalars['String']>;
/**
- * The unique identifier of protein families and domains in the Pfam database.
- *
+ * The value of _pdbx_reference_molecule.prd_id is the unique identifier
+ * for the reference molecule in this family.
+ *
+ * By convention this ID uniquely identifies the reference molecule in
+ * in the PDB reference dictionary.
+ *
+ * The ID has the template form PRD_dddddd (e.g. PRD_000001)
+ *
* Examples:
- * RhoGEF, Clathrin, Peptidase_C14
+ * PRD_000001, PRD_0000010
+ *
*/
- readonly rcsb_pfam_identifier?: Maybe<Scalars['String']>;
+ readonly prd_id: Scalars['String'];
/**
- * Pfam-A is the manually curated portion of the Pfam database.
- *
+ * Defines the current PDB release status for this molecule definition.
+ *
* Allowable values:
- * Pfam-A
+ * HOLD, OBS, REL, WAIT
+ *
*/
- readonly rcsb_pfam_provenance_code?: Maybe<Scalars['String']>;
+ readonly release_status?: Maybe<Scalars['String']>;
+ /** Assigns the identifier of the reference molecule that has replaced this molecule. */
+ readonly replaced_by?: Maybe<Scalars['String']>;
/**
- * Pfam entries are classified into six different categories, depending on the length and nature of the sequence regions included in the entry: family, domain, repeats, motifs, coiled-coil, and disordered.
- *
+ * Assigns the identifier for the reference molecule which have been replaced
+ * by this reference molecule.
+ * Multiple molecule identifier codes should be separated by commas.
+ */
+ readonly replaces?: Maybe<Scalars['String']>;
+ /**
+ * Defines how this entity is represented in PDB data files.
+ *
* Allowable values:
- * Family, Domain, Repeat, Motif, Disordered, Coiled-coil
+ * branched, polymer, single molecule
+ *
*/
- readonly rcsb_pfam_seed_source?: Maybe<Scalars['String']>;
+ readonly represent_as?: Maybe<Scalars['String']>;
+ /** The PDB accession code for the entry containing a representative example of this molecule. */
+ readonly representative_PDB_id_code?: Maybe<Scalars['String']>;
+ /**
+ * Defines the structural classification of the entity.
+ *
+ * Allowable values:
+ * Amino acid, Aminoglycoside, Ansamycin, Anthracycline, Anthraquinone, Chalkophore, Chalkophore, Polypeptide, Chromophore, Cyclic depsipeptide, Cyclic lipopeptide, Cyclic peptide, Glycopeptide, Heterocyclic, Imino sugar, Keto acid, Lipoglycopeptide, Lipopeptide, Macrolide, Non-polymer, Nucleoside, Oligopeptide, Oligosaccharide, Peptaibol, Peptide-like, Polycyclic, Polypeptide, Polysaccharide, Quinolone, Siderophore, Thiolactone, Thiopeptide, Unknown
+ *
+ */
+ readonly type?: Maybe<Scalars['String']>;
+ /** Evidence for the assignment of _pdbx_reference_molecule.type */
+ readonly type_evidence_code?: Maybe<Scalars['String']>;
};
-export type EmImageRecording = {
+export type PdbxReferenceMoleculeAnnotation = {
/**
- * The average exposure time for each image.
- *
- * Examples:
- * 2.0
+ * The value of _pdbx_reference_molecule_annotation.family_prd_id is a reference to
+ * _pdbx_reference_molecule_list.family_prd_id in category PDBX_REFERENCE_MOLECULE_FAMILY_LIST.
*/
- readonly average_exposure_time?: Maybe<Scalars['Float']>;
+ readonly family_prd_id: Scalars['String'];
+ /** This data item distinguishes anotations for this entity. */
+ readonly ordinal: Scalars['Int'];
/**
- * The electron dose received by the specimen per image (electrons per square angstrom).
- *
- * Examples:
- * 30.0
+ * This data item is a pointer to _pdbx_reference_molecule.prd_id in the
+ * PDB_REFERENCE_MOLECULE category.
*/
- readonly avg_electron_dose_per_image?: Maybe<Scalars['Float']>;
+ readonly prd_id?: Maybe<Scalars['String']>;
/**
- * Any additional details about image recording.
- *
+ * The source of the annoation for this entity.
+ *
* Examples:
- * Images were collected in movie-mode at 17 frames per second
- */
- readonly details?: Maybe<Scalars['String']>;
- /**
- * The detector mode used during image recording.
- *
- * Allowable values:
- * COUNTING, INTEGRATING, OTHER, SUPER-RESOLUTION
+ * depositor provided, from UniProt Entry P200311
+ *
*/
- readonly detector_mode?: Maybe<Scalars['String']>;
+ readonly source?: Maybe<Scalars['String']>;
/**
- * The detector type used for recording images.
- * Usually film or CCD camera.
+ * Text describing the annotation for this entity.
+ *
+ * Examples:
+ * antigen binding, glucose transporter activity
+ *
*/
- readonly film_or_detector_model?: Maybe<Scalars['String']>;
+ readonly text?: Maybe<Scalars['String']>;
/**
- * The item _em_image_recording.id uniquely identifies
- * a set of recorded images.
+ * Type of annotation for this entity.
+ *
+ * Examples:
+ * Function, Use, Pharmacology, Mechanism_of_Action, Biological_Activity, Inhibitor_Class, Therapeutic_Category, Research_Use, Other_annotation
+ *
*/
- readonly id: Scalars['String'];
- /** This data item the id of the microscopy settings used in the imaging. */
- readonly imaging_id: Scalars['String'];
- /** The number of diffraction images collected. */
- readonly num_diffraction_images?: Maybe<Scalars['Int']>;
- /** Number of grids in the microscopy session */
- readonly num_grids_imaged?: Maybe<Scalars['Int']>;
- /** The number of micrograph images collected. */
- readonly num_real_images?: Maybe<Scalars['Int']>;
+ readonly type?: Maybe<Scalars['String']>;
};
-export type RcsbBirdCitation = {
+export type PdbxReferenceMoleculeDetails = {
/**
- * The value of _rcsb_bird_citation.id must uniquely identify a record in the
- * rcsb_bird_citation list.
- *
- * Examples:
- * 1, 2
+ * The value of _pdbx_reference_molecule_details.family_prd_id is a reference to
+ * _pdbx_reference_molecule_list.family_prd_id' in category PDBX_REFERENCE_MOLECULE_FAMILY.
*/
- readonly id: Scalars['String'];
+ readonly family_prd_id: Scalars['String'];
/**
- * Abbreviated name of the cited journal as given in the
- * Chemical Abstracts Service Source Index.
- *
- * Examples:
- * J.Mol.Biol., J. Mol. Biol.
+ * The value of _pdbx_reference_molecule_details.ordinal is an ordinal that
+ * distinguishes each descriptive text for this entity.
*/
- readonly journal_abbrev?: Maybe<Scalars['String']>;
+ readonly ordinal: Scalars['Int'];
+ /** A data source of this information (e.g. PubMed, Merck Index) */
+ readonly source?: Maybe<Scalars['String']>;
+ /** A identifier within the data source for this information. */
+ readonly source_id?: Maybe<Scalars['String']>;
+ /** The text of the description of special aspects of the entity. */
+ readonly text?: Maybe<Scalars['String']>;
+};
+
+export type PdbxReferenceMoleculeFamily = {
/**
- * Volume number of the journal cited; relevant for journal
- * articles.
- *
+ * The value of _pdbx_reference_entity.family_prd_id must uniquely identify a record in the
+ * PDBX_REFERENCE_MOLECULE_FAMILY list.
+ *
+ * By convention this ID uniquely identifies the reference family in
+ * in the PDB reference dictionary.
+ *
+ * The ID has the template form FAM_dddddd (e.g. FAM_000001)
+ */
+ readonly family_prd_id: Scalars['String'];
+ /**
+ * The entity family name.
+ *
* Examples:
- * 174
+ * actinomycin, adriamycin
+ *
*/
- readonly journal_volume?: Maybe<Scalars['String']>;
+ readonly name?: Maybe<Scalars['String']>;
/**
- * The first page of the rcsb_bird_citation; relevant for journal
- * articles, books and book chapters.
+ * Assigns the current PDB release status for this family.
+ *
+ * Allowable values:
+ * HOLD, OBS, REL, WAIT
+ *
*/
- readonly page_first?: Maybe<Scalars['String']>;
+ readonly release_status?: Maybe<Scalars['String']>;
+ /** Assigns the identifier of the family that has replaced this component. */
+ readonly replaced_by?: Maybe<Scalars['String']>;
/**
- * The last page of the rcsb_bird_citation; relevant for journal
- * articles, books and book chapters.
+ * Assigns the identifier for the family which have been replaced by this family.
+ * Multiple family identifier codes should be separated by commas.
*/
- readonly page_last?: Maybe<Scalars['String']>;
+ readonly replaces?: Maybe<Scalars['String']>;
+};
+
+export type PdbxReferenceMoleculeFeatures = {
/**
- * Document Object Identifier used by doi.org to uniquely
- * specify bibliographic entry.
- *
- * Examples:
- * 10.2345/S1384107697000225
+ * The value of _pdbx_reference_molecule_features.family_prd_id is a reference to
+ * _pdbx_reference_molecule_list.family_prd_id in category PDBX_REFERENCE_MOLECULE_FAMILY_LIST.
*/
- readonly pdbx_database_id_DOI?: Maybe<Scalars['String']>;
+ readonly family_prd_id: Scalars['String'];
/**
- * Ascession number used by PubMed to categorize a specific
- * bibliographic entry.
- *
- * Examples:
- * 12627512
+ * The value of _pdbx_reference_molecule_features.ordinal distinguishes
+ * each feature for this entity.
*/
- readonly pdbx_database_id_PubMed?: Maybe<Scalars['Int']>;
+ readonly ordinal: Scalars['Int'];
/**
- * Names of the authors of the citation; relevant for journal
- * articles, books and book chapters. Names are separated by vertical bars.
- *
- * The family name(s), followed by a comma and including any
- * dynastic components, precedes the first name(s) or initial(s).
+ * The value of _pdbx_reference_molecule_features.prd_id is a reference
+ * _pdbx_reference_molecule.prd_id in the PDBX_REFERENCE_MOLECULE category.
*/
- readonly rcsb_authors?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
+ readonly prd_id: Scalars['String'];
/**
- * The title of the rcsb_bird_citation; relevant for journal articles, books
- * and book chapters.
- *
+ * The information source for the component feature.
+ *
* Examples:
- * Structure of diferric duck ovotransferrin
- * at 2.35 Angstroms resolution.
+ * PDB, CHEBI, DRUGBANK, PUBCHEM
+ *
*/
- readonly title?: Maybe<Scalars['String']>;
+ readonly source?: Maybe<Scalars['String']>;
/**
- * The year of the rcsb_bird_citation; relevant for journal articles, books
- * and book chapters.
- *
+ * The value of _pdbx_reference_molecule_features.source_ordinal provides
+ * the priority order of features from a particular source or database.
+ */
+ readonly source_ordinal?: Maybe<Scalars['Int']>;
+ /**
+ * The entity feature type.
+ *
* Examples:
- * 1984
+ * FUNCTION, ENZYME INHIBITED, STRUCTURE IMAGE URL
+ *
*/
- readonly year?: Maybe<Scalars['Int']>;
-};
-
-export type RcsbBranchedInstanceAnnotationAnnotationLineage = {
- /** Members of the annotation lineage as parent lineage depth (1-N) */
- readonly depth?: Maybe<Scalars['Int']>;
- /** Members of the annotation lineage as parent class identifiers. */
- readonly id?: Maybe<Scalars['String']>;
- /** Members of the annotation lineage as parent class names. */
- readonly name?: Maybe<Scalars['String']>;
-};
-
-export type RcsbNonpolymerInstanceAnnotationAnnotationLineage = {
- /** Members of the annotation lineage as parent lineage depth (1-N) */
- readonly depth?: Maybe<Scalars['Int']>;
- /** Members of the annotation lineage as parent class identifiers. */
- readonly id?: Maybe<Scalars['String']>;
- /** Members of the annotation lineage as parent class names. */
- readonly name?: Maybe<Scalars['String']>;
+ readonly type?: Maybe<Scalars['String']>;
+ /** The entity feature value. */
+ readonly value?: Maybe<Scalars['String']>;
};
-export type RcsbUniprotProteinName = {
- /** Historical record of the data attribute. */
- readonly provenance_code: Scalars['String'];
- /** Name that allows to unambiguously identify a protein. */
- readonly value: Scalars['String'];
+export type PdbxReferenceMoleculeList = {
+ /**
+ * The value of _pdbx_reference_molecule_list.family_prd_id is a reference to
+ * _pdbx_reference_molecule_family.family_prd_id' in category PDBX_REFERENCE_MOLECULE_FAMILY.
+ */
+ readonly family_prd_id: Scalars['String'];
+ /**
+ * The value of _pdbx_reference_molecule_list.prd_id is the unique identifier
+ * for the reference molecule in this family.
+ *
+ * By convention this ID uniquely identifies the reference molecule in
+ * in the PDB reference dictionary.
+ *
+ * The ID has the template form PRD_dddddd (e.g. PRD_000001)
+ */
+ readonly prd_id: Scalars['String'];
};
-export type EmEmbedding = {
+export type PdbxReferenceMoleculeRelatedStructures = {
+ /** A link to related reference information in the citation category. */
+ readonly citation_id?: Maybe<Scalars['String']>;
/**
- * Staining procedure used in the specimen preparation.
- *
+ * The database accession code for the related structure reference.
+ *
* Examples:
- * The crystal suspension was injected into the lens of a drop of buffer containing
- * 1 % tannin sitting on a carbon film supported by a molybdenum grid. An equal volume
- * of 1% glucose was then added and the solution thoroughly but gently mixed. The grid
- * was then blotted, air dried, and frozen in LN2.
+ * 143108
+ *
*/
- readonly details?: Maybe<Scalars['String']>;
- /** This data item is the primary key of the category. */
- readonly id: Scalars['String'];
+ readonly db_accession?: Maybe<Scalars['String']>;
/**
- * The embedding material.
- *
+ * The database identifier code for the related structure reference.
+ *
* Examples:
- * tannin and glucose
+ * QEFHUE
+ *
*/
- readonly material?: Maybe<Scalars['String']>;
- /** Foreign key relationship to the EMD SPECIMEN category */
- readonly specimen_id?: Maybe<Scalars['String']>;
-};
-
-export type PdbxReferenceEntitySrcNat = {
- /** The Americal Tissue Culture Collection code for organism from which the entity was isolated. */
- readonly atcc?: Maybe<Scalars['String']>;
- /** The database code for this source information */
readonly db_code?: Maybe<Scalars['String']>;
- /** The database name for this source information */
+ /**
+ * The database name for the related structure reference.
+ *
+ * Examples:
+ * CCDC
+ *
+ */
readonly db_name?: Maybe<Scalars['String']>;
/**
- * The value of _pdbx_reference_entity_src_nat.ordinal distinguishes
- * source details for this entity.
+ * The value of _pdbx_reference_molecule_related_structures.family_prd_id is a reference to
+ * _pdbx_reference_molecule_list.family_prd_id in category PDBX_REFERENCE_MOLECULE_FAMILY_LIST.
*/
- readonly ordinal: Scalars['Int'];
+ readonly family_prd_id: Scalars['String'];
/**
- * The scientific name of the organism from which the entity was isolated.
- *
+ * The formula for the reference entity. Formulae are written
+ * according to the rules:
+ *
+ * 1. Only recognised element symbols may be used.
+ *
+ * 2. Each element symbol is followed by a 'count' number. A count
+ * of '1' may be omitted.
+ *
+ * 3. A space or parenthesis must separate each element symbol and
+ * its count, but in general parentheses are not used.
+ *
+ * 4. The order of elements depends on whether or not carbon is
+ * present. If carbon is present, the order should be: C, then
+ * H, then the other elements in alphabetical order of their
+ * symbol. If carbon is not present, the elements are listed
+ * purely in alphabetic order of their symbol. This is the
+ * 'Hill' system used by Chemical Abstracts.
+ *
* Examples:
- * Mus musculus
+ * C18 H19 N7 O8 S
+ *
*/
- readonly organism_scientific?: Maybe<Scalars['String']>;
+ readonly formula?: Maybe<Scalars['String']>;
/**
- * The value of _pdbx_reference_entity_src_nat.prd_id is a reference
- * _pdbx_reference_entity_list.prd_id in the PDBX_REFERENCE_ENTITY_LIST category.
+ * The chemical name for the structure entry in the related database
+ *
+ * Examples:
+ * actinomycn
+ *
*/
- readonly prd_id: Scalars['String'];
+ readonly name?: Maybe<Scalars['String']>;
/**
- * The value of _pdbx_reference_entity_src_nat.ref_entity_id is a reference
- * to _pdbx_reference_entity_list.ref_entity_id in PDBX_REFERENCE_ENTITY_LIST category.
+ * The value of _pdbx_reference_molecule_related_structures.ordinal distinguishes
+ * related structural data for each entity.
*/
- readonly ref_entity_id: Scalars['String'];
- /** The data source for this information. */
- readonly source?: Maybe<Scalars['String']>;
- /** A identifier within the data source for this information. */
- readonly source_id?: Maybe<Scalars['String']>;
- /** The NCBI TaxId of the organism from which the entity was isolated. */
- readonly taxid?: Maybe<Scalars['String']>;
+ readonly ordinal: Scalars['Int'];
};
-export type EmDiffractionStats = {
- /**
- * Any addition details about the structure factor measurements
- *
- * Examples:
- * Phases were obtained from micrograph images of the 2D crystals
- */
- readonly details?: Maybe<Scalars['String']>;
+export type PdbxReferenceMoleculeSynonyms = {
/**
- * Completeness of the structure factor data within the defined space group
- * at the reported resolution (percent).
- *
- * Examples:
- * 89.3
+ * The value of _pdbx_reference_molecule_synonyms.family_prd_id is a reference to
+ * _pdbx_reference_molecule_list.family_prd_id in category PDBX_REFERENCE_MOLECULE_FAMILY_LIST.
*/
- readonly fourier_space_coverage?: Maybe<Scalars['Float']>;
+ readonly family_prd_id: Scalars['String'];
/**
- * High resolution limit of the structure factor data, in Angstroms
- *
+ * A synonym name for the entity.
+ *
* Examples:
- * 7.5
+ * thiostrepton
+ *
*/
- readonly high_resolution?: Maybe<Scalars['Float']>;
- /** Identifier for this category */
- readonly id: Scalars['String'];
- /** Pointer to _em_image_processing.id */
- readonly image_processing_id?: Maybe<Scalars['String']>;
+ readonly name?: Maybe<Scalars['String']>;
/**
- * Total number of diffraction intensities measured (before averaging)
- *
- * Examples:
- * 1590
+ * The value of _pdbx_reference_molecule_synonyms.ordinal is an ordinal
+ * to distinguish synonyms for this entity.
*/
- readonly num_intensities_measured?: Maybe<Scalars['Int']>;
+ readonly ordinal: Scalars['Int'];
/**
- * Number of structure factors obtained (merged amplitudes + phases)
- *
- * Examples:
- * 325
+ * The value of _pdbx_reference_molecule_synonyms.prd_id is a reference
+ * _pdbx_reference_molecule.prd_id in the PDBX_REFERENCE_MOLECULE category.
*/
- readonly num_structure_factors?: Maybe<Scalars['Int']>;
+ readonly prd_id: Scalars['String'];
/**
- * Overall phase error in degrees
- *
+ * The source of this synonym name for the entity.
+ *
* Examples:
- * 17.5
+ * CAS
+ *
*/
- readonly overall_phase_error?: Maybe<Scalars['Float']>;
+ readonly source?: Maybe<Scalars['String']>;
+};
+
+export type PdbxRelatedExpDataSet = {
/**
- * Overall phase residual in degrees
- *
+ * A DOI reference to the related data set.
+ *
* Examples:
- * 17.5
+ * 10.000/10002/image_data/cif
+ *
*/
- readonly overall_phase_residual?: Maybe<Scalars['Float']>;
+ readonly data_reference?: Maybe<Scalars['String']>;
/**
- * Criteria used to reject phases
- *
+ * The type of the experimenatal data set.
+ *
* Examples:
- * Structure factors with phase errors higher than 20 degrees were omitted from refinement
+ * diffraction image data, NMR free induction decay data
+ *
*/
- readonly phase_error_rejection_criteria?: Maybe<Scalars['String']>;
+ readonly data_set_type?: Maybe<Scalars['String']>;
/**
- * Rmerge value (percent)
- *
- * Examples:
- * 19.8
+ * Additional details describing the content of the related data set and its application to
+ * the current investigation.
*/
- readonly r_merge?: Maybe<Scalars['Float']>;
+ readonly details?: Maybe<Scalars['String']>;
/**
- * Rsym value (percent)
- *
+ * A DOI reference to the metadata decribing the related data set.
+ *
* Examples:
- * 24.4
+ * 10.000/10002/image_data/txt
+ *
*/
- readonly r_sym?: Maybe<Scalars['Float']>;
+ readonly metadata_reference?: Maybe<Scalars['String']>;
};
-export type PdbxAuditRevisionItem = {
+export type PdbxSgProject = {
/**
- * The type of file that the pdbx_audit_revision_history record refers to.
- *
+ * The value identifies the full name of center.
+ *
* Allowable values:
- * Chemical component, NMR restraints, NMR shifts, Structure factors, Structure model
+ * Accelerated Technologies Center for Gene to 3D Structure, Assembly, Dynamics and Evolution of Cell-Cell and Cell-Matrix Adhesions, Atoms-to-Animals: The Immune Function Network, Bacterial targets at IGS-CNRS, France, Berkeley Structural Genomics Center, Center for Eukaryotic Structural Genomics, Center for High-Throughput Structural Biology, Center for Membrane Proteins of Infectious Diseases, Center for Structural Genomics of Infectious Diseases, Center for Structures of Membrane Proteins, Center for the X-ray Structure Determination of Human Transporters, Chaperone-Enabled Studies of Epigenetic Regulation Enzymes, Enzyme Discovery for Natural Product Biosynthesis, GPCR Network, Integrated Center for Structure and Function Innovation, Israel Structural Proteomics Center, Joint Center for Structural Genomics, Marseilles Structural Genomics Program @ AFMB, Medical Structural Genomics of Pathogenic Protozoa, Membrane Protein Structural Biology Consortium, Membrane Protein Structures by Solution NMR, Midwest Center for Macromolecular Research, Midwest Center for Structural Genomics, Mitochondrial Protein Partnership, Montreal-Kingston Bacterial Structural Genomics Initiative, Mycobacterium Tuberculosis Structural Proteomics Project, New York Consortium on Membrane Protein Structure, New York SGX Research Center for Structural Genomics, New York Structural GenomiX Research Consortium, New York Structural Genomics Research Consortium, Northeast Structural Genomics Consortium, Nucleocytoplasmic Transport: a Target for Cellular Control, Ontario Centre for Structural Proteomics, Oxford Protein Production Facility, Paris-Sud Yeast Structural Genomics, Partnership for Nuclear Receptor Signaling Code Biology, Partnership for Stem Cell Biology, Partnership for T-Cell Biology, Program for the Characterization of Secreted Effector Proteins, Protein Structure Factory, RIKEN Structural Genomics/Proteomics Initiative, Scottish Structural Proteomics Facility, Seattle Structural Genomics Center for Infectious Disease, South Africa Structural Targets Annotation Database, Southeast Collaboratory for Structural Genomics, Structural Genomics Consortium, Structural Genomics Consortium for Research on Gene Expression, Structural Genomics of Pathogenic Protozoa Consortium, Structural Proteomics in Europe, Structural Proteomics in Europe 2, Structure 2 Function Project, Structure, Dynamics and Activation Mechanisms of Chemokine Receptors, Structure-Function Analysis of Polymorphic CDI Toxin-Immunity Protein Complexes, Structure-Function Studies of Tight Junction Membrane Proteins, Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors, TB Structural Genomics Consortium, Transcontinental EM Initiative for Membrane Protein Structure, Transmembrane Protein Center
+ *
*/
- readonly data_content_type: Scalars['String'];
+ readonly full_name_of_center?: Maybe<Scalars['String']>;
/**
- * A high level explanation the author has provided for submitting a revision.
- *
- * Examples:
- * _atom_site.type_symbol
+ * A unique integer identifier for this center
+ *
+ * Allowable values:
+ * 1, 2, 3, 4, 5, 6, 7, 8, 9, 10
+ *
*/
- readonly item?: Maybe<Scalars['String']>;
+ readonly id: Scalars['Int'];
+ /**
+ * The value identifies the full name of center.
+ *
+ * Allowable values:
+ * ATCG3D, BIGS, BSGC, BSGI, CEBS, CELLMAT, CESG, CHSAM, CHTSB, CSGID, CSMP, GPCR, IFN, ISFI, ISPC, JCSG, MCMR, MCSG, MPID, MPP, MPSBC, MPSbyNMR, MSGP, MSGPP, MTBI, NESG, NHRs, NPCXstals, NYCOMPS, NYSGRC, NYSGXRC, NatPro, OCSP, OPPF, PCSEP, PSF, RSGI, S2F, SASTAD, SECSG, SGC, SGCGES, SGPP, SPINE, SPINE-2, SSGCID, SSPF, STEMCELL, TBSGC, TCELL, TEMIMPS, TJMP, TMPC, TransportPDB, UC4CDI, XMTB, YSG
+ *
+ */
+ readonly initial_of_center?: Maybe<Scalars['String']>;
+ /**
+ * The value identifies the Structural Genomics project.
+ *
+ * Allowable values:
+ * Enzyme Function Initiative, NIAID, National Institute of Allergy and Infectious Diseases, NPPSFA, National Project on Protein Structural and Functional Analyses, PSI, Protein Structure Initiative, PSI:Biology
+ *
+ */
+ readonly project_name?: Maybe<Scalars['String']>;
+};
+
+export type PdbxSerialCrystallographyDataReduction = {
+ /**
+ * For experiments in which samples are provided in a
+ * continuous stream, the total number of frames collected
+ * in which the crystal was hit.
+ */
+ readonly crystal_hits?: Maybe<Scalars['Int']>;
/**
- * A unique identifier for the pdbx_audit_revision_item record.
- *
+ * The data item is a pointer to _diffrn.id in the DIFFRN
+ * category.
+ *
* Examples:
* 1
+ *
*/
- readonly ordinal: Scalars['Int'];
+ readonly diffrn_id: Scalars['String'];
+ /**
+ * For experiments in which samples are provided in a
+ * continuous stream, the total number of frames collected
+ * in which a droplet was hit.
+ */
+ readonly droplet_hits?: Maybe<Scalars['Int']>;
+ /**
+ * For experiments in which samples are provided in a
+ * continuous stream, the total number of data frames collected
+ * in which the sample was hit.
+ */
+ readonly frame_hits?: Maybe<Scalars['Int']>;
+ /**
+ * For experiments in which samples are provided in a
+ * continuous stream, the total number of data frames collected
+ * that contained a "hit" but failed to index.
+ */
+ readonly frames_failed_index?: Maybe<Scalars['Int']>;
+ /**
+ * For experiments in which samples are provided in a
+ * continuous stream, the total number of data frames collected
+ * that were indexed.
+ */
+ readonly frames_indexed?: Maybe<Scalars['Int']>;
+ /**
+ * The total number of data frames collected for this
+ * data set.
+ */
+ readonly frames_total?: Maybe<Scalars['Int']>;
+ /**
+ * For experiments in which samples are provided in a
+ * continuous stream, the total number of lattices indexed.
+ */
+ readonly lattices_indexed?: Maybe<Scalars['Int']>;
+ /** For FEL experiments, the number of pulse events in the dataset. */
+ readonly xfel_pulse_events?: Maybe<Scalars['Int']>;
+ /**
+ * For FEL experiments, in which data collection was performed
+ * in batches, indicates which subset of the data collected
+ * were used in producing this dataset.
+ */
+ readonly xfel_run_numbers?: Maybe<Scalars['String']>;
+};
+
+export type PdbxSerialCrystallographyMeasurement = {
+ /**
+ * The total number of hours required to measure this data set.
+ *
+ * Examples:
+ * null
+ *
+ */
+ readonly collection_time_total?: Maybe<Scalars['Float']>;
/**
- * A pointer to _pdbx_audit_revision_history.ordinal
- *
+ * The collimation or type of focusing optics applied to the radiation.
+ *
+ * Examples:
+ * Kirkpatrick-Baez mirrors, Beryllium compound refractive lenses, Fresnel zone plates
+ *
+ */
+ readonly collimation?: Maybe<Scalars['String']>;
+ /**
+ * The data item is a pointer to _diffrn.id in the DIFFRN
+ * category.
+ *
* Examples:
* 1
+ *
*/
- readonly revision_ordinal: Scalars['Int'];
+ readonly diffrn_id: Scalars['String'];
+ /**
+ * The focal spot size of the beam
+ * impinging on the sample (micrometres squared).
+ */
+ readonly focal_spot_size?: Maybe<Scalars['Float']>;
+ /** The photons per pulse measured in (tera photons (10^(12)^)/pulse units). */
+ readonly photons_per_pulse?: Maybe<Scalars['Float']>;
+ /**
+ * The average duration (femtoseconds)
+ * of the pulse energy measured at the sample.
+ */
+ readonly pulse_duration?: Maybe<Scalars['Float']>;
+ /** The energy/pulse of the X-ray pulse impacting the sample measured in microjoules. */
+ readonly pulse_energy?: Maybe<Scalars['Float']>;
+ /** The photon energy of the X-ray pulse measured in KeV. */
+ readonly pulse_photon_energy?: Maybe<Scalars['Float']>;
+ /** The distance from source to the sample along the optical axis (metres). */
+ readonly source_distance?: Maybe<Scalars['Float']>;
+ /** The dimension of the source beam measured at the source (micrometres squared). */
+ readonly source_size?: Maybe<Scalars['Float']>;
+ /** For FEL experiments, the pulse repetition rate measured in cycles per seconds. */
+ readonly xfel_pulse_repetition_rate?: Maybe<Scalars['Float']>;
};
export type PdbxSerialCrystallographySampleDelivery = {
/**
* The description of the mechanism by which the specimen in placed in the path
* of the source.
- *
+ *
* Examples:
* fixed target, electrospin, MESH, CoMESH, gas dynamic virtual nozzle, LCP injector, addressable microarray
+ *
*/
readonly description?: Maybe<Scalars['String']>;
/**
* The data item is a pointer to _diffrn.id in the DIFFRN
* category.
- *
+ *
* Examples:
* 1
+ *
*/
readonly diffrn_id: Scalars['String'];
/**
* The description of the mechanism by which the specimen in placed in the path
* of the source.
- *
+ *
* Allowable values:
* fixed target, injection
+ *
*/
readonly method?: Maybe<Scalars['String']>;
};
-export type Em3dReconstruction = {
+export type PdbxSerialCrystallographySampleDeliveryFixedTarget = {
+ /** The number of crystals per dropplet or pore in fixed target */
+ readonly crystals_per_unit?: Maybe<Scalars['Int']>;
+ /** For a fixed target sample, a description of sample preparation */
+ readonly description?: Maybe<Scalars['String']>;
+ /** Any details pertinent to the fixed sample target */
+ readonly details?: Maybe<Scalars['String']>;
/**
- * The actual pixel size of projection set of images.
- *
+ * The data item is a pointer to _diffrn.id in the DIFFRN
+ * category.
+ *
* Examples:
- * 2.8, 5.76
+ * 1
+ *
*/
- readonly actual_pixel_size?: Maybe<Scalars['Float']>;
- /** The algorithm used project from 2D orientations to 3D map. */
- readonly algorithm?: Maybe<Scalars['String']>;
+ readonly diffrn_id: Scalars['String'];
/**
- * Any additional details used in the 3d reconstruction.
- *
+ * Device used to control movement of the fixed sample
+ *
* Examples:
- * a modified version of SPIDER program was used for the reconstruction
+ * DMC-4080
+ *
*/
- readonly details?: Maybe<Scalars['String']>;
+ readonly motion_control?: Maybe<Scalars['String']>;
/**
- * The value of _em_3d_reconstruction.id must
- * uniquely identify the 3d reconstruction.
+ * Method to prevent dehydration of sample
+ *
+ * Examples:
+ * seal, humidifed gas, flash freezing
+ *
*/
- readonly id: Scalars['String'];
- /** Foreign key to the EM_IMAGE_PROCESSING category */
- readonly image_processing_id: Scalars['String'];
+ readonly sample_dehydration_prevention?: Maybe<Scalars['String']>;
/**
- * The magnification calibration method for the 3d reconstruction.
- *
+ * For a fixed target sample, mechanism to hold sample in the beam
+ *
* Examples:
- * TMV images
+ * mesh, loop, grid
+ *
*/
- readonly magnification_calibration?: Maybe<Scalars['String']>;
+ readonly sample_holding?: Maybe<Scalars['String']>;
+ /** The sample solution content and concentration */
+ readonly sample_solvent?: Maybe<Scalars['String']>;
/**
- * The algorithm method used for the 3d-reconstruction.
- *
- * Examples:
- * cross-common lines, polar Fourier transform (PFT)
+ * Size of pore in grid supporting sample. Diameter or length in micrometres,
+ * e.g. pore diameter
*/
- readonly method?: Maybe<Scalars['String']>;
+ readonly sample_unit_size?: Maybe<Scalars['Float']>;
/**
- * The nominal pixel size of the projection set of images.
- *
+ * Type of base holding the support
+ *
* Examples:
- * 3.11, 6.78
+ * goniometer
+ *
*/
- readonly nominal_pixel_size?: Maybe<Scalars['Float']>;
+ readonly support_base?: Maybe<Scalars['String']>;
+ /** Velocity of sample horizontally relative to a perpendicular beam in millimetres/second */
+ readonly velocity_horizontal?: Maybe<Scalars['Float']>;
+ /** Velocity of sample vertically relative to a perpendicular beam in millimetres/second */
+ readonly velocity_vertical?: Maybe<Scalars['Float']>;
+};
+
+export type PdbxSerialCrystallographySampleDeliveryInjection = {
/**
- * This item was correspondence to two type of em dataset
- * processing_emDataSet_singleParticle.numClassAverages
- * processing_emDataSet_icosahedral.numClassAverages
+ * For continuous sample flow experiments, the carrier buffer used
+ * to move the sample into the beam. Should include protein
+ * concentration.
+ *
+ * Examples:
+ * LCP, grease, liquid
+ *
*/
- readonly num_class_averages?: Maybe<Scalars['Int']>;
- /** The number of 2D projections or 3D subtomograms used in the 3d reconstruction */
- readonly num_particles?: Maybe<Scalars['Int']>;
+ readonly carrier_solvent?: Maybe<Scalars['String']>;
/**
- * type of refinement performed in order to determine map resolution
- *
- * Allowable values:
- * HALF-MAPS REFINED AGAINST SAME DATA, HALF-MAPS REFINED INDEPENDENTLY, HALF-MAPS REFINED INDEPENDENTLY WITH FREQUENCY RANGE OMITTED, HALF-MAPS REFINED WITH FREQUENCY RANGE OMITTED, OTHER
+ * For continuous sample flow experiments, the concentration of
+ * crystals in the solution being injected.
+ *
+ * The concentration is measured in million crystals/ml.
*/
- readonly refinement_type?: Maybe<Scalars['String']>;
+ readonly crystal_concentration?: Maybe<Scalars['Float']>;
/**
- * The final resolution (in Angstroms)of the 3D reconstruction.
- *
+ * For continuous sample flow experiments, a description of the injector used
+ * to move the sample into the beam.
+ *
* Examples:
- * 8.9, 10.0
+ * microextrusion injector
+ *
*/
- readonly resolution?: Maybe<Scalars['Float']>;
+ readonly description?: Maybe<Scalars['String']>;
/**
- * The method used to determine the final resolution
- * of the 3d reconstruction.
- * The Fourier Shell Correlation criterion as a measure of
- * resolution is based on the concept of splitting the (2D)
- * data set into two halves; averaging each and comparing them
- * using the Fourier Ring Correlation (FRC) technique.
- *
+ * The data item is a pointer to _diffrn.id in the DIFFRN
+ * category.
+ *
* Examples:
- * FSC at 0.5 cut-off
+ * 1
+ *
*/
- readonly resolution_method?: Maybe<Scalars['String']>;
+ readonly diffrn_id: Scalars['String'];
+ /** The size of filter in micrometres in filtering crystals */
+ readonly filter_size?: Maybe<Scalars['Float']>;
/**
- * The type of symmetry applied to the reconstruction
- *
- * Allowable values:
- * 2D CRYSTAL, 3D CRYSTAL, HELICAL, POINT
+ * For continuous sample flow experiments, the flow rate of
+ * solution being injected measured in ul/min.
*/
- readonly symmetry_type?: Maybe<Scalars['String']>;
-};
-
-export type EmParticleSelection = {
+ readonly flow_rate?: Maybe<Scalars['Float']>;
/**
- * Any additional details used for selecting particles
- *
+ * For continuous sample flow experiments, the diameter of the
+ * injector in micrometres.
+ */
+ readonly injector_diameter?: Maybe<Scalars['Float']>;
+ /**
+ * The type of nozzle to deliver and focus sample jet
+ *
* Examples:
- * negative monitor contrast facilitated particle picking
+ * gas, GDVN
+ *
*/
- readonly details?: Maybe<Scalars['String']>;
- /** Ordinal identifier */
- readonly id: Scalars['String'];
+ readonly injector_nozzle?: Maybe<Scalars['String']>;
/**
- * The value of _em_particle_selection.image_processing_id points to
- * the EM_IMAGE_PROCESSING category.
+ * For continuous sample flow experiments, the mean pressure
+ * in kilopascals at which the sample is injected into the beam.
*/
- readonly image_processing_id: Scalars['String'];
+ readonly injector_pressure?: Maybe<Scalars['Float']>;
/**
- * The number of particles selected from the projection set of images.
- *
- * Examples:
- * 840
+ * For continuous sample flow experiments, the temperature in
+ * Kelvins of the speciman injected. This may be different from
+ * the temperature of the sample.
*/
- readonly num_particles_selected?: Maybe<Scalars['Int']>;
-};
-
-export type CoreChemComp = {
- readonly chem_comp?: Maybe<ChemComp>;
- /** Get DrubBank entry associated with this chemical component. */
- readonly drugbank?: Maybe<CoreDrugbank>;
- readonly pdbx_chem_comp_audit?: Maybe<ReadonlyArray<Maybe<PdbxChemCompAudit>>>;
- readonly pdbx_chem_comp_descriptor?: Maybe<ReadonlyArray<Maybe<PdbxChemCompDescriptor>>>;
- readonly pdbx_chem_comp_feature?: Maybe<ReadonlyArray<Maybe<PdbxChemCompFeature>>>;
- readonly pdbx_chem_comp_identifier?: Maybe<ReadonlyArray<Maybe<PdbxChemCompIdentifier>>>;
- readonly pdbx_family_prd_audit?: Maybe<ReadonlyArray<Maybe<PdbxFamilyPrdAudit>>>;
- readonly pdbx_prd_audit?: Maybe<ReadonlyArray<Maybe<PdbxPrdAudit>>>;
- readonly pdbx_reference_entity_list?: Maybe<ReadonlyArray<Maybe<PdbxReferenceEntityList>>>;
- readonly pdbx_reference_entity_poly?: Maybe<ReadonlyArray<Maybe<PdbxReferenceEntityPoly>>>;
- readonly pdbx_reference_entity_poly_link?: Maybe<ReadonlyArray<Maybe<PdbxReferenceEntityPolyLink>>>;
- readonly pdbx_reference_entity_poly_seq?: Maybe<ReadonlyArray<Maybe<PdbxReferenceEntityPolySeq>>>;
- readonly pdbx_reference_entity_sequence?: Maybe<ReadonlyArray<Maybe<PdbxReferenceEntitySequence>>>;
- readonly pdbx_reference_entity_src_nat?: Maybe<ReadonlyArray<Maybe<PdbxReferenceEntitySrcNat>>>;
- readonly pdbx_reference_molecule?: Maybe<PdbxReferenceMolecule>;
- readonly pdbx_reference_molecule_annotation?: Maybe<ReadonlyArray<Maybe<PdbxReferenceMoleculeAnnotation>>>;
- readonly pdbx_reference_molecule_details?: Maybe<ReadonlyArray<Maybe<PdbxReferenceMoleculeDetails>>>;
- readonly pdbx_reference_molecule_family?: Maybe<PdbxReferenceMoleculeFamily>;
- readonly pdbx_reference_molecule_features?: Maybe<ReadonlyArray<Maybe<PdbxReferenceMoleculeFeatures>>>;
- readonly pdbx_reference_molecule_list?: Maybe<ReadonlyArray<Maybe<PdbxReferenceMoleculeList>>>;
- readonly pdbx_reference_molecule_related_structures?: Maybe<ReadonlyArray<Maybe<PdbxReferenceMoleculeRelatedStructures>>>;
- readonly pdbx_reference_molecule_synonyms?: Maybe<ReadonlyArray<Maybe<PdbxReferenceMoleculeSynonyms>>>;
- readonly rcsb_bird_citation?: Maybe<ReadonlyArray<Maybe<RcsbBirdCitation>>>;
- readonly rcsb_chem_comp_annotation?: Maybe<ReadonlyArray<Maybe<RcsbChemCompAnnotation>>>;
- readonly rcsb_chem_comp_container_identifiers?: Maybe<RcsbChemCompContainerIdentifiers>;
- readonly rcsb_chem_comp_descriptor?: Maybe<RcsbChemCompDescriptor>;
- readonly rcsb_chem_comp_info?: Maybe<RcsbChemCompInfo>;
- readonly rcsb_chem_comp_related?: Maybe<ReadonlyArray<Maybe<RcsbChemCompRelated>>>;
- readonly rcsb_chem_comp_synonyms?: Maybe<ReadonlyArray<Maybe<RcsbChemCompSynonyms>>>;
- readonly rcsb_chem_comp_target?: Maybe<ReadonlyArray<Maybe<RcsbChemCompTarget>>>;
- /** A unique identifier for the chemical definition in this container. */
- readonly rcsb_id: Scalars['String'];
- readonly rcsb_schema_container_identifiers?: Maybe<ReadonlyArray<Maybe<RcsbSchemaContainerIdentifiers>>>;
-};
-
-export type EmExperiment = {
- /**
- * The aggregation/assembly state of the imaged specimen.
- *
- * Allowable values:
- * 2D ARRAY, 3D ARRAY, CELL, FILAMENT, HELICAL ARRAY, PARTICLE, TISSUE
- */
- readonly aggregation_state?: Maybe<Scalars['String']>;
- /** Foreign key to the EM_ENTITY_ASSEMBLY category */
- readonly entity_assembly_id?: Maybe<Scalars['String']>;
- /** Placeholder ID. */
- readonly id?: Maybe<Scalars['String']>;
+ readonly injector_temperature?: Maybe<Scalars['Float']>;
+ /** Diameter in micrometres of jet stream of sample delivery */
+ readonly jet_diameter?: Maybe<Scalars['Float']>;
/**
- * The reconstruction method used in the EM experiment.
- *
- * Allowable values:
- * CRYSTALLOGRAPHY, HELICAL, SINGLE PARTICLE, SUBTOMOGRAM AVERAGING, TOMOGRAPHY
+ * Sample deliver driving force, e.g. Gas, Electronic Potential
+ *
+ * Examples:
+ * syringe, gas, electronic potential
+ *
*/
- readonly reconstruction_method?: Maybe<Scalars['String']>;
-};
-
-export type PdbxStructAssemblyProp = {
- /** The identifier for the assembly used in category PDBX_STRUCT_ASSEMBLY. */
- readonly assembly_id?: Maybe<Scalars['String']>;
- /** The identifier for the assembly used in category PDBX_STRUCT_ASSEMBLY. */
- readonly biol_id: Scalars['String'];
+ readonly power_by?: Maybe<Scalars['String']>;
/**
- * The property type for the assembly.
- *
- * Allowable values:
- * ABSA (A^2), MORE, SSA (A^2)
+ * Details of crystal growth and preparation of the crystals
+ *
+ * Examples:
+ * Crystals transfered to carrier solvent at room temperature
+ *
*/
- readonly type: Scalars['String'];
- /** The value of the assembly property. */
- readonly value?: Maybe<Scalars['String']>;
+ readonly preparation?: Maybe<Scalars['String']>;
};
-export type PdbxNmrSoftware = {
+export type PdbxSolnScatter = {
/**
- * The name of the authors of the software used in this
- * procedure.
- *
+ * The name of the buffer used for the sample in the solution scattering
+ * experiment.
+ *
* Examples:
- * Brunger, Guentert
+ * acetic acid
+ *
*/
- readonly authors?: Maybe<Scalars['String']>;
+ readonly buffer_name?: Maybe<Scalars['String']>;
/**
- * The purpose of the software.
- *
+ * The concentration range (mg/mL) of the complex in the
+ * sample used in the solution scattering experiment to
+ * determine the mean radius of structural elongation.
+ *
* Examples:
- * collection, processing, data analysis, structure solution, refinement, iterative matrix relaxation
+ * 0.7 - 14
+ *
*/
- readonly classification?: Maybe<Scalars['String']>;
+ readonly concentration_range?: Maybe<Scalars['String']>;
/**
- * The name of the software used for the task.
- *
+ * A list of the software used in the data analysis
+ *
* Examples:
- * ANSIG, AURELIA, AZARA, CHARMM, CoMAND, CORMA, DIANA, DYANA, DSPACE, DISGEO, DGII, DISMAN, DINOSAUR, DISCOVER, FELIX, FT_NMR, GROMOS, IRMA, MARDIGRAS, NMRPipe, SA, UXNMR, VNMR, X-PLOR, XWINNMR
+ * SCTPL5 GNOM
+ *
*/
- readonly name?: Maybe<Scalars['String']>;
+ readonly data_analysis_software_list?: Maybe<Scalars['String']>;
/**
- * An ordinal index for this category
- *
+ * A list of the software used in the data reduction
+ *
* Examples:
- * 1, 2
+ * OTOKO
+ *
*/
- readonly ordinal: Scalars['Int'];
+ readonly data_reduction_software_list?: Maybe<Scalars['String']>;
/**
- * The version of the software.
- *
- * Examples:
- * 940501.3, 2.1
+ * The particular radiation detector. In general this will be a
+ * manufacturer, description, model number or some combination of
+ * these.
*/
- readonly version?: Maybe<Scalars['String']>;
-};
-
-export type RcsbUniprotAnnotationAnnotationLineage = {
- /** Members of the annotation lineage as parent lineage depth (1-N) */
- readonly depth?: Maybe<Scalars['Int']>;
- /** Members of the annotation lineage as parent class identifiers. */
- readonly id?: Maybe<Scalars['String']>;
- /** Members of the annotation lineage as parent class names. */
- readonly name?: Maybe<Scalars['String']>;
-};
-
-export type Diffrn = {
+ readonly detector_specific?: Maybe<Scalars['String']>;
+ /** The general class of the radiation detector. */
+ readonly detector_type?: Maybe<Scalars['String']>;
/**
- * The mean hydrostatic pressure in kilopascals at which the
- * intensities were measured.
+ * The value of _pdbx_soln_scatter.id must
+ * uniquely identify the sample in the category PDBX_SOLN_SCATTER
*/
- readonly ambient_pressure?: Maybe<Scalars['Float']>;
+ readonly id: Scalars['String'];
/**
- * The mean temperature in kelvins at which the intensities were
- * measured.
+ * The maximum mean radius of structural elongation of the sample.
+ * In a given solute-solvent contrast, the radius of gyration
+ * R_G is a measure of structural elongation if the internal
+ * inhomogeneity of scattering densities has no effect. Guiner
+ * analysis at low Q give the R_G and the forward scattering at
+ * zero angle I(0).
+ *
+ * lnl(Q) = lnl(0) - R_G^2Q^2/3
+ *
+ * where
+ * Q = 4(pi)sin(theta/lamda)
+ * 2theta = scattering angle
+ * lamda = wavelength
+ *
+ * The above expression is valid in a QR_G range for extended
+ * rod-like particles. The relative I(0)/c values ( where
+ * c = sample concentration) for sample measurements in a
+ * constant buffer for a single sample data session, gives the
+ * relative masses of the protein(s) studied when referenced
+ * against a standard.
+ *
+ * see:
+ * O.Glatter & O.Kratky, (1982). Editors of "Small angle
+ * X-ray Scattering, Academic Press, New York.
+ * O.Kratky. (1963). X-ray small angle scattering with
+ * substances of biological interest in diluted solutions.
+ * Prog. Biophys. Chem., 13, 105-173.
+ * G.D.Wignall & F.S.Bates, (1987). The small-angle approximation
+ * of X-ray and neutron scatter from rigid rods of non-uniform
+ * cross section and finite length. J.Appl. Crystallog., 18, 452-460.
+ *
+ * If the structure is elongated, the mean radius of gyration
+ * of the cross-sectional structure R_XS and the mean cross sectional
+ * intensity at zero angle [I(Q).Q]_Q->0 is obtained from
+ * ln[I(Q).Q] = ln[l(Q).(Q)]_Q->0 - ((R_XS)^2Q^2)/2
*/
- readonly ambient_temp?: Maybe<Scalars['Float']>;
+ readonly max_mean_cross_sectional_radii_gyration?: Maybe<Scalars['Float']>;
/**
- * A description of special aspects of temperature control during
- * data collection.
+ * The estimated standard deviation for the
+ * minimum mean radius of structural elongation of the sample.
+ * In a given solute-solvent contrast, the radius of gyration
+ * R_G is a measure of structural elongation if the internal
+ * inhomogeneity of scattering densities has no effect. Guiner
+ * analysis at low Q give the R_G and the forward scattering at
+ * zero angle I(0).
+ *
+ * lnl(Q) = lnl(0) - R_G^2Q^2/3
+ *
+ * where
+ * Q = 4(pi)sin(theta/lamda)
+ * 2theta = scattering angle
+ * lamda = wavelength
+ *
+ * The above expression is valid in a QR_G range for extended
+ * rod-like particles. The relative I(0)/c values ( where
+ * c = sample concentration) for sample measurements in a
+ * constant buffer for a single sample data session, gives the
+ * relative masses of the protein(s) studied when referenced
+ * against a standard.
+ *
+ * see:
+ * O.Glatter & O.Kratky, (1982). Editors of "Small angle
+ * X-ray Scattering, Academic Press, New York.
+ * O.Kratky. (1963). X-ray small angle scattering with
+ * substances of biological interest in diluted solutions.
+ * Prog. Biophys. Chem., 13, 105-173.
+ * G.D.Wignall & F.S.Bates, (1987). The small-angle approximation
+ * of X-ray and neutron scatter from rigid rods of non-uniform
+ * cross section and finite length. J.Appl. Crystallog., 18, 452-460.
+ *
+ * If the structure is elongated, the mean radius of gyration
+ * of the cross-sectional structure R_XS and the mean cross sectional
+ * intensity at zero angle [I(Q).Q]_Q->0 is obtained from
+ * ln[I(Q).Q] = ln[l(Q).(Q)]_Q->0 - ((R_XS)^2Q^2)/2
*/
- readonly ambient_temp_details?: Maybe<Scalars['String']>;
+ readonly max_mean_cross_sectional_radii_gyration_esd?: Maybe<Scalars['Float']>;
/**
- * This data item is a pointer to _exptl_crystal.id in the
- * EXPTL_CRYSTAL category.
+ * The mean radius of structural elongation of the sample.
+ * In a given solute-solvent contrast, the radius of gyration
+ * R_G is a measure of structural elongation if the internal
+ * inhomogeneity of scattering densities has no effect. Guiner
+ * analysis at low Q gives the R_G and the forward scattering at
+ * zero angle I(0).
+ *
+ * lnl(Q) = lnl(0) - R_G^2Q^2/3
+ *
+ * where
+ * Q = 4(pi)sin(theta/lamda)
+ * 2theta = scattering angle
+ * lamda = wavelength
+ *
+ * The above expression is valid in a QR_G range for extended
+ * rod-like particles. The relative I(0)/c values ( where
+ * c = sample concentration) for sample measurements in a
+ * constant buffer for a single sample data session, gives the
+ * relative masses of the protein(s) studied when referenced
+ * against a standard.
+ *
+ * see: O.Glatter & O.Kratky, (1982). Editors of "Small angle
+ * X-ray Scattering, Academic Press, New York.
+ * O.Kratky. (1963). X-ray small angle scattering with
+ * substances of biological interest in diluted solutions.
+ * Prog. Biophys. Chem., 13, 105-173.
+ *
+ * G.D.Wignall & F.S.Bates, (1987). The small-angle approximation
+ * of X-ray and neutron scatter from rigid rods of non-uniform
+ * cross section and finite length. J.Appl. Crystallog., 18, 452-460.
+ *
+ * If the structure is elongated, the mean radius of gyration
+ * of the cross-sectional structure R_XS and the mean cross sectional
+ * intensity at zero angle [I(Q).Q]_Q->0 is obtained from
+ *
+ * ln[I(Q).Q] = ln[l(Q).(Q)]_Q->0 - ((R_XS)^2Q^2)/2
*/
- readonly crystal_id?: Maybe<Scalars['String']>;
+ readonly mean_guiner_radius?: Maybe<Scalars['Float']>;
/**
- * The physical device used to support the crystal during data
- * collection.
- *
- * Examples:
- * glass capillary, quartz capillary, fiber, metal loop
+ * The estimated standard deviation for the
+ * mean radius of structural elongation of the sample.
+ * In a given solute-solvent contrast, the radius of gyration
+ * R_G is a measure of structural elongation if the internal
+ * inhomogeneity of scattering densities has no effect. Guiner
+ * analysis at low Q give the R_G and the forward scattering at
+ * zero angle I(0).
+ *
+ * lnl(Q) = lnl(0) - R_G^2Q^2/3
+ *
+ * where
+ * Q = 4(pi)sin(theta/lamda)
+ * 2theta = scattering angle
+ * lamda = wavelength
+ *
+ * The above expression is valid in a QR_G range for extended
+ * rod-like particles. The relative I(0)/c values ( where
+ * c = sample concentration) for sample measurements in a
+ * constant buffer for a single sample data session, gives the
+ * relative masses of the protein(s) studied when referenced
+ * against a standard.
+ *
+ * see:
+ * O.Glatter & O.Kratky, (1982). Editors of "Small angle
+ * X-ray Scattering, Academic Press, New York.
+ * O.Kratky. (1963). X-ray small angle scattering with
+ * substances of biological interest in diluted solutions.
+ * Prog. Biophys. Chem., 13, 105-173.
+ * G.D.Wignall & F.S.Bates, (1987). The small-angle approximation
+ * of X-ray and neutron scatter from rigid rods of non-uniform
+ * cross section and finite length. J.Appl. Crystallog., 18, 452-460.
+ *
+ * If the structure is elongated, the mean radius of gyration
+ * of the cross-sectional structure R_XS and the mean cross sectional
+ * intensity at zero angle [I(Q).Q]_Q->0 is obtained from
+ * ln[I(Q).Q] = ln[l(Q).(Q)]_Q->0 - ((R_XS)^2Q^2)/2
*/
- readonly crystal_support?: Maybe<Scalars['String']>;
+ readonly mean_guiner_radius_esd?: Maybe<Scalars['Float']>;
/**
- * Special details of the diffraction measurement process. Should
- * include information about source instability, crystal motion,
- * degradation and so on.
- */
- readonly details?: Maybe<Scalars['String']>;
+ * The minimum mean radius of structural elongation of the sample.
+ * In a given solute-solvent contrast, the radius of gyration
+ * R_G is a measure of structural elongation if the internal
+ * inhomogeneity of scattering densities has no effect. Guiner
+ * analysis at low Q give the R_G and the forward scattering at
+ * zero angle I(0).
+ *
+ * lnl(Q) = lnl(0) - R_G^2Q^2/3
+ *
+ * where
+ * Q = 4(pi)sin(theta/lamda)
+ * 2theta = scattering angle
+ * lamda = wavelength
+ *
+ * The above expression is valid in a QR_G range for extended
+ * rod-like particles. The relative I(0)/c values ( where
+ * c = sample concentration) for sample measurements in a
+ * constant buffer for a single sample data session, gives the
+ * relative masses of the protein(s) studied when referenced
+ * against a standard.
+ *
+ * see:
+ * O.Glatter & O.Kratky, (1982). Editors of "Small angle
+ * X-ray Scattering, Academic Press, New York.
+ * O.Kratky. (1963). X-ray small angle scattering with
+ * substances of biological interest in diluted solutions.
+ * Prog. Biophys. Chem., 13, 105-173.
+ * G.D.Wignall & F.S.Bates, (1987). The small-angle approximation
+ * of X-ray and neutron scatter from rigid rods of non-uniform
+ * cross section and finite length. J.Appl. Crystallog., 18, 452-460.
+ *
+ * If the structure is elongated, the mean radius of gyration
+ * of the cross-sectional structure R_XS and the mean cross sectional
+ * intensity at zero angle [I(Q).Q]_Q->0 is obtained from
+ * ln[I(Q).Q] = ln[l(Q).(Q)]_Q->0 - ((R_XS)^2Q^2)/2
+ */
+ readonly min_mean_cross_sectional_radii_gyration?: Maybe<Scalars['Float']>;
/**
- * This data item uniquely identifies a set of diffraction
- * data.
+ * The estimated standard deviation for the
+ * minimum mean radius of structural elongation of the sample.
+ * In a given solute-solvent contrast, the radius of gyration
+ * R_G is a measure of structural elongation if the internal
+ * inhomogeneity of scattering densities has no effect. Guiner
+ * analysis at low Q give the R_G and the forward scattering at
+ * zero angle I(0).
+ *
+ * lnl(Q) = lnl(0) - R_G^2Q^2/3
+ *
+ * where
+ * Q = 4(pi)sin(theta/lamda)
+ * 2theta = scattering angle
+ * lamda = wavelength
+ *
+ * The above expression is valid in a QR_G range for extended
+ * rod-like particles. The relative I(0)/c values ( where
+ * c = sample concentration) for sample measurements in a
+ * constant buffer for a single sample data session, gives the
+ * relative masses of the protein(s) studied when referenced
+ * against a standard.
+ *
+ * see:
+ * O.Glatter & O.Kratky, (1982). Editors of "Small angle
+ * X-ray Scattering, Academic Press, New York.
+ * O.Kratky. (1963). X-ray small angle scattering with
+ * substances of biological interest in diluted solutions.
+ * Prog. Biophys. Chem., 13, 105-173.
+ * G.D.Wignall & F.S.Bates, (1987). The small-angle approximation
+ * of X-ray and neutron scatter from rigid rods of non-uniform
+ * cross section and finite length. J.Appl. Crystallog., 18, 452-460.
+ *
+ * If the structure is elongated, the mean radius of gyration
+ * of the cross-sectional structure R_XS and the mean cross sectional
+ * intensity at zero angle [I(Q).Q]_Q->0 is obtained from
+ *
+ * ln[I(Q).Q] = ln[l(Q).(Q)]_Q->0 - ((R_XS)^2Q^2)/2
*/
- readonly id: Scalars['String'];
+ readonly min_mean_cross_sectional_radii_gyration_esd?: Maybe<Scalars['Float']>;
+ /** The number of time frame solution scattering images used. */
+ readonly num_time_frames?: Maybe<Scalars['Int']>;
/**
- * Y/N if using serial crystallography experiment in which multiple crystals contribute to each diffraction frame in the experiment.
- *
+ * The length (or range) of the protein sample under study.
+ * If the solution structure is approximated as an elongated elliptical
+ * cyclinder the length L is determined from,
+ *
+ * L = sqrt [12( (R_G)^2 - (R_XS)^2 ) ]
+ *
+ * The length should also be given by
+ *
+ * L = pi I(0) / [ I(Q).Q]_Q->0
+ */
+ readonly protein_length?: Maybe<Scalars['String']>;
+ /** The pH value of the buffered sample. */
+ readonly sample_pH?: Maybe<Scalars['Float']>;
+ /** The beamline name used for the experiment */
+ readonly source_beamline?: Maybe<Scalars['String']>;
+ /** The instrumentation used on the beamline */
+ readonly source_beamline_instrument?: Maybe<Scalars['String']>;
+ /**
+ * The general class of the radiation source.
+ *
* Examples:
- * Y, N
+ * neutron source, synchrotron
+ *
*/
- readonly pdbx_serial_crystal_experiment?: Maybe<Scalars['String']>;
+ readonly source_class?: Maybe<Scalars['String']>;
+ /** The make, model, name or beamline of the source of radiation. */
+ readonly source_type?: Maybe<Scalars['String']>;
+ /**
+ * The temperature in kelvins at which the experiment
+ * was conducted
+ */
+ readonly temperature?: Maybe<Scalars['Float']>;
+ /**
+ * The type of solution scattering experiment carried out
+ *
+ * Allowable values:
+ * modelling, neutron, x-ray
+ *
+ */
+ readonly type?: Maybe<Scalars['String']>;
};
-export type PdbxNmrExptlSampleConditions = {
+export type PdbxSolnScatterModel = {
/**
- * The condition number as defined above.
- *
- * Examples:
- * 1, 2, 3
+ * A description of the conformer selection criteria
+ * used.
+ *
+ * Examples:
+ * The modelled scattering curves were assessed by calculation of the
+ * RG, RSX-1 and RXS-2 values in the same Q ranges
+ * used in the experimental Guinier fits. models were
+ * then ranked using a goodness-of-fit R-factor
+ * defined by analogy with protein crystallography
+ * and based on the experimental curves in the Q range
+ * extending to 1.4 nm-1.
+ *
*/
- readonly conditions_id: Scalars['String'];
+ readonly conformer_selection_criteria?: Maybe<Scalars['String']>;
/**
- * General details describing conditions of both the sample and the environment
- * during measurements.
- *
+ * A description of any additional details concerning the experiment.
+ *
* Examples:
- * The high salinity of the sample may have contributed to overheating of the sample during experiments with long saturation periods like the TOCSY experiments.
+ * Homology models were built for
+ * the 17 SCR domains and energy minimisations were
+ * performed to improve the connectivity in the fh model.
+ * triantennary complex-type carbohydrate structures
+ * (MAN3GLCNAC6GAL3FUC3NEUNAC1) were added to each of the
+ * N-linked glycosylation sites. a library of linker peptide
+ * conformations was used in domain modelling constrained
+ * by the solution scattering fits. modelling with the
+ * scattering data was also carried out by rotational
+ * search methods. the x-ray and neutron scattering curve
+ * I(Q) was calculated assuming a uniform scattering density
+ * for the spheres using the debye equation as adapted to
+ * spheres. x-ray curves were calculated from the hydrated
+ * sphere models without corrections for wavelength spread or
+ * beam divergence, while these corrections were applied for
+ * the neutron curves but now using unhydrated models.
+ *
*/
readonly details?: Maybe<Scalars['String']>;
/**
- * The ionic strength at which the NMR data were collected -in lieu of
- * this enter the concentration and identity of the salt in the sample.
- */
- readonly ionic_strength?: Maybe<Scalars['String']>;
- /**
- * Estimate of the standard error for the value for the sample ionic strength.
- *
+ * A list of the entries used to fit the model
+ * to the scattering data
+ *
* Examples:
- * 0.2
+ * PDB CODE 1HFI, 1HCC, 1HFH, 1VCC
+ *
*/
- readonly ionic_strength_err?: Maybe<Scalars['Float']>;
+ readonly entry_fitting_list?: Maybe<Scalars['String']>;
/**
- * Units for the value of the sample condition ionic strength..
- *
- * Allowable values:
- * M, Not defined, mM
+ * The value of _pdbx_soln_scatter_model.id must
+ * uniquely identify the sample in the category PDBX_SOLN_SCATTER_MODEL
*/
- readonly ionic_strength_units?: Maybe<Scalars['String']>;
+ readonly id: Scalars['String'];
/**
- * A descriptive label that uniquely identifies this set of sample conditions.
- *
+ * A description of the methods used in the modelling
+ *
* Examples:
- * conditions_1
+ * Constrained scattering fitting of homology models
+ *
*/
- readonly label?: Maybe<Scalars['String']>;
+ readonly method?: Maybe<Scalars['String']>;
+ /** The number of model conformers calculated. */
+ readonly num_conformers_calculated?: Maybe<Scalars['Int']>;
+ /** The number of model conformers submitted in the entry */
+ readonly num_conformers_submitted?: Maybe<Scalars['Int']>;
+ /** The index of the representative conformer among the submitted conformers for the entry */
+ readonly representative_conformer?: Maybe<Scalars['Int']>;
+ /** This data item is a pointer to _pdbx_soln_scatter.id in the PDBX_SOLN_SCATTER category. */
+ readonly scatter_id: Scalars['String'];
/**
- * The pH at which the NMR data were collected.
- *
+ * A list of the software authors
+ *
* Examples:
- * 3.1, 7.0
+ * MSI
+ *
*/
- readonly pH?: Maybe<Scalars['String']>;
+ readonly software_author_list?: Maybe<Scalars['String']>;
/**
- * Estimate of the standard error for the value for the sample pH.
- *
+ * A list of the software used in the modeeling
+ *
* Examples:
- * 0.05
- */
- readonly pH_err?: Maybe<Scalars['Float']>;
- /**
- * Units for the value of the sample condition pH.
- *
- * Allowable values:
- * Not defined, pD, pH, pH*
+ * INSIGHT II, HOMOLOGY, DISCOVERY, BIOPOLYMER, DELPHI
+ *
*/
- readonly pH_units?: Maybe<Scalars['String']>;
+ readonly software_list?: Maybe<Scalars['String']>;
+};
+
+export type PdbxStructAssembly = {
/**
- * The pressure at which NMR data were collected.
- *
+ * A description of special aspects of the macromolecular assembly.
+ *
* Examples:
- * 1, ambient, 1atm
+ * The icosahedral virus particle.
+ *
*/
- readonly pressure?: Maybe<Scalars['String']>;
+ readonly details?: Maybe<Scalars['String']>;
/**
- * Estimate of the standard error for the value for the sample pressure.
- *
- * Examples:
- * 0.01
+ * The value of _pdbx_struct_assembly.id must uniquely identify a record in
+ * the PDBX_STRUCT_ASSEMBLY list.
*/
- readonly pressure_err?: Maybe<Scalars['Float']>;
+ readonly id: Scalars['String'];
/**
- * The units of pressure at which NMR data were collected.
- *
- * Examples:
- * Pa, atm, Torr
+ * Provides details of the method used to determine or
+ * compute the assembly.
*/
- readonly pressure_units?: Maybe<Scalars['String']>;
+ readonly method_details?: Maybe<Scalars['String']>;
+ /** The number of polymer molecules in the assembly. */
+ readonly oligomeric_count?: Maybe<Scalars['Int']>;
/**
- * The temperature (in Kelvin) at which NMR data were
- * collected.
- *
+ * Provides the details of the oligomeric state of the assembly.
+ *
* Examples:
- * 298
+ * monomer, octameric, tetradecameric, eicosameric, 21-meric, 60-meric, 180-meric, helical
+ *
*/
- readonly temperature?: Maybe<Scalars['String']>;
+ readonly oligomeric_details?: Maybe<Scalars['String']>;
/**
- * Estimate of the standard error for the value for the sample temperature.
- *
- * Examples:
- * 0.2
+ * Candidate macromolecular assembly.
+ *
+ * Excludes the following cases classified in pdbx_struct_asembly.details:
+ *
+ * 'crystal asymmetric unit', 'crystal asymmetric unit, crystal frame', 'helical asymmetric unit',
+ * 'helical asymmetric unit, std helical frame','icosahedral 23 hexamer', 'icosahedral asymmetric unit',
+ * 'icosahedral asymmetric unit, std point frame','icosahedral pentamer', 'pentasymmetron capsid unit',
+ * 'point asymmetric unit', 'point asymmetric unit, std point frame','trisymmetron capsid unit',
+ * and 'deposited_coordinates'.
+ *
+ * Allowable values:
+ * N, Y
+ *
*/
- readonly temperature_err?: Maybe<Scalars['Float']>;
+ readonly rcsb_candidate_assembly?: Maybe<Scalars['String']>;
/**
- * Units for the value of the sample condition temperature.
- *
+ * A filtered description of the macromolecular assembly.
+ *
* Allowable values:
- * C, K, Not defined
+ * author_and_software_defined_assembly, author_defined_assembly, software_defined_assembly
+ *
*/
- readonly temperature_units?: Maybe<Scalars['String']>;
+ readonly rcsb_details?: Maybe<Scalars['String']>;
};
-export type Refine = {
+export type PdbxStructAssemblyAuthEvidence = {
+ /** This item references an assembly in pdbx_struct_assembly */
+ readonly assembly_id: Scalars['String'];
/**
- * The maximum isotropic displacement parameter (B value)
- * found in the coordinate set.
+ * Provides any additional information regarding the evidence of this assembly
+ *
+ * Examples:
+ * Homology to bacteriorhodopsin, Helical filament was observed by negative staining and Cryo-EM
+ *
*/
- readonly B_iso_max?: Maybe<Scalars['Float']>;
+ readonly details?: Maybe<Scalars['String']>;
/**
- * The mean isotropic displacement parameter (B value)
- * for the coordinate set.
+ * Provides the experimental method to determine the state of this assembly
+ *
+ * Allowable values:
+ * NMR Distance Restraints, NMR relaxation study, SAXS, assay for oligomerization, cross-linking, electron microscopy, equilibrium centrifugation, fluorescence resonance energy transfer, gel filtration, homology, immunoprecipitation, isothermal titration calorimetry, light scattering, mass spectrometry, microscopy, native gel electrophoresis, none, scanning transmission electron microscopy, surface plasmon resonance
+ *
*/
- readonly B_iso_mean?: Maybe<Scalars['Float']>;
+ readonly experimental_support?: Maybe<Scalars['String']>;
+ /** Identifies a unique record in pdbx_struct_assembly_auth_evidence. */
+ readonly id: Scalars['String'];
+};
+
+export type PdbxStructAssemblyGen = {
/**
- * The minimum isotropic displacement parameter (B value)
- * found in the coordinate set.
+ * This data item is a pointer to _pdbx_struct_assembly.id in the
+ * PDBX_STRUCT_ASSEMBLY category.
*/
- readonly B_iso_min?: Maybe<Scalars['Float']>;
+ readonly assembly_id?: Maybe<Scalars['String']>;
/**
- * The [1][1] element of the matrix that defines the overall
- * anisotropic displacement model if one was refined for this
- * structure.
+ * This data item is a pointer to _struct_asym.id in
+ * the STRUCT_ASYM category.
+ *
+ * This item may be expressed as a comma separated list of identifiers.
*/
- readonly aniso_B_1_1?: Maybe<Scalars['Float']>;
+ readonly asym_id_list?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
/**
- * The [1][2] element of the matrix that defines the overall
- * anisotropic displacement model if one was refined for this
- * structure.
+ * Identifies the operation of collection of operations
+ * from category PDBX_STRUCT_OPER_LIST.
+ *
+ * Operation expressions may have the forms:
+ *
+ * (1) the single operation 1
+ * (1,2,5) the operations 1, 2, 5
+ * (1-4) the operations 1,2,3 and 4
+ * (1,2)(3,4) the combinations of operations
+ * 3 and 4 followed by 1 and 2 (i.e.
+ * the cartesian product of parenthetical
+ * groups applied from right to left)
+ *
+ * Examples:
+ * (1), (1,2,5), (1-60), (1-60)(61)
+ *
*/
- readonly aniso_B_1_2?: Maybe<Scalars['Float']>;
+ readonly oper_expression?: Maybe<Scalars['String']>;
/**
- * The [1][3] element of the matrix that defines the overall
- * anisotropic displacement model if one was refined for this
- * structure.
+ * This data item is an ordinal index for the
+ * PDBX_STRUCT_ASSEMBLY category.
*/
- readonly aniso_B_1_3?: Maybe<Scalars['Float']>;
+ readonly ordinal: Scalars['Int'];
+};
+
+export type PdbxStructAssemblyProp = {
+ /** The identifier for the assembly used in category PDBX_STRUCT_ASSEMBLY. */
+ readonly assembly_id?: Maybe<Scalars['String']>;
+ /** The identifier for the assembly used in category PDBX_STRUCT_ASSEMBLY. */
+ readonly biol_id: Scalars['String'];
/**
- * The [2][2] element of the matrix that defines the overall
- * anisotropic displacement model if one was refined for this
- * structure.
+ * The property type for the assembly.
+ *
+ * Allowable values:
+ * ABSA (A^2), MORE, SSA (A^2)
+ *
*/
- readonly aniso_B_2_2?: Maybe<Scalars['Float']>;
+ readonly type: Scalars['String'];
+ /** The value of the assembly property. */
+ readonly value?: Maybe<Scalars['String']>;
+};
+
+export type PdbxStructOperList = {
/**
- * The [2][3] element of the matrix that defines the overall
- * anisotropic displacement model if one was refined for this
- * structure.
+ * This identifier code must uniquely identify a
+ * record in the PDBX_STRUCT_OPER_LIST list.
*/
- readonly aniso_B_2_3?: Maybe<Scalars['Float']>;
+ readonly id: Scalars['String'];
/**
- * The [3][3] element of the matrix that defines the overall
- * anisotropic displacement model if one was refined for this
- * structure.
+ * The [1][1] element of the 3x3 matrix component of the
+ * transformation operation.
*/
- readonly aniso_B_3_3?: Maybe<Scalars['Float']>;
+ readonly matrix_1_1?: Maybe<Scalars['Float']>;
/**
- * The correlation coefficient between the observed and
- * calculated structure factors for reflections included in
- * the refinement.
- *
- * The correlation coefficient is scale-independent and gives
- * an idea of the quality of the refined model.
- *
- * sum~i~(Fo~i~ Fc~i~ - <Fo><Fc>)
- * R~corr~ = ------------------------------------------------------------
- * SQRT{sum~i~(Fo~i~)^2^-<Fo>^2^} SQRT{sum~i~(Fc~i~)^2^-<Fc>^2^}
- *
- * Fo = observed structure factors
- * Fc = calculated structure factors
- * <> denotes average value
- *
- * summation is over reflections included in the refinement
+ * The [1][2] element of the 3x3 matrix component of the
+ * transformation operation.
*/
- readonly correlation_coeff_Fo_to_Fc?: Maybe<Scalars['Float']>;
+ readonly matrix_1_2?: Maybe<Scalars['Float']>;
/**
- * The correlation coefficient between the observed and
- * calculated structure factors for reflections not included
- * in the refinement (free reflections).
- *
- * The correlation coefficient is scale-independent and gives
- * an idea of the quality of the refined model.
- *
- * sum~i~(Fo~i~ Fc~i~ - <Fo><Fc>)
- * R~corr~ = ------------------------------------------------------------
- * SQRT{sum~i~(Fo~i~)^2^-<Fo>^2^} SQRT{sum~i~(Fc~i~)^2^-<Fc>^2^}
- *
- * Fo = observed structure factors
- * Fc = calculated structure factors
- * <> denotes average value
- *
- * summation is over reflections not included
- * in the refinement (free reflections)
+ * The [1][3] element of the 3x3 matrix component of the
+ * transformation operation.
*/
- readonly correlation_coeff_Fo_to_Fc_free?: Maybe<Scalars['Float']>;
- /** Description of special aspects of the refinement process. */
- readonly details?: Maybe<Scalars['String']>;
+ readonly matrix_1_3?: Maybe<Scalars['Float']>;
/**
- * Residual factor R for reflections that satisfy the resolution
- * limits established by _refine.ls_d_res_high and
- * _refine.ls_d_res_low and the observation limit established by
- * _reflns.observed_criterion, and that were used as the test
- * reflections (i.e. were excluded from the refinement) when the
- * refinement included the calculation of a 'free' R factor.
- * Details of how reflections were assigned to the working and
- * test sets are given in _reflns.R_free_details.
- *
- * sum|F~obs~ - F~calc~|
- * R = ---------------------
- * sum|F~obs~|
- *
- * F~obs~ = the observed structure-factor amplitudes
- * F~calc~ = the calculated structure-factor amplitudes
- *
- * sum is taken over the specified reflections
+ * The [2][1] element of the 3x3 matrix component of the
+ * transformation operation.
*/
- readonly ls_R_factor_R_free?: Maybe<Scalars['Float']>;
+ readonly matrix_2_1?: Maybe<Scalars['Float']>;
/**
- * The estimated error in _refine.ls_R_factor_R_free.
- * The method used to estimate the error is described in the
- * item _refine.ls_R_factor_R_free_error_details.
+ * The [2][2] element of the 3x3 matrix component of the
+ * transformation operation.
*/
- readonly ls_R_factor_R_free_error?: Maybe<Scalars['Float']>;
+ readonly matrix_2_2?: Maybe<Scalars['Float']>;
/**
- * Special aspects of the method used to estimated the error in
- * _refine.ls_R_factor_R_free.
+ * The [2][3] element of the 3x3 matrix component of the
+ * transformation operation.
*/
- readonly ls_R_factor_R_free_error_details?: Maybe<Scalars['String']>;
+ readonly matrix_2_3?: Maybe<Scalars['Float']>;
/**
- * Residual factor R for reflections that satisfy the resolution
- * limits established by _refine.ls_d_res_high and
- * _refine.ls_d_res_low and the observation limit established by
- * _reflns.observed_criterion, and that were used as the working
- * reflections (i.e. were included in the refinement) when the
- * refinement included the calculation of a 'free' R factor.
- * Details of how reflections were assigned to the working and
- * test sets are given in _reflns.R_free_details.
- *
- * _refine.ls_R_factor_obs should not be confused with
- * _refine.ls_R_factor_R_work; the former reports the results of a
- * refinement in which all observed reflections were used, the
- * latter a refinement in which a subset of the observed
- * reflections were excluded from refinement for the calculation
- * of a 'free' R factor. However, it would be meaningful to quote
- * both values if a 'free' R factor were calculated for most of
- * the refinement, but all of the observed reflections were used
- * in the final rounds of refinement; such a protocol should be
- * explained in _refine.details.
- *
- * sum|F~obs~ - F~calc~|
- * R = ---------------------
- * sum|F~obs~|
- *
- * F~obs~ = the observed structure-factor amplitudes
- * F~calc~ = the calculated structure-factor amplitudes
- *
- * sum is taken over the specified reflections
+ * The [3][1] element of the 3x3 matrix component of the
+ * transformation operation.
*/
- readonly ls_R_factor_R_work?: Maybe<Scalars['Float']>;
+ readonly matrix_3_1?: Maybe<Scalars['Float']>;
/**
- * Residual factor R for all reflections that satisfy the resolution
- * limits established by _refine.ls_d_res_high and
- * _refine.ls_d_res_low.
- *
- * sum|F~obs~ - F~calc~|
- * R = ---------------------
- * sum|F~obs~|
- *
- * F~obs~ = the observed structure-factor amplitudes
- * F~calc~ = the calculated structure-factor amplitudes
- *
- * sum is taken over the specified reflections
+ * The [3][2] element of the 3x3 matrix component of the
+ * transformation operation.
*/
- readonly ls_R_factor_all?: Maybe<Scalars['Float']>;
+ readonly matrix_3_2?: Maybe<Scalars['Float']>;
/**
- * Residual factor R for reflections that satisfy the resolution
- * limits established by _refine.ls_d_res_high and
- * _refine.ls_d_res_low and the observation limit established by
- * _reflns.observed_criterion.
- *
- * _refine.ls_R_factor_obs should not be confused with
- * _refine.ls_R_factor_R_work; the former reports the results of a
- * refinement in which all observed reflections were used, the
- * latter a refinement in which a subset of the observed
- * reflections were excluded from refinement for the calculation
- * of a 'free' R factor. However, it would be meaningful to quote
- * both values if a 'free' R factor were calculated for most of
- * the refinement, but all of the observed reflections were used
- * in the final rounds of refinement; such a protocol should be
- * explained in _refine.details.
- *
- * sum|F~obs~ - F~calc~|
- * R = ---------------------
- * sum|F~obs~|
- *
- * F~obs~ = the observed structure-factor amplitudes
- * F~calc~ = the calculated structure-factor amplitudes
- *
- * sum is taken over the specified reflections
+ * The [3][3] element of the 3x3 matrix component of the
+ * transformation operation.
*/
- readonly ls_R_factor_obs?: Maybe<Scalars['Float']>;
+ readonly matrix_3_3?: Maybe<Scalars['Float']>;
/**
- * The smallest value for the interplanar spacings for the
- * reflection data used in the refinement in angstroms. This is
- * called the highest resolution.
+ * A descriptive name for the transformation operation.
+ *
+ * Examples:
+ * 1_555, two-fold rotation
+ *
*/
- readonly ls_d_res_high?: Maybe<Scalars['Float']>;
+ readonly name?: Maybe<Scalars['String']>;
/**
- * The largest value for the interplanar spacings for
- * the reflection data used in the refinement in angstroms.
- * This is called the lowest resolution.
+ * The symmetry operation corresponding to the transformation operation.
+ *
+ * Examples:
+ * x,y,z, x+1/2,y,-z
+ *
*/
- readonly ls_d_res_low?: Maybe<Scalars['Float']>;
+ readonly symmetry_operation?: Maybe<Scalars['String']>;
/**
- * Type of matrix used to accumulate the least-squares derivatives.
- *
+ * A code to indicate the type of operator.
+ *
* Allowable values:
- * atomblock, diagonal, full, fullcycle, sparse, userblock
+ * 2D crystal symmetry operation, 3D crystal symmetry operation, build 2D crystal asymmetric unit, build 3D crystal asymmetric unit, build helical asymmetric unit, build point asymmetric unit, crystal symmetry operation, helical symmetry operation, identity operation, point symmetry operation, transform to 2D crystal frame, transform to 3D crystal frame, transform to crystal frame, transform to helical frame, transform to point frame
+ *
*/
- readonly ls_matrix_type?: Maybe<Scalars['String']>;
+ readonly type?: Maybe<Scalars['String']>;
/**
- * The number of parameters refined in the least-squares process.
- * If possible, this number should include some contribution from
- * the restrained parameters. The restrained parameters are
- * distinct from the constrained parameters (where one or more
- * parameters are linearly dependent on the refined value of
- * another). Least-squares restraints often depend on geometry or
- * energy considerations and this makes their direct contribution
- * to this number, and to the goodness-of-fit calculation,
- * difficult to assess.
+ * The [1] element of the three-element vector component of the
+ * transformation operation.
*/
- readonly ls_number_parameters?: Maybe<Scalars['Int']>;
+ readonly vector_1?: Maybe<Scalars['Float']>;
/**
- * The number of reflections that satisfy the resolution limits
- * established by _refine.ls_d_res_high and _refine.ls_d_res_low
- * and the observation limit established by
- * _reflns.observed_criterion, and that were used as the test
- * reflections (i.e. were excluded from the refinement) when the
- * refinement included the calculation of a 'free' R factor.
- * Details of how reflections were assigned to the working and
- * test sets are given in _reflns.R_free_details.
+ * The [2] element of the three-element vector component of the
+ * transformation operation.
*/
- readonly ls_number_reflns_R_free?: Maybe<Scalars['Int']>;
+ readonly vector_2?: Maybe<Scalars['Float']>;
/**
- * The number of reflections that satisfy the resolution limits
- * established by _refine.ls_d_res_high and _refine.ls_d_res_low
- * and the observation limit established by
- * _reflns.observed_criterion, and that were used as the working
- * reflections (i.e. were included in the refinement) when the
- * refinement included the calculation of a 'free' R factor.
- * Details of how reflections were assigned to the working and
- * test sets are given in _reflns.R_free_details.
+ * The [3] element of the three-element vector component of the
+ * transformation operation.
*/
- readonly ls_number_reflns_R_work?: Maybe<Scalars['Int']>;
+ readonly vector_3?: Maybe<Scalars['Float']>;
+};
+
+export type PdbxStructSpecialSymmetry = {
/**
- * The number of reflections that satisfy the resolution limits
- * established by _refine.ls_d_res_high and _refine.ls_d_res_low.
+ * Part of the identifier for the molecular component.
+ *
+ * This data item is a pointer to _atom_site.pdbx_PDB_model_num in the
+ * ATOM_SITE category.
*/
- readonly ls_number_reflns_all?: Maybe<Scalars['Int']>;
+ readonly PDB_model_num?: Maybe<Scalars['Int']>;
/**
- * The number of reflections that satisfy the resolution limits
- * established by _refine.ls_d_res_high and _refine.ls_d_res_low
- * and the observation limit established by
- * _reflns.observed_criterion.
+ * Part of the identifier for the molecular component.
+ *
+ * This data item is a pointer to _atom_site.auth_seq_id in the
+ * ATOM_SITE category.
*/
- readonly ls_number_reflns_obs?: Maybe<Scalars['Int']>;
+ readonly auth_seq_id?: Maybe<Scalars['String']>;
/**
- * The number of restrained parameters. These are parameters which
- * are not directly dependent on another refined parameter.
- * Restrained parameters often involve geometry or energy
- * dependencies.
- * See also _atom_site.constraints and _atom_site.refinement_flags.
- * A general description of refinement constraints may appear in
- * _refine.details.
+ * The value of _pdbx_struct_special_symmetry.id must uniquely identify
+ * each item in the PDBX_STRUCT_SPECIAL_SYMMETRY list.
+ *
+ * This is an integer serial number.
*/
- readonly ls_number_restraints?: Maybe<Scalars['Int']>;
+ readonly id: Scalars['Int'];
/**
- * The number of reflections that satisfy the resolution limits
- * established by _refine.ls_d_res_high and _refine.ls_d_res_low
- * and the observation limit established by
- * _reflns.observed_criterion, and that were used as the test
- * reflections (i.e. were excluded from the refinement) when the
- * refinement included the calculation of a 'free' R factor,
- * expressed as a percentage of the number of geometrically
- * observable reflections that satisfy the resolution limits.
+ * Part of the identifier for the molecular component.
+ *
+ * This data item is a pointer to _atom_site.label_asym_id in the
+ * ATOM_SITE category.
*/
- readonly ls_percent_reflns_R_free?: Maybe<Scalars['Float']>;
+ readonly label_asym_id?: Maybe<Scalars['String']>;
/**
- * The number of reflections that satisfy the resolution limits
- * established by _refine.ls_d_res_high and _refine.ls_d_res_low
- * and the observation limit established by
- * _reflns.observed_criterion, expressed as a percentage of the
- * number of geometrically observable reflections that satisfy
- * the resolution limits.
+ * Part of the identifier for the molecular component.
+ *
+ * This data item is a pointer to _atom_site.label_comp_id in the
+ * ATOM_SITE category.
*/
- readonly ls_percent_reflns_obs?: Maybe<Scalars['Float']>;
+ readonly label_comp_id?: Maybe<Scalars['String']>;
+};
+
+export type PdbxVrptSummary = {
/**
- * The ratio of the total number of observations of the
- * reflections that satisfy the resolution limits established by
- * _refine.ls_d_res_high and _refine.ls_d_res_low to the number
- * of crystallographically unique reflections that satisfy the
- * same limits.
+ * String for B_factor_type either "PARTIAL" or "FULL".
+ *
+ * Allowable values:
+ * FULL, PARTIAL
+ *
*/
- readonly ls_redundancy_reflns_all?: Maybe<Scalars['Float']>;
+ readonly B_factor_type?: Maybe<Scalars['String']>;
/**
- * The ratio of the total number of observations of the
- * reflections that satisfy the resolution limits established by
- * _refine.ls_d_res_high and _refine.ls_d_res_low and the
- * observation limit established by _reflns.observed_criterion to
- * the number of crystallographically unique reflections that
- * satisfy the same limits.
+ * REFMAC scaling parameter as reported in log output line starting 'bulk solvent: scale'.
+ * Example: X-ray entry specific, obtained in the eds step from REFMAC calculation.
*/
- readonly ls_redundancy_reflns_obs?: Maybe<Scalars['Float']>;
+ readonly Babinet_b?: Maybe<Scalars['Float']>;
/**
- * Weighted residual factor wR for reflections that satisfy the
- * resolution limits established by _refine.ls_d_res_high and
- * _refine.ls_d_res_low and the observation limit established by
- * _reflns.observed_criterion, and that were used as the test
- * reflections (i.e. were excluded from the refinement) when the
- * refinement included the calculation of a 'free' R factor.
- * Details of how reflections were assigned to the working and
- * test sets are given in _reflns.R_free_details.
- *
- * ( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^
- * wR = ( ---------------------------- )
- * ( sum|w Y~obs~^2^| )
- *
- * Y~obs~ = the observed amplitude specified by
- * _refine.ls_structure_factor_coef
- * Y~calc~ = the calculated amplitude specified by
- * _refine.ls_structure_factor_coef
- * w = the least-squares weight
- *
- * sum is taken over the specified reflections
+ * REFMAC scaling parameter as reported in log output line starting 'bulk solvent: scale'.
+ * Example: X-ray entry specific, obtained in the eds step from REFMAC calculation.
*/
- readonly ls_wR_factor_R_free?: Maybe<Scalars['Float']>;
+ readonly Babinet_k?: Maybe<Scalars['Float']>;
/**
- * Weighted residual factor wR for reflections that satisfy the
- * resolution limits established by _refine.ls_d_res_high and
- * _refine.ls_d_res_low and the observation limit established by
- * _reflns.observed_criterion, and that were used as the working
- * reflections (i.e. were included in the refinement) when the
- * refinement included the calculation of a 'free' R factor.
- * Details of how reflections were assigned to the working and
- * test sets are given in _reflns.R_free_details.
- *
- * ( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^
- * wR = ( ---------------------------- )
- * ( sum|w Y~obs~^2^| )
- *
- * Y~obs~ = the observed amplitude specified by
- * _refine.ls_structure_factor_coef
- * Y~calc~ = the calculated amplitude specified by
- * _refine.ls_structure_factor_coef
- * w = the least-squares weight
- *
- * sum is taken over the specified reflections
+ * The string "yes".
+ *
+ * Allowable values:
+ * yes
+ *
*/
- readonly ls_wR_factor_R_work?: Maybe<Scalars['Float']>;
- /** The maximum value for occupancy found in the coordinate set. */
- readonly occupancy_max?: Maybe<Scalars['Float']>;
- /** The minimum value for occupancy found in the coordinate set. */
- readonly occupancy_min?: Maybe<Scalars['Float']>;
+ readonly CA_ONLY?: Maybe<Scalars['String']>;
/**
- * Average figure of merit of phases of reflections not included
- * in the refinement.
- *
- * This value is derived from the likelihood function.
- *
- * FOM = I~1~(X)/I~0~(X)
- *
- * I~0~, I~1~ = zero- and first-order modified Bessel functions
- * of the first kind
- * X = sigma~A~ |E~o~| |E~c~|/SIGMA
- * E~o~, E~c~ = normalized observed and calculated structure
- * factors
- * sigma~A~ = <cos 2 pi s delta~x~> SQRT(Sigma~P~/Sigma~N~)
- * estimated using maximum likelihood
- * Sigma~P~ = sum~{atoms in model}~ f^2^
- * Sigma~N~ = sum~{atoms in crystal}~ f^2^
- * f = form factor of atoms
- * delta~x~ = expected error
- * SIGMA = (sigma~{E;exp}~)^2^ + epsilon [1-(sigma~A~)^2^]
- * sigma~{E;exp}~ = uncertainties of normalized observed
- * structure factors
- * epsilon = multiplicity of the diffracting plane
- *
- * Ref: Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997).
- * Acta Cryst. D53, 240-255.
+ * The overall R-factor from a DCC recalculation of an electron density map.
+ * Example: Currently value is rounded to 2 decimal places.
+ * X-ray entry specific, obtained from the DCC program.
*/
- readonly overall_FOM_free_R_set?: Maybe<Scalars['Float']>;
+ readonly DCC_R?: Maybe<Scalars['Float']>;
+ /** Either a decimal number or the string "NotAvailable". */
+ readonly DCC_Rfree?: Maybe<Scalars['Float']>;
/**
- * Average figure of merit of phases of reflections included in
- * the refinement.
- *
- * This value is derived from the likelihood function.
- *
- * FOM = I~1~(X)/I~0~(X)
- *
- * I~0~, I~1~ = zero- and first-order modified Bessel functions
- * of the first kind
- * X = sigma~A~ |E~o~| |E~c~|/SIGMA
- * E~o~, E~c~ = normalized observed and calculated structure
- * factors
- * sigma~A~ = <cos 2 pi s delta~x~> SQRT(Sigma~P~/Sigma~N~)
- * estimated using maximum likelihood
- * Sigma~P~ = sum~{atoms in model}~ f^2^
- * Sigma~N~ = sum~{atoms in crystal}~ f^2^
- * f = form factor of atoms
- * delta~x~ = expected error
- * SIGMA = (sigma~{E;exp}~)^2^ + epsilon [1-(sigma~A~)^2^]
- * sigma~{E;exp}~ = uncertainties of normalized observed
- * structure factors
- * epsilon = multiplicity of the diffracting plane
- *
- * Ref: Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997).
- * Acta Cryst. D53, 240-255.
+ * The pdbx_vrpt_software used by DCC to perform the recaluclation of the electron density maps.
+ *  Currently one of "CNS", "REFMAC" or "PHENIX".
+ * Example: X-ray entry specific, obtained from the DCC program.
*/
- readonly overall_FOM_work_R_set?: Maybe<Scalars['Float']>;
+ readonly DCC_refinement_program?: Maybe<Scalars['String']>;
/**
- * The overall standard uncertainty (estimated standard deviation)
- * of the displacement parameters based on a maximum-likelihood
- * residual.
- *
- * The overall standard uncertainty (sigma~B~)^2^ gives an idea
- * of the uncertainty in the B values of averagely defined
- * atoms (atoms with B values equal to the average B value).
- *
- * N~a~
- * (sigma~B~)^2^ = 8 ----------------------------------------------
- * sum~i~ {[1/Sigma - (E~o~)^2^ (1-m^2^)](SUM_AS)s^4^}
- *
- * N~a~ = number of atoms
- * E~o~ = normalized structure factors
- * m = figure of merit of phases of reflections
- * included in the summation
- * s = reciprocal-space vector
- *
- * SUM_AS = (sigma~A~)^2^/Sigma^2^
- * Sigma = (sigma~{E;exp}~)^2^ + epsilon [1-(sigma~A~)^2^]
- * sigma~{E;exp}~ = experimental uncertainties of normalized
- * structure factors
- * sigma~A~ = <cos 2 pi s delta~x~> SQRT(Sigma~P~/Sigma~N~)
- * estimated using maximum likelihood
- * Sigma~P~ = sum~{atoms in model}~ f^2^
- * Sigma~N~ = sum~{atoms in crystal}~ f^2^
- * f = atom form factor
- * delta~x~ = expected error
- * epsilon = multiplicity of diffracting plane
- *
- * summation is over all reflections included in refinement
- *
- * Ref: (sigma~A~ estimation) "Refinement of macromolecular
- * structures by the maximum-likelihood method",
- * Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997).
- * Acta Cryst. D53, 240-255.
- *
- * (SU B estimation) Murshudov, G. N. & Dodson,
- * E. J. (1997). Simplified error estimation a la
- * Cruickshank in macromolecular crystallography.
- * CCP4 Newsletter on Protein Crystallography, No. 33,
- * January 1997, pp. 31-39.
- *
- * http://www.ccp4.ac.uk/newsletters/newsletter33/murshudov.html
+ * The overall R factor from the EDS REFMAC calculation (no free set is used in this).
+ * Example: Currently value is rounded to 2 decimal places.
+ * X-ray entry specific, obtained in the eds step from REFMAC calculation.
*/
- readonly overall_SU_B?: Maybe<Scalars['Float']>;
+ readonly EDS_R?: Maybe<Scalars['Float']>;
/**
- * The overall standard uncertainty (estimated standard deviation)
- * of the positional parameters based on a maximum likelihood
- * residual.
- *
- * The overall standard uncertainty (sigma~X~)^2^ gives an
- * idea of the uncertainty in the position of averagely
- * defined atoms (atoms with B values equal to average B value)
- *
- * 3 N~a~
- * (sigma~X~)^2^ = ---------------------------------------------------------
- * 8 pi^2^ sum~i~ {[1/Sigma - (E~o~)^2^ (1-m^2^)](SUM_AS)s^2^}
- *
- * N~a~ = number of atoms
- * E~o~ = normalized structure factors
- * m = figure of merit of phases of reflections
- * included in the summation
- * s = reciprocal-space vector
- *
- * SUM_AS = (sigma~A~)^2^/Sigma^2^
- * Sigma = (sigma~{E;exp}~)^2^ + epsilon [1-(sigma~A~)^2^]
- * sigma~{E;exp}~ = experimental uncertainties of normalized
- * structure factors
- * sigma~A~ = <cos 2 pi s delta~x~> SQRT(Sigma~P~/Sigma~N~)
- * estimated using maximum likelihood
- * Sigma~P~ = sum~{atoms in model}~ f^2^
- * Sigma~N~ = sum~{atoms in crystal}~ f^2^
- * f = atom form factor
- * delta~x~ = expected error
- * epsilon = multiplicity of diffracting plane
- *
- * summation is over all reflections included in refinement
- *
- * Ref: (sigma_A estimation) "Refinement of macromolecular
- * structures by the maximum-likelihood method",
- * Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997).
- * Acta Cryst. D53, 240-255.
- *
- * (SU ML estimation) Murshudov, G. N. & Dodson,
- * E. J. (1997). Simplified error estimation a la
- * Cruickshank in macromolecular crystallography.
- * CCP4 Newsletter on Protein Crystallography, No. 33,
- * January 1997, pp. 31-39.
- *
- * http://www.ccp4.ac.uk/newsletters/newsletter33/murshudov.html
+ * The data high resolution diffraction limit, in Angstroms, found in the input structure factor file.
+ * Example: X-ray entry specific, obtained in the eds step.
*/
- readonly overall_SU_ML?: Maybe<Scalars['Float']>;
+ readonly EDS_resolution?: Maybe<Scalars['Float']>;
/**
- * The overall standard uncertainty (estimated standard deviation)
- * of the displacement parameters based on the crystallographic
- * R value, expressed in a formalism known as the dispersion
- * precision indicator (DPI).
- *
- * The overall standard uncertainty (sigma~B~) gives an idea
- * of the uncertainty in the B values of averagely defined
- * atoms (atoms with B values equal to the average B value).
- *
- * N~a~
- * (sigma~B~)^2^ = 0.65 ---------- (R~value~)^2^ (D~min~)^2^ C^-2/3^
- * (N~o~-N~p~)
- *
- *
- * N~a~ = number of atoms included in refinement
- * N~o~ = number of observations
- * N~p~ = number of parameters refined
- * R~value~ = conventional crystallographic R value
- * D~min~ = maximum resolution
- * C = completeness of data
- *
- * Ref: Cruickshank, D. W. J. (1999). Acta Cryst. D55, 583-601.
- *
- * Murshudov, G. N. & Dodson,
- * E. J. (1997). Simplified error estimation a la
- * Cruickshank in macromolecular crystallography.
- * CCP4 Newsletter on Protein Crystallography, No. 33,
- * January 1997, pp. 31-39.
- *
- * http://www.ccp4.ac.uk/newsletters/newsletter33/murshudov.html
+ * The data low resolution diffraction limit, in Angstroms, found in the input structure factor file.
+ * Example: X-ray entry specific, obtained in the eds step.
*/
- readonly overall_SU_R_Cruickshank_DPI?: Maybe<Scalars['Float']>;
+ readonly EDS_resolution_low?: Maybe<Scalars['Float']>;
/**
- * The overall standard uncertainty (estimated standard deviation)
- * of the displacement parameters based on the free R value.
- *
- * The overall standard uncertainty (sigma~B~) gives an idea
- * of the uncertainty in the B values of averagely defined
- * atoms (atoms with B values equal to the average B value).
- *
- * N~a~
- * (sigma~B~)^2^ = 0.65 ---------- (R~free~)^2^ (D~min~)^2^ C^-2/3^
- * (N~o~-N~p~)
- *
- *
- * N~a~ = number of atoms included in refinement
- * N~o~ = number of observations
- * N~p~ = number of parameters refined
- * R~free~ = conventional free crystallographic R value calculated
- * using reflections not included in refinement
- * D~min~ = maximum resolution
- * C = completeness of data
- *
- * Ref: Cruickshank, D. W. J. (1999). Acta Cryst. D55, 583-601.
- *
- * Murshudov, G. N. & Dodson,
- * E. J. (1997). Simplified error estimation a la
- * Cruickshank in macromolecular crystallography.
- * CCP4 Newsletter on Protein Crystallography, No. 33,
- * January 1997, pp. 31-39.
- *
- * http://www.ccp4.ac.uk/newsletters/newsletter33/murshudov.html
+ * Date in yyyy-mm-dd format when map was deposited to the EMDB.
+ * Reports produced by the validation server or during the initial deposition process should not have this item.
+ * If there is a difficulty parsing the item then "unknown" will be given.
*/
- readonly overall_SU_R_free?: Maybe<Scalars['Float']>;
+ readonly EMDB_deposition_date?: Maybe<Scalars['Date']>;
+ /** Either a decimal number or the string "NotAvailable". */
+ readonly EMDB_resolution?: Maybe<Scalars['Float']>;
/**
- * Details of the manner in which the cross validation
- * reflections were selected.
- *
- * Examples:
- * Random selection
+ * Fo,Fc correlation: The difference between the observed structure factors (Fo) and the
+ * calculated structure factors (Fc) measures the correlation between the PDB_model_num and the i
+ * experimental data.
+ * Example: X-ray entry specific, obtained in the eds step from REFMAC calculation.
*/
- readonly pdbx_R_Free_selection_details?: Maybe<Scalars['String']>;
+ readonly Fo_Fc_correlation?: Maybe<Scalars['Float']>;
/**
- * A flag for TLS refinements identifying the type of atomic displacement parameters stored
- * in _atom_site.B_iso_or_equiv.
- *
- * Allowable values:
- * LIKELY RESIDUAL, UNVERIFIED
+ * Each reflection has an intensity (I) and an uncertainty in measurement
+ * (sigma(I)), so I/sigma(I) is the signal-to-noise ratio. This
+ * ratio decreases at higher resolution. <I/sigma(I)> is the mean of individual I/sigma(I)
+ * values. Value for outer resolution shell is given in parentheses. In case
+ * structure factor amplitudes are deposited, Xtriage estimates the intensities
+ * first and then calculates this metric. When intensities are available in the
+ * deposited file, these are converted to amplitudes and then back to intensity
+ * estimate before calculating the metric.
+ * Example X-ray entry specific, calculated by Phenix Xtriage program.
*/
- readonly pdbx_TLS_residual_ADP_flag?: Maybe<Scalars['String']>;
+ readonly I_over_sigma?: Maybe<Scalars['String']>;
+ /** Either a decimal number or the string "NotAvailable". */
+ readonly PDB_R?: Maybe<Scalars['Float']>;
+ /** Either a decimal number or the string "NotAvailable". */
+ readonly PDB_Rfree?: Maybe<Scalars['Float']>;
/**
- * Average Fourier Shell Correlation (avgFSC) between model and
- * observed structure factors for reflections not included in refinement.
- *
- * The average FSC is a measure of the agreement between observed
- * and calculated structure factors.
- *
- * sum(N~i~ FSC~free-i~)
- * avgFSC~free~ = ---------------------
- * sum(N~i~)
- *
- *
- * N~i~ = the number of free reflections in the resolution shell i
- * FSC~free-i~ = FSC for free reflections in the i-th resolution shell calculated as:
- *
- * (sum(|F~o~| |F~c~| fom cos(phi~c~-phi~o~)))
- * FSC~free-i~ = -------------------------------------------
- * (sum(|F~o~|^2^) (sum(|F~c~|^2^)))^1/2^
- *
- * |F~o~| = amplitude of observed structure factor
- * |F~c~| = amplitude of calculated structure factor
- * phi~o~ = phase of observed structure factor
- * phi~c~ = phase of calculated structure factor
- * fom = figure of merit of the experimental phases.
- *
- * Summation of FSC~free-i~ is carried over all free reflections in the resolution shell.
- *
- * Summation of avgFSC~free~ is carried over all resolution shells.
- *
- *
- * Ref: Rosenthal P.B., Henderson R.
- * "Optimal determination of particle orientation, absolute hand,
- * and contrast loss in single-particle electron cryomicroscopy.
- * Journal of Molecular Biology. 2003;333(4):721-745, equation (A6).
+ * Date in yyyy-mm-dd format when structure was deposited to the PDB.
+ * Obtained from mmCIF table _database_PDB_rev item _database_PDB_rev.date_original
+ * Reports produced by the validation server or during the initial deposition process should not have this item.
+ * If there is a difficulty parsing the item then "unknown" will be given.
*/
- readonly pdbx_average_fsc_free?: Maybe<Scalars['Float']>;
+ readonly PDB_deposition_date?: Maybe<Scalars['Date']>;
+ /** Either a decimal number or the string "NotAvailable". */
+ readonly PDB_resolution?: Maybe<Scalars['Float']>;
+ /** Either a decimal number or the string "NotAvailable". */
+ readonly PDB_resolution_low?: Maybe<Scalars['Float']>;
/**
- * Overall average Fourier Shell Correlation (avgFSC) between model and
- * observed structure factors for all reflections.
- *
- * The average FSC is a measure of the agreement between observed
- * and calculated structure factors.
- *
- * sum(N~i~ FSC~i~)
- * avgFSC = ----------------
- * sum(N~i~)
- *
- *
- * N~i~ = the number of all reflections in the resolution shell i
- * FSC~i~ = FSC for all reflections in the i-th resolution shell calculated as:
- *
- * (sum(|F~o~| |F~c~| fom cos(phi~c~-phi~o~)))
- * FSC~i~ = -------------------------------------------
- * (sum(|F~o~|^2^) (sum(|F~c~|^2^)))^1/2^
- *
- * |F~o~| = amplitude of observed structure factor
- * |F~c~| = amplitude of calculated structure factor
- * phi~o~ = phase of observed structure factor
- * phi~c~ = phase of calculated structure factor
- * fom = figure of merit of the experimental phases.
- *
- * Summation of FSC~i~ is carried over all reflections in the resolution shell.
- *
- * Summation of avgFSC is carried over all resolution shells.
- *
- *
- * Ref: Rosenthal P.B., Henderson R.
- * "Optimal determination of particle orientation, absolute hand,
- * and contrast loss in single-particle electron cryomicroscopy.
- * Journal of Molecular Biology. 2003;333(4):721-745, equation (A6).
+ * Date in yyyy-mm-dd format when the structure was last revised by PDB.
+ * Obtained from mmCIF table _database_PDB_rev item _database_PDB_rev.date
+ * Reports produced by the validation server or during the initial depositon process should not have this item.
+ * If there is a difficulty parsing the item then "unknown" will be given.
*/
- readonly pdbx_average_fsc_overall?: Maybe<Scalars['Float']>;
+ readonly PDB_revision_date?: Maybe<Scalars['Date']>;
/**
- * Average Fourier Shell Correlation (avgFSC) between model and
- * observed structure factors for reflections included in refinement.
- *
- * The average FSC is a measure of the agreement between observed
- * and calculated structure factors.
- *
- * sum(N~i~ FSC~work-i~)
- * avgFSC~work~ = ---------------------
- * sum(N~i~)
- *
- *
- * N~i~ = the number of working reflections in the resolution shell i
- * FSC~work-i~ = FSC for working reflections in the i-th resolution shell calculated as:
- *
- * (sum(|F~o~| |F~c~| fom cos(phi~c~-phi~o~)))
- * FSC~work-i~ = -------------------------------------------
- * (sum(|F~o~|^2^) (sum(|F~c~|^2^)))^1/2^
- *
- * |F~o~| = amplitude of observed structure factor
- * |F~c~| = amplitude of calculated structure factor
- * phi~o~ = phase of observed structure factor
- * phi~c~ = phase of calculated structure factor
- * fom = figure of merit of the experimental phases.
- *
- * Summation of FSC~work-i~ is carried over all working reflections in the resolution shell.
- *
- * Summation of avgFSC~work~ is carried over all resolution shells.
- *
- *
- * Ref: Rosenthal P.B., Henderson R.
- * "Optimal determination of particle orientation, absolute hand,
- * and contrast loss in single-particle electron cryomicroscopy.
- * Journal of Molecular Biology. 2003;333(4):721-745, equation (A6).
+ * The last highest number that appears in mmCIF item _database_PDB_rev.num.
+ * Data items in the DATABASE_PDB_REV category record details about the history of the data block as archived by the Protein Data Bank (PDB).
+ * If the input mmCIF coordinate file lacks the information then a value of -1 is supplied.
*/
- readonly pdbx_average_fsc_work?: Maybe<Scalars['Float']>;
+ readonly PDB_revision_number?: Maybe<Scalars['Float']>;
/**
- * Value of F at "high end" of data cutoff.
- *
- * Examples:
- * 17600
+ * The MolProbity conformer-match quality parameter for RNA structures.
+ * Low values are worse.
+ * Example: Specific to structures that contain RNA polymers.
*/
- readonly pdbx_data_cutoff_high_absF?: Maybe<Scalars['Float']>;
+ readonly RNA_suiteness?: Maybe<Scalars['Float']>;
/**
- * Value of RMS |F| used as high data cutoff.
- *
- * Examples:
- * 205.1
+ * Result of absolute likelihood based Wilson scaling,
+ * The anisotropic B value of the data is determined using a likelihood based approach.
+ * The resulting B tensor is reported, the 3 diagonal values are given first, followed
+ * by the 3 off diagonal values.
+ * A large spread in (especially the diagonal) values indicates anisotropy.
+ * Example: X-ray entry specific, calculated by Phenix Xtriage program.
*/
- readonly pdbx_data_cutoff_high_rms_absF?: Maybe<Scalars['Float']>;
+ readonly Wilson_B_aniso?: Maybe<Scalars['String']>;
/**
- * Value of F at "low end" of data cutoff.
- *
- * Examples:
- * 0.30
+ * An estimate of the overall B-value of the structure, calculated from the diffraction data.
+ * Units Angstroms squared.
+ * It serves as an indicator of the degree of order in the crystal and the value is usually
+ * not hugely different from the average B-value calculated from the model.
+ * Example: X-ray entry specific, calculated by Phenix Xtriage program.
*/
- readonly pdbx_data_cutoff_low_absF?: Maybe<Scalars['Float']>;
+ readonly Wilson_B_estimate?: Maybe<Scalars['Float']>;
/**
- * An identifier for the diffraction data set used in this refinement.
- *
- * Multiple diffraction data sets specified as a comma separated list.
+ * Structures are judged in comparison to previously deposited PDB entries.
+ * The comparison is carried out by calculation of the percentile rank, i.e. the percentage of entries
+ * that are equal or poorer than this structure in terms of a quality indicator.
+ * Percentile ranks range from 0 (the worst) to 100 (the best).
*/
- readonly pdbx_diffrn_id?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
+ readonly absolute_percentile_DCC_Rfree?: Maybe<Scalars['Float']>;
/**
- * Whether the structure was refined with indvidual
- * isotropic, anisotropic or overall temperature factor.
- *
- * Examples:
- * Isotropic, Overall
+ * Structures are judged in comparison to previously deposited PDB entries.
+ * The comparison is carried out by calculation of the percentile rank, i.e. the percentage of entries
+ * that are equal or poorer than this structure in terms of a quality indicator.
+ * Percentile ranks range from 0 (the worst) to 100 (the best).
*/
- readonly pdbx_isotropic_thermal_model?: Maybe<Scalars['String']>;
+ readonly absolute_percentile_RNA_suiteness?: Maybe<Scalars['Float']>;
/**
- * Whether the cross validataion method was used through
- * out or only at the end.
- *
- * Examples:
- * FREE R-VALUE
+ * Structures are judged in comparison to previously deposited PDB entries.
+ * The comparison is carried out by calculation of the percentile rank, i.e. the percentage of entries
+ * that are equal or poorer than this structure in terms of a quality indicator.
+ * Percentile ranks range from 0 (the worst) to 100 (the best).
*/
- readonly pdbx_ls_cross_valid_method?: Maybe<Scalars['String']>;
- /** Data cutoff (SIGMA(F)) */
- readonly pdbx_ls_sigma_F?: Maybe<Scalars['Float']>;
- /** Data cutoff (SIGMA(F^2)) */
- readonly pdbx_ls_sigma_Fsqd?: Maybe<Scalars['Float']>;
- /** Data cutoff (SIGMA(I)) */
- readonly pdbx_ls_sigma_I?: Maybe<Scalars['Float']>;
+ readonly absolute_percentile_clashscore?: Maybe<Scalars['Float']>;
/**
- * Method(s) used to determine the structure.
- *
- * Examples:
- * AB INITIO PHASING, DM, ISAS, ISIR, ISIRAS, MAD, MIR, MIRAS, MR, SIR, SIRAS
+ * Structures are judged in comparison to previously deposited PDB entries.
+ * The comparison is carried out by calculation of the percentile rank, i.e. the percentage of entries
+ * that are equal or poorer than this structure in terms of a quality indicator.
+ * Percentile ranks range from 0 (the worst) to 100 (the best).
*/
- readonly pdbx_method_to_determine_struct?: Maybe<Scalars['String']>;
+ readonly absolute_percentile_percent_RSRZ_outliers?: Maybe<Scalars['Float']>;
/**
- * Overall estimated standard uncertainties of positional
- * parameters based on R value.
+ * Structures are judged in comparison to previously deposited PDB entries.
+ * The comparison is carried out by calculation of the percentile rank, i.e. the percentage of entries
+ * that are equal or poorer than this structure in terms of a quality indicator.
+ * Percentile ranks range from 0 (the worst) to 100 (the best).
*/
- readonly pdbx_overall_ESU_R?: Maybe<Scalars['Float']>;
- /** Overall estimated standard uncertainties of positional parameters based on R free value. */
- readonly pdbx_overall_ESU_R_Free?: Maybe<Scalars['Float']>;
+ readonly absolute_percentile_percent_ramachandran_outliers?: Maybe<Scalars['Float']>;
/**
- * The overall standard uncertainty (estimated standard deviation)
- * of the displacement parameters based on the crystallographic
- * R value, expressed in a formalism known as the dispersion
- * precision indicator (DPI).
- *
- * Ref: Blow, D (2002) Acta Cryst. D58, 792-797
+ * Structures are judged in comparison to previously deposited PDB entries.
+ * The comparison is carried out by calculation of the percentile rank, i.e. the percentage of entries
+ * that are equal or poorer than this structure in terms of a quality indicator.
+ * Percentile ranks range from 0 (the worst) to 100 (the best).
*/
- readonly pdbx_overall_SU_R_Blow_DPI?: Maybe<Scalars['Float']>;
+ readonly absolute_percentile_percent_rotamer_outliers?: Maybe<Scalars['Float']>;
/**
- * The overall standard uncertainty (estimated standard deviation)
- * of the displacement parameters based on the crystallographic
- * R-free value, expressed in a formalism known as the dispersion
- * precision indicator (DPI).
- *
- * Ref: Blow, D (2002) Acta Cryst. D58, 792-797
+ * The number of acentric reflections that Xtriage identifies as outliers on the basis
+ * of Wilson statistics. Note that if pseudo translational symmetry is present,
+ * a large number of 'outliers' will be present.
+ * Example: X-ray entry specific, calculated by Phenix Xtriage program.
*/
- readonly pdbx_overall_SU_R_free_Blow_DPI?: Maybe<Scalars['Float']>;
+ readonly acentric_outliers?: Maybe<Scalars['Int']>;
/**
- * The overall standard uncertainty (estimated standard deviation)
- * of the displacement parameters based on the crystallographic
- * R-free value, expressed in a formalism known as the dispersion
- * precision indicator (DPI).
- *
- * Ref: Cruickshank, D. W. J. (1999). Acta Cryst. D55, 583-601.
- */
- readonly pdbx_overall_SU_R_free_Cruickshank_DPI?: Maybe<Scalars['Float']>;
+ * The overall root mean square of the Z-score for deviations of bond angles in comparison to
+ * "standard geometry" made using the MolProbity dangle program.
+ * Standard geometry parameters are taken from Engh and Huber (2001) and Parkinson et al. (1996).
+ * This value is for all chains in the structure.
+ */
+ readonly angles_RMSZ?: Maybe<Scalars['Float']>;
+ /** The proportion of all non hydrogen atoms within density. */
+ readonly atom_inclusion_all_atoms?: Maybe<Scalars['Float']>;
+ /** The proportion of backbone atoms within density. */
+ readonly atom_inclusion_backbone?: Maybe<Scalars['Float']>;
+ /**
+ * The steps that were attempted by the validation pipeline software.
+ * A step typically involves running a 3rd party validation tool, for instance "mogul"
+ * Each step that was successfully completed will result in a pdbx_vrpt_software element in the pdbx_vrpt_sotfware_notused list.
+ */
+ readonly attempted_validation_steps?: Maybe<Scalars['String']>;
+ /** The resolution from the intersection of the author provided fsc and the indicator curve halfbit. */
+ readonly author_provided_fsc_resolution_by_cutoff_halfbit?: Maybe<Scalars['Float']>;
+ /** The resolution from the intersection of the author provided fsc and the indicator curve onebit. */
+ readonly author_provided_fsc_resolution_by_cutoff_onebit?: Maybe<Scalars['Float']>;
+ /** The resolution from the intersection of the author provided fsc and the indicator curve 0.5. */
+ readonly author_provided_fsc_resolution_by_cutoff_pt_5?: Maybe<Scalars['Float']>;
+ /** The resolution from the intersection of the author provided fsc and the indicator curve 0.143. */
+ readonly author_provided_fsc_resolution_by_cutoff_pt_143?: Maybe<Scalars['Float']>;
+ /** The resolution from the intersection of the author provided fsc and the indicator curve 0.333. */
+ readonly author_provided_fsc_resolution_by_cutoff_pt_333?: Maybe<Scalars['Float']>;
+ /** The resolution from the intersection of the author provided fsc and the indicator curve threesigma. */
+ readonly author_provided_fsc_resolution_by_cutoff_threesigma?: Maybe<Scalars['Float']>;
+ /**
+ * The overall root mean square of the Z-score for deviations of bond lengths in comparison to
+ * "standard geometry" made using the MolProbity dangle program.
+ * Standard geometry parameters are taken from Engh and Huber (2001) and Parkinson et al. (1996).
+ * This value is for all chains in the structure.
+ */
+ readonly bonds_RMSZ?: Maybe<Scalars['Float']>;
+ /**
+ * REFMAC scaling parameter as reported in log output line starting
+ * 'Partial structure 1: scale.'
+ * Example: X-ray entry specific, obtained in the eds step from REFMAC calculation.
+ */
+ readonly bulk_solvent_b?: Maybe<Scalars['Float']>;
+ /**
+ * REFMAC scaling parameter as reported in log output line starting
+ * 'Partial structure 1: scale.'
+ * Example: X-ray entry specific, obtained in the eds step from REFMAC calculation.
+ */
+ readonly bulk_solvent_k?: Maybe<Scalars['Float']>;
+ /** The resolution from the intersection of the fsc curve generated by from the provided halfmaps and the indicator curve halfbit. */
+ readonly calculated_fsc_resolution_by_cutoff_halfbit?: Maybe<Scalars['Float']>;
+ /** The resolution from the intersection of the fsc curve generated by from the provided halfmaps and the indicator curve onebit. */
+ readonly calculated_fsc_resolution_by_cutoff_onebit?: Maybe<Scalars['Float']>;
+ /** The resolution from the intersection of the fsc curve generated by from the provided halfmaps and the indicator curve 0.5. */
+ readonly calculated_fsc_resolution_by_cutoff_pt_5?: Maybe<Scalars['Float']>;
+ /** The resolution from the intersection of the fsc curve generated by from the provided halfmaps and the indicator curve 0.143. */
+ readonly calculated_fsc_resolution_by_cutoff_pt_143?: Maybe<Scalars['Float']>;
+ /** The resolution from the intersection of the fsc curve generated by from the provided halfmaps and the indicator curve 0.333. */
+ readonly calculated_fsc_resolution_by_cutoff_pt_333?: Maybe<Scalars['Float']>;
+ /** The resolution from the intersection of the fsc curve generated by from the provided halfmaps and the indicator curve threesigma. */
+ readonly calculated_fsc_resolution_by_cutoff_threesigma?: Maybe<Scalars['Float']>;
+ /**
+ * The version of CCP4 suite pdbx_vrpt_sotfware_notused used in the analysis.
+ * Example: X-ray entry specific, obtained from the eds step.
+ */
+ readonly ccp4version?: Maybe<Scalars['String']>;
+ /**
+ * The number of centric reflections that Xtriage identifies as outliers.
+ * Example: X-ray entry specific, calculated by Phenix Xtriage program.
+ */
+ readonly centric_outliers?: Maybe<Scalars['Float']>;
+ /**
+ * Overall completeness of the chemical shift assignments for the well-defined
+ * regions of the structure.
+ */
+ readonly chemical_shift_completeness?: Maybe<Scalars['Float']>;
+ /**
+ * Overall completeness of the chemical shift assignments for the full
+ * macromolecule or complex as suggested by the molecular description of an entry
+ * (whether some portion of it is modelled or not).
+ */
+ readonly chemical_shift_completeness_full_length?: Maybe<Scalars['Float']>;
+ /**
+ * The filename for the input chemical shifts file given to the validation pipeline.
+ * Not reported for runs at the annotation or release stage.
+ */
+ readonly chemical_shifts_input_filename?: Maybe<Scalars['String']>;
+ /**
+ * This score is derived from the number of pairs of atoms in the PDB_model_num that are unusually close to each other.
+ * It is calculated by the MolProbity pdbx_vrpt_software and expressed as the number or such clashes per thousand atoms.
+ * For structures determined by NMR the clashscore value here will only consider label_atom_id pairs in the
+ * well-defined (core) residues from ensemble analysis.
+ */
+ readonly clashscore?: Maybe<Scalars['Float']>;
+ /** Only given for structures determined by NMR. The MolProbity pdbx_vrpt_clashes score for all label_atom_id pairs. */
+ readonly clashscore_full_length?: Maybe<Scalars['Float']>;
+ /** The recommended contour level for the primary map of this deposition. */
+ readonly contour_level_primary_map?: Maybe<Scalars['String']>;
+ /**
+ * The filename for the input mmCIF coordinate file given to the validation pipeline.
+ * Not reported for runs at the annotation or release stage.
+ */
+ readonly coordinates_input_filename?: Maybe<Scalars['String']>;
+ /**
+ * Diagnostic message from the wrapper of Cyrange software which identifies the
+ * well-defined cores (domains) of NMR protein structures.
+ */
+ readonly cyrange_error?: Maybe<Scalars['String']>;
+ /** Total number of well-defined cores (domains) identified by Cyrange */
+ readonly cyrange_number_of_domains?: Maybe<Scalars['Int']>;
+ /** Reference for the Cyrange software. */
+ readonly cyrange_version?: Maybe<Scalars['String']>;
+ /**
+ * The ratio (Bmax ‑ Bmin) / Bmean where Bmax, Bmin and Bmean are computed from the B-values
+ * associated with the principal axes of the anisotropic thermal ellipsoid.
+ * This ratio is usually less than 0.5; for only 1% of PDB entries it is more than 1.0 (Read et al., 2011).
+ * Example: X-ray entry specific, obtained from the Xtriage program.
+ */
+ readonly data_anisotropy?: Maybe<Scalars['Float']>;
+ /** A percentage, Normally percent proportion of the total number. Between 0% and 100%. */
+ readonly data_completeness?: Maybe<Scalars['Float']>;
+ /**
+ * An identifier for the map
+ * For released or annotated structures this will be the EMDB ID EMD-\d{4-5} eg "EMD-1001", "EMD-12325"
+ */
+ readonly emdb_id?: Maybe<Scalars['String']>;
+ /**
+ * The resolution bin limit in Angstroms for PDB depositions used in the comparison when calculating
+ * the attribute "relative-percentile-DCC_Rfree".
+ * Note that the "high_resol_relative_percentile_DCC_Rfree" value is numerically smaller than the
+ * corresponding low-* value.
+ * Example: X-ray entry specific, produced by the percentiles step of the validation pipeline software.
+ */
+ readonly high_resol_relative_percentile_DCC_Rfree?: Maybe<Scalars['Float']>;
+ /**
+ * The resolution bin limit in Angstroms for PDB depositions used in the comparison when calculating
+ * the attribute "relative-percentile-RNAsuiteness".
+ * Note that the "high_resol_relative_percentile_RNA_suiteness" value is numerically smaller than the
+ * corresponding low value.
+ * Example: Specific to entries that contain RNA polymers (and have a RNA_suiteness attribute),
+ * and have been determined by X-ray crystallography.
+ * Produced by the percentiles step of the validation pipeline software.
+ */
+ readonly high_resol_relative_percentile_RNA_suiteness?: Maybe<Scalars['Float']>;
+ /**
+ * The resolution bin limit in Angstroms for PDB depositions used in the comparison when calculating
+ * the attribute "relative-percentile-clashscore".
+ * Note that the "high_resol_relative_percentile_clashscore" value is numerically smaller than the
+ * corresponding low value.
+ * Example: Specific to that have a clashscore attribute and have been determined by X-ray crystallography.
+ * Produced by the percentiles step of the validation pipeline software.
+ */
+ readonly high_resol_relative_percentile_clashscore?: Maybe<Scalars['Float']>;
+ /**
+ * The resolution bin limit in Angstroms for PDB depositions used in the comparison when calculating
+ * the attribute "relative-percentile-percent-RSRZ-outliers".
+ * Note that the "high_resol_relative_percentile_percent_RSRZ_outliers" value is numerically smaller than the
+ * corresponding low-* value.
+ * Example: X-ray entry specific, produced by the percentiles step of the validation pipeline software.
+ */
+ readonly high_resol_relative_percentile_percent_RSRZ_outliers?: Maybe<Scalars['Float']>;
+ /**
+ * The resolution bin limit in Angstroms for PDB depositions used in the comparison when calculating
+ * the attribute "relative-percentile-percent-rama-outliers".
+ * Note that the "high_resol_relative_percentile_percent_ramachandran_outliers" value is numerically smaller than the
+ * corresponding low value.
+ * Example: Specific to structures that have a percent_ramachandran_outliers attribute and have been determined by X-ray crystallography.
+ * Produced by the percentiles step of the validation pipeline software.
+ */
+ readonly high_resol_relative_percentile_percent_ramachandran_outliers?: Maybe<Scalars['Float']>;
+ /**
+ * The resolution bin limit in Angstroms for PDB depositions used in the comparison when calculating
+ * the attribute "relative-percentile-percent-rota-outliers".
+ * Note that the "high_resol_relative_percentile_percent_rotamer_outliers" value is numerically smaller than the
+ * corresponding low value.
+ * Example: Specific to that have a percent_rotamer_outliers attribute and have been determined by X-ray crystallography.
+ * Produced by the percentiles step of the validation pipeline software.
+ */
+ readonly high_resol_relative_percentile_percent_rotamer_outliers?: Maybe<Scalars['Float']>;
+ /**
+ * The string "yes".
+ *
+ * Allowable values:
+ * yes
+ *
+ */
+ readonly ligands_for_buster_report?: Maybe<Scalars['String']>;
+ /**
+ * The resolution bin limit in Angstroms for PDB depositions used in the comparison when calculating
+ * the attribute "relative-percentile-DCC_Rfree".
+ * Note that the "low_resol_relative_percentile_DCC_Rfree" value is numerically greater than the
+ * corresponding high value.
+ * Example: X-ray entry specific, produced by the percentiles step of the validation pipeline software.
+ */
+ readonly low_resol_relative_percentile_DCC_Rfree?: Maybe<Scalars['Float']>;
+ /**
+ * The resolution bin limit in Angstroms for PDB depositions used in the comparison when calculating
+ * the attribute "relative-percentile-RNAsuiteness".
+ * Note that the "low_resol_relative_percentile_RNA_suiteness" value is numerically greater than the
+ * corresponding high value.
+ * Example: Specific to entries that contain RNA polymers (and have a RNA_suiteness attribute),
+ * and have been determined by X-ray crystallography.
+ * Produced by the percentiles step of the validation pipeline software.
+ */
+ readonly low_resol_relative_percentile_RNA_suiteness?: Maybe<Scalars['Float']>;
+ /**
+ * The resolution bin limit in Angstroms for PDB depositions used in the comparison when calculating
+ * the attribute "relative-percentile-clashscore".
+ * Note that the "low_resol_relative_percentile_clashscore" value is numerically greater than the
+ * corresponding high value.
+ * Example: Specific to that have a clashscore attribute and have been determined by X-ray crystallography.
+ * Produced by the percentiles step of the validation pipeline software.
+ */
+ readonly low_resol_relative_percentile_clashscore?: Maybe<Scalars['Float']>;
+ /**
+ * The resolution bin limit in Angstroms for PDB depositions used in the comparison when calculating
+ * the attribute "relative-percentile-percent-RSRZ-outliers".
+ * Note that the "low_resol_relative_percentile_percent_RSRZ_outliers" value is numerically greater than the
+ * corresponding high value.
+ * Example: X-ray entry specific, produced by the percentiles step of the validation pipeline software.
+ */
+ readonly low_resol_relative_percentile_percent_RSRZ_outliers?: Maybe<Scalars['Float']>;
+ /**
+ * The resolution bin limit in Angstroms for PDB depositions used in the comparison when calculating
+ * the attribute "relative-percentile-percent-rama-outliers".
+ * Note that the "low_resol_relative_percentile_percent_ramachandran_outliers" value is numerically greater than the
+ * corresponding high value.
+ * Example: Specific to that have a percent_ramachandran_outliers attribute and have been determined by X-ray crystallography.
+ * Produced by the percentiles step of the validation pipeline software.
+ */
+ readonly low_resol_relative_percentile_percent_ramachandran_outliers?: Maybe<Scalars['Float']>;
+ /**
+ * The resolution bin limit in Angstroms for PDB depositions used in the comparison when calculating
+ * the attribute "relative-percentile-percent-rota-outliers".
+ * Note that the "low_resol_relative_percentile_percent_rotamer_outliers" value is numerically greater than the
+ * corresponding high value.
+ * Example: Specific to that have a percent_rotamer_outliers attribute and have been determined by X-ray crystallography.
+ * Produced by the percentiles step of the validation pipeline software.
+ */
+ readonly low_resol_relative_percentile_percent_rotamer_outliers?: Maybe<Scalars['Float']>;
+ /**
+ * For each Cyrange well-defined core ("cyrange_domain") the id of the PDB_model_num which is most
+ * similar to other models as measured by pairwise RMSDs over the domain.
+ * For the whole entry ("Entry"), the medoid PDB_model_num of the largest core is taken as an overall
+ * representative of the structure.
+ */
+ readonly medoid_model?: Maybe<Scalars['Int']>;
+ /**
+ * A flag indicating if all models in the NMR ensemble contain the exact
+ * same atoms ("True") or if the models differ in this respect ("False").
+ */
+ readonly nmr_models_consistency_flag?: Maybe<Scalars['String']>;
+ /** Diagnostic message from the wrapper of NMRClust software which clusters NMR models. */
+ readonly nmrclust_error?: Maybe<Scalars['String']>;
+ /** Total number of clusters in the NMR ensemble identified by NMRClust. */
+ readonly nmrclust_number_of_clusters?: Maybe<Scalars['Int']>;
+ /**
+ * Number of models analysed by NMRClust - should in almost all cases be the
+ * same as the number of models in the NMR ensemble.
+ */
+ readonly nmrclust_number_of_models?: Maybe<Scalars['Int']>;
+ /** Number of models that do not belong to any cluster as deemed by NMRClust. */
+ readonly nmrclust_number_of_outliers?: Maybe<Scalars['Int']>;
+ /** Overall representative PDB_model_num of the NMR ensemble as identified by NMRClust. */
+ readonly nmrclust_representative_model?: Maybe<Scalars['Int']>;
+ /** Reference for the NMRClust software. */
+ readonly nmrclust_version?: Maybe<Scalars['String']>;
+ /**
+ * The string "yes".
+ *
+ * Allowable values:
+ * yes
+ *
+ */
+ readonly no_ligands_for_buster_report?: Maybe<Scalars['String']>;
+ /**
+ * The string "yes".
+ *
+ * Allowable values:
+ * yes
+ *
+ */
+ readonly no_ligands_for_mogul?: Maybe<Scalars['String']>;
+ /**
+ * Will be set to "true" if no property was found to do percentile analysis on.
+ * Please note that currently due to a bug that this attribute is "true" erronously for NMR structures.
+ */
+ readonly no_percentile_property?: Maybe<Scalars['String']>;
+ /**
+ * This is the number of hydrogen atoms added and optimized by the MolProbity reduce pdbx_vrpt_software as part of the
+ * all-atom clashscore.
+ */
+ readonly num_H_reduce?: Maybe<Scalars['Float']>;
+ /**
+ * The number of PDB depositions used in the comparison when calculating the attribute
+ * "absolute-percentile-DCC_Rfree".
+ * Example: X-ray entry specific, produced by the percentiles step of the validation pipeline software.
+ */
+ readonly num_PDBids_absolute_percentile_DCC_Rfree?: Maybe<Scalars['Int']>;
+ /**
+ * The number of PDB depositions used in the comparison when calculating the attribute
+ * "absolute-percentile-RNAsuiteness".
+ * Example: Specific to entries that contain RNA polymers (and have a RNA_suiteness attribute).
+ * Produced by the percentiles step of the validation pipeline software.
+ */
+ readonly num_PDBids_absolute_percentile_RNA_suiteness?: Maybe<Scalars['Int']>;
+ /**
+ * The number of PDB depositions used in the comparison when calculating the attribute
+ * "absolute-percentile-clashscore"
+ * Example: Produced by the percentiles step of the validation pipeline software.
+ */
+ readonly num_PDBids_absolute_percentile_clashscore?: Maybe<Scalars['Int']>;
+ /**
+ * The number of PDB depositions used in the comparison when calculating the attribute
+ * "absolute-percentile-percent-RSRZ-outliers".
+ * Example: X-ray entry specific, produced by the percentiles step of the validation pipeline software.
+ */
+ readonly num_PDBids_absolute_percentile_percent_RSRZ_outliers?: Maybe<Scalars['Int']>;
+ /**
+ * The number of PDB depositions used in the comparison when calculating the attribute
+ * "absolute-percentile-percent-rama-outliers"
+ * Example: Produced by the percentiles step of the validation pipeline software.
+ */
+ readonly num_PDBids_absolute_percentile_percent_ramachandran_outliers?: Maybe<Scalars['Int']>;
+ /**
+ * The number of PDB depositions used in the comparison when calculating the attribute
+ * "absolute-percentile-percent-rota-outliers"
+ * Example: Produced by the percentiles step of the validation pipeline software.
+ */
+ readonly num_PDBids_absolute_percentile_percent_rotamer_outliers?: Maybe<Scalars['Int']>;
+ /**
+ * The number of PDB depositions used in the comparison when calculating the attribute
+ * "relative-percentile-DCC_Rfree".
+ * Example: X-ray entry specific, produced by the percentiles step of the validation pipeline software.
+ */
+ readonly num_PDBids_relative_percentile_DCC_Rfree?: Maybe<Scalars['Int']>;
+ /**
+ * The number of PDB depositions used in the comparison when calculating the attribute
+ * "relative-percentile-RNAsuiteness".
+ * Example: Specific to entries that contain RNA polymers (and have a RNA_suiteness attribute).
+ * Produced by the percentiles step of the validation pipeline software.
+ */
+ readonly num_PDBids_relative_percentile_RNA_suiteness?: Maybe<Scalars['Int']>;
+ /**
+ * The number of PDB depositions used in the comparison when calculating the attribute
+ * "relative-percentile-clashscore"
+ * Example: Produced by the percentiles step of the validation pipeline software.
+ */
+ readonly num_PDBids_relative_percentile_clashscore?: Maybe<Scalars['Int']>;
+ /**
+ * The number of PDB depositions used in the comparison when calculating the attribute
+ * "relative-percentile-percent-RSRZ-outliers".
+ * Example: X-ray entry specific, produced by the percentiles step of the validation pipeline software.
+ */
+ readonly num_PDBids_relative_percentile_percent_RSRZ_outliers?: Maybe<Scalars['Int']>;
+ /**
+ * The number of PDB depositions used in the comparison when calculating the attribute
+ * "relative-percentile-percent-rama-outliers"
+ * Example: Produced by the percentiles step of the validation pipeline software.
+ */
+ readonly num_PDBids_relative_percentile_percent_ramachandran_outliers?: Maybe<Scalars['Int']>;
+ /**
+ * The number of PDB depositions used in the comparison when calculating the attribute
+ * "relative-percentile-percent-rota-outliers"
+ * Example: Produced by the percentiles step of the validation pipeline software.
+ */
+ readonly num_PDBids_relative_percentile_percent_rotamer_outliers?: Maybe<Scalars['Int']>;
+ /**
+ * The number of bond angless compared to "standard geometry" made using the MolProbity dangle program.
+ * Standard geometry parameters are taken from Engh and Huber (2001) and Parkinson et al. (1996).
+ * This value is for all chains in the structure.
+ */
+ readonly num_angles_RMSZ?: Maybe<Scalars['Int']>;
+ /**
+ * The number of bond lengths compared to "standard geometry" made using the MolProbity dangle program.
+ * Standard geometry parameters are taken from Engh and Huber (2001) and Parkinson et al. (1996).
+ * This value is for all chains in the structure.
+ */
+ readonly num_bonds_RMSZ?: Maybe<Scalars['Int']>;
+ /**
+ * The number of reflections in the free set as defined in the input structure factor file supplied to the validation pipeline.
+ * example: X-ray entry specific, obtained from the DCC program.
+ */
+ readonly num_free_reflections?: Maybe<Scalars['Int']>;
+ /**
+ * The number of Miller Indices reported by the Xtriage program. This should be the same as the
+ * number of _refln in the input structure factor file.
+ * Example: X-ray entry specific, calculated by Phenix Xtriage program.
+ */
+ readonly num_miller_indices?: Maybe<Scalars['Int']>;
+ /** Reference for the PANAV software. */
+ readonly panav_version?: Maybe<Scalars['String']>;
+ /** A percentage, Normally percent proportion of the total number. Between 0% and 100%. */
+ readonly percent_RSRZ_outliers?: Maybe<Scalars['Float']>;
+ /** A percentage, Normally percent proportion of the total number. Between 0% and 100%. */
+ readonly percent_free_reflections?: Maybe<Scalars['Float']>;
+ /** A percentage, Normally percent proportion of the total number. Between 0% and 100%. */
+ readonly percent_ramachandran_outliers?: Maybe<Scalars['Float']>;
+ /** A percentage, Normally percent proportion of the total number. Between 0% and 100%. */
+ readonly percent_ramachandran_outliers_full_length?: Maybe<Scalars['Float']>;
+ /** A percentage, Normally percent proportion of the total number. Between 0% and 100%. */
+ readonly percent_rotamer_outliers?: Maybe<Scalars['Float']>;
+ /** A percentage, Normally percent proportion of the total number. Between 0% and 100%. */
+ readonly percent_rotamer_outliers_full_length?: Maybe<Scalars['Float']>;
+ /**
+ * The percentile bins that this structure would contribute to in a recalculation of
+ * percentile. The string is a comma separated list.
+ * Example: An X-ray entry with a resolution of 1.8 Angstroms,
+ * that would contribute to bins all structures, what ever bin 1.8 Angstrom resolution is in and
+ * the all xray bin.
+ * Example #2: An EM entry that would contribute to all and em structures bins.
+ * Example #3: A NMR entry hat would contribute to all and nmr structures bins.
+ */
+ readonly percentilebins?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
+ /**
+ * Comma separated list of the _entity.id's for the molecular entities that are present in the structure
+ * and have _entity_poly.type indicating that they are protein, RNA or DNA: that is in the list
+ * 'polypeptide(L)', 'polypeptide(D)', 'polyribonucleotide, 'polydeoxyribonucleotide' or
+ * 'polydeoxyribonucleotide/polyribonucleotide hybrid'.
+ * Normally the entity.id's are integer numbers but not necessarily so.
+ * Example
+ */
+ readonly protein_DNA_RNA_entities?: Maybe<Scalars['String']>;
+ /** Version and reference of the RCI software */
+ readonly rci_version?: Maybe<Scalars['String']>;
+ /**
+ * The filename for the input mmCIF format reflection file given to the validation pipeline.
+ * Not reported for runs at the annotation or release stage.
+ */
+ readonly reflections_input_filename?: Maybe<Scalars['String']>;
+ /**
+ * Version of the REFMAC pdbx_vrpt_software used in the EDS step.
+ * Example: X-ray entry specific, obtained in the eds step from REFMAC calculation.
+ */
+ readonly refmac_version?: Maybe<Scalars['String']>;
+ /**
+ * Structures are judged in comparison to previously deposited PDB entries.
+ * The comparison is carried out by calculation of the percentile rank, i.e. the percentage of entries
+ * that are equal or poorer than this structure in terms of a quality indicator.
+ * Percentile ranks range from 0 (the worst) to 100 (the best).
+ */
+ readonly relative_percentile_DCC_Rfree?: Maybe<Scalars['Float']>;
+ /**
+ * Structures are judged in comparison to previously deposited PDB entries.
+ * The comparison is carried out by calculation of the percentile rank, i.e. the percentage of entries
+ * that are equal or poorer than this structure in terms of a quality indicator.
+ * Percentile ranks range from 0 (the worst) to 100 (the best).
+ */
+ readonly relative_percentile_RNA_suiteness?: Maybe<Scalars['Float']>;
+ /**
+ * Structures are judged in comparison to previously deposited PDB entries.
+ * The comparison is carried out by calculation of the percentile rank, i.e. the percentage of entries
+ * that are equal or poorer than this structure in terms of a quality indicator.
+ * Percentile ranks range from 0 (the worst) to 100 (the best).
+ */
+ readonly relative_percentile_clashscore?: Maybe<Scalars['Float']>;
+ /**
+ * Structures are judged in comparison to previously deposited PDB entries.
+ * The comparison is carried out by calculation of the percentile rank, i.e. the percentage of entries
+ * that are equal or poorer than this structure in terms of a quality indicator.
+ * Percentile ranks range from 0 (the worst) to 100 (the best).
+ */
+ readonly relative_percentile_percent_RSRZ_outliers?: Maybe<Scalars['Float']>;
+ /**
+ * Structures are judged in comparison to previously deposited PDB entries.
+ * The comparison is carried out by calculation of the percentile rank, i.e. the percentage of entries
+ * that are equal or poorer than this structure in terms of a quality indicator.
+ * Percentile ranks range from 0 (the worst) to 100 (the best).
+ */
+ readonly relative_percentile_percent_ramachandran_outliers?: Maybe<Scalars['Float']>;
+ /**
+ * Structures are judged in comparison to previously deposited PDB entries.
+ * The comparison is carried out by calculation of the percentile rank, i.e. the percentage of entries
+ * that are equal or poorer than this structure in terms of a quality indicator.
+ * Percentile ranks range from 0 (the worst) to 100 (the best).
+ */
+ readonly relative_percentile_percent_rotamer_outliers?: Maybe<Scalars['Float']>;
+ /**
+ * The date, time and time-zone that the validation XML file was created.
+ * The string will be formatted like "Feb 7, 2017 -- 12:32 pm GMT".
+ */
+ readonly report_creation_date?: Maybe<Scalars['String']>;
+ /**
+ * The data high resolution diffraction limit, in Angstroms, obtained from cif item
+ * _reflns.d_resolution_high.
+ * X-ray entry specific.
+ */
+ readonly resol_high_from_reflectionsfile?: Maybe<Scalars['Float']>;
+ /**
+ * The data low resolution diffraction limit, in Angstroms, obtained from cif item
+ * _reflns.d_resolution_low.
+ * X-ray entry specific.
+ */
+ readonly resol_low_from_reflectionsfile?: Maybe<Scalars['Float']>;
+ /**
+ * This is a comma separated list of the residue types whose bond lengths and bond angles have
+ * not been checked against "standard geometry" using the MolProbity dangle program.
+ * Standard geometry parameters are taken from Engh and Huber (2001) and Parkinson et al. (1996)
+ */
+ readonly restypes_notchecked_for_bond_angle_geometry?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
+ /**
+ * Version of the software for chemical shift outlier detection - currently
+ * same as revision number of the validation pipeline.
+ */
+ readonly shiftchecker_version?: Maybe<Scalars['String']>;
+ /**
+ * A sentence giving the result of Xtriage’s analysis on translational NCS.
+ * Example: largest off-origin peak in the Patterson function is 8.82% of the height of the origin peak. No significant pseudotranslation is detected."
+ * X-ray entry specific, obtained from the Xtriage program.
+ */
+ readonly trans_NSC?: Maybe<Scalars['String']>;
+ /**
+ * Padilla and Yeates twinning parameter <|L|>.
+ * Theoretical values is 0.5 in the untwinned case, and 0.375 in the perfectly twinned case.
+ * Example: X-ray entry specific, obtained from the Xtriage program.
+ */
+ readonly twin_L?: Maybe<Scalars['Float']>;
+ /**
+ * Padilla and Yeates twinning parameter <|L**2|>.
+ * Theoretical values is 0.333 in the untwinned case, and 0.2 in the perfectly twinned case.
+ * Example: X-ray entry specific, obtained from the Xtriage program.
+ */
+ readonly twin_L2?: Maybe<Scalars['Float']>;
+ /**
+ * Estimated twinning fraction for operators as identified by Xtriage. A semicolon separated
+ * list of operators with fractions is givens
+ * Example: X-ray entry specific, obtained from the Xtriage program.
+ */
+ readonly twin_fraction?: Maybe<Scalars['String']>;
/**
- * The overall phase error for all reflections after refinement using
- * the current refinement target.
- *
+ * The mmCIF item names of the _refln columns used as input to the Xtriage program.
+ * Example X-ray entry specific, calculated by Phenix Xtriage program.
+ */
+ readonly xtriage_input_columns?: Maybe<Scalars['String']>;
+};
+
+/** Query root */
+export type Query = {
+ /** Get a list of assemblies given the list of ASSEMBLY IDs. Here an ASSEMBLY ID is a compound identifier that includes entry_id and assembly_id separated by '-', e.g. 1XXX-1. */
+ readonly assemblies?: Maybe<ReadonlyArray<Maybe<CoreAssembly>>>;
+ /** Get an assembly given the PDB ID and ASSEMBLY ID. Here ASSEMBLY ID is '1', '2', '3', etc. or 'deposited' for deposited coordinates. */
+ readonly assembly?: Maybe<CoreAssembly>;
+ /** Get a list of PDB branched entities given a list of ENTITY IDs. Here ENTITY ID is a compound identifier that includes entry_id and entity_id separated by '_', e.g. 1XXX_1. */
+ readonly branched_entities?: Maybe<ReadonlyArray<Maybe<CoreBranchedEntity>>>;
+ /** Get a PDB branched entity, given the PDB ID and ENTITY ID. Here ENTITY ID is a '1', '2', '3', etc. */
+ readonly branched_entity?: Maybe<CoreBranchedEntity>;
+ /** Get a PDB branched entity instance (chain), given the PDB ID and ENTITY INSTANCE ID. Here ENTITY INSTANCE ID identifies structural element in the asymmetric unit, e.g. 'A', 'B', etc. */
+ readonly branched_entity_instance?: Maybe<CoreBranchedEntityInstance>;
+ /** Get a list of PDB branched entity instances (chains), given the list of ENTITY INSTANCE IDs. Here ENTITY INSTANCE ID identifies structural element in the asymmetric unit, e.g. 'A', 'B', etc. */
+ readonly branched_entity_instances?: Maybe<ReadonlyArray<Maybe<CoreBranchedEntityInstance>>>;
+ /** Get a chemical component given the CHEMICAL COMPONENT ID, e.g. 'CFF', 'HEM', 'FE'.For nucleic acid polymer entities, use the one-letter code for the base. */
+ readonly chem_comp?: Maybe<CoreChemComp>;
+ /** Get a list of chemical components given the list of CHEMICAL COMPONENT ID, e.g. 'CFF', 'HEM', 'FE'.For nucleic acid polymer entities, use the one-letter code for the base. */
+ readonly chem_comps?: Maybe<ReadonlyArray<Maybe<CoreChemComp>>>;
+ /** Get a list of PDB entries given a list of PDB IDs. */
+ readonly entries?: Maybe<ReadonlyArray<Maybe<CoreEntry>>>;
+ /** Get PDB entry given the PDB id. */
+ readonly entry?: Maybe<CoreEntry>;
+ /** Get a list of PDB non-polymer entities given a list of ENTITY IDs. Here ENTITY ID is a compound identifier that includes entry_id and entity_id separated by '_', e.g. 1XXX_1. */
+ readonly nonpolymer_entities?: Maybe<ReadonlyArray<Maybe<CoreNonpolymerEntity>>>;
+ /** Get a PDB non-polymer entity, given the PDB ID and ENTITY ID. Here ENTITY ID is a '1', '2', '3', etc. */
+ readonly nonpolymer_entity?: Maybe<CoreNonpolymerEntity>;
+ /** Get a PDB non-polymer entity instance (chain), given the PDB ID and ENTITY INSTANCE ID. Here ENTITY INSTANCE ID identifies structural element in the asymmetric unit, e.g. 'A', 'B', etc. */
+ readonly nonpolymer_entity_instance?: Maybe<CoreNonpolymerEntityInstance>;
+ /** Get a list of PDB non-polymer entity instances (chains), given the list of ENTITY INSTANCE IDs. Here ENTITY INSTANCE ID identifies structural element in the asymmetric unit, e.g. 'A', 'B', etc. */
+ readonly nonpolymer_entity_instances?: Maybe<ReadonlyArray<Maybe<CoreNonpolymerEntityInstance>>>;
+ /** Get a list of PDB polymer entities given a list of ENTITY IDs. Here ENTITY ID is a compound identifier that includes entry_id and entity_id separated by '_', e.g. 1XXX_1. */
+ readonly polymer_entities?: Maybe<ReadonlyArray<Maybe<CorePolymerEntity>>>;
+ /** Get a PDB polymer entity, given the PDB ID and ENTITY ID. Here ENTITY ID is a '1', '2', '3', etc. */
+ readonly polymer_entity?: Maybe<CorePolymerEntity>;
+ /** Get a PDB polymer entity instance (chain), given the PDB ID and ENTITY INSTANCE ID. Here ENTITY INSTANCE ID identifies structural element in the asymmetric unit, e.g. 'A', 'B', etc. */
+ readonly polymer_entity_instance?: Maybe<CorePolymerEntityInstance>;
+ /** Get a list of PDB polymer entity instances (chains), given the list of ENTITY INSTANCE IDs. Here ENTITY INSTANCE ID identifies structural element in the asymmetric unit, e.g. 'A', 'B', etc. */
+ readonly polymer_entity_instances?: Maybe<ReadonlyArray<Maybe<CorePolymerEntityInstance>>>;
+ /** Get literature information from PubMed database given the PubMed identifier. */
+ readonly pubmed?: Maybe<CorePubmed>;
+ /** Get UniProt KB entry given the UniProt primary accession. */
+ readonly uniprot?: Maybe<CoreUniprot>;
+};
+
+
+/** Query root */
+export type QueryAssembliesArgs = {
+ assembly_ids: ReadonlyArray<Maybe<Scalars['String']>>;
+};
+
+
+/** Query root */
+export type QueryAssemblyArgs = {
+ assembly_id: Scalars['String'];
+ entry_id: Scalars['String'];
+};
+
+
+/** Query root */
+export type QueryBranched_EntitiesArgs = {
+ entity_ids: ReadonlyArray<Scalars['String']>;
+};
+
+
+/** Query root */
+export type QueryBranched_EntityArgs = {
+ entity_id: Scalars['String'];
+ entry_id: Scalars['String'];
+};
+
+
+/** Query root */
+export type QueryBranched_Entity_InstanceArgs = {
+ asym_id: Scalars['String'];
+ entry_id: Scalars['String'];
+};
+
+
+/** Query root */
+export type QueryBranched_Entity_InstancesArgs = {
+ instance_ids: ReadonlyArray<Maybe<Scalars['String']>>;
+};
+
+
+/** Query root */
+export type QueryChem_CompArgs = {
+ comp_id: Scalars['String'];
+};
+
+
+/** Query root */
+export type QueryChem_CompsArgs = {
+ comp_ids: ReadonlyArray<Maybe<Scalars['String']>>;
+};
+
+
+/** Query root */
+export type QueryEntriesArgs = {
+ entry_ids: ReadonlyArray<Scalars['String']>;
+};
+
+
+/** Query root */
+export type QueryEntryArgs = {
+ entry_id: Scalars['String'];
+};
+
+
+/** Query root */
+export type QueryNonpolymer_EntitiesArgs = {
+ entity_ids: ReadonlyArray<Scalars['String']>;
+};
+
+
+/** Query root */
+export type QueryNonpolymer_EntityArgs = {
+ entity_id: Scalars['String'];
+ entry_id: Scalars['String'];
+};
+
+
+/** Query root */
+export type QueryNonpolymer_Entity_InstanceArgs = {
+ asym_id: Scalars['String'];
+ entry_id: Scalars['String'];
+};
+
+
+/** Query root */
+export type QueryNonpolymer_Entity_InstancesArgs = {
+ instance_ids: ReadonlyArray<Maybe<Scalars['String']>>;
+};
+
+
+/** Query root */
+export type QueryPolymer_EntitiesArgs = {
+ entity_ids: ReadonlyArray<Scalars['String']>;
+};
+
+
+/** Query root */
+export type QueryPolymer_EntityArgs = {
+ entity_id: Scalars['String'];
+ entry_id: Scalars['String'];
+};
+
+
+/** Query root */
+export type QueryPolymer_Entity_InstanceArgs = {
+ asym_id: Scalars['String'];
+ entry_id: Scalars['String'];
+};
+
+
+/** Query root */
+export type QueryPolymer_Entity_InstancesArgs = {
+ instance_ids: ReadonlyArray<Maybe<Scalars['String']>>;
+};
+
+
+/** Query root */
+export type QueryPubmedArgs = {
+ pubmed_id: Scalars['Int'];
+};
+
+
+/** Query root */
+export type QueryUniprotArgs = {
+ uniprot_id: Scalars['String'];
+};
+
+export type RcsbAccessionInfo = {
+ /**
+ * The entry deposition date.
+ *
* Examples:
- * 0.30
+ * 2020-07-11, 2013-10-01
+ *
*/
- readonly pdbx_overall_phase_error?: Maybe<Scalars['Float']>;
+ readonly deposit_date?: Maybe<Scalars['Date']>;
/**
- * This data item uniquely identifies a refinement within an entry.
- * _refine.pdbx_refine_id can be used to distinguish the results of
- * joint refinements.
+ * A code indicating the current availibility of experimental data in the repository.
+ *
+ * Allowable values:
+ * N, Y
+ *
*/
- readonly pdbx_refine_id: Scalars['String'];
- /** For bulk solvent mask calculation, the amount that the ionic radii of atoms, which can be ions, are increased used. */
- readonly pdbx_solvent_ion_probe_radii?: Maybe<Scalars['Float']>;
- /** For bulk solvent mask calculation, amount mask is shrunk after taking away atoms with new radii and a constant value assigned to this new region. */
- readonly pdbx_solvent_shrinkage_radii?: Maybe<Scalars['Float']>;
- /** For bulk solvent mask calculation, the value by which the vdw radii of non-ion atoms (like carbon) are increased and used. */
- readonly pdbx_solvent_vdw_probe_radii?: Maybe<Scalars['Float']>;
+ readonly has_released_experimental_data?: Maybe<Scalars['String']>;
/**
- * Starting model for refinement. Starting model for
- * molecular replacement should refer to a previous
- * structure or experiment.
- *
+ * The entry initial release date.
+ *
* Examples:
- * 1XYZ, 2XYZ, BDL001
+ * 2020-01-10, 2018-01-23
+ *
*/
- readonly pdbx_starting_model?: Maybe<Scalars['String']>;
+ readonly initial_release_date?: Maybe<Scalars['Date']>;
+ /** The latest entry major revision number. */
+ readonly major_revision?: Maybe<Scalars['Int']>;
+ /** The latest entry minor revision number. */
+ readonly minor_revision?: Maybe<Scalars['Int']>;
/**
- * Special case of stereochemistry target values used
- * in SHELXL refinement.
+ * The latest entry revision date.
+ *
+ * Examples:
+ * 2020-02-11, 2018-10-23
+ *
*/
- readonly pdbx_stereochem_target_val_spec_case?: Maybe<Scalars['String']>;
- /** Stereochemistry target values used in refinement. */
- readonly pdbx_stereochemistry_target_values?: Maybe<Scalars['String']>;
- /** Special aspects of the solvent model used during refinement. */
- readonly solvent_model_details?: Maybe<Scalars['String']>;
+ readonly revision_date?: Maybe<Scalars['Date']>;
/**
- * The value of the BSOL solvent-model parameter describing
- * the average isotropic displacement parameter of disordered
- * solvent atoms.
- *
- * This is one of the two parameters (the other is
- * _refine.solvent_model_param_ksol) in Tronrud's method of
- * modelling the contribution of bulk solvent to the
- * scattering. The standard scale factor is modified according
- * to the expression
- *
- * k0 exp(-B0 * s^2^)[1-KSOL * exp(-BSOL * s^2^)]
- *
- * where k0 and B0 are the scale factors for the protein.
- *
- * Ref: Tronrud, D. E. (1997). Methods Enzymol. 277, 243-268.
+ * The release status for the entry.
+ *
+ * Allowable values:
+ * AUCO, AUTH, HOLD, HPUB', POLC, PROC, REFI, REL, REPL, WAIT, WDRN
+ *
*/
- readonly solvent_model_param_bsol?: Maybe<Scalars['Float']>;
+ readonly status_code?: Maybe<Scalars['String']>;
+};
+
+export type RcsbAssemblyContainerIdentifiers = {
/**
- * The value of the KSOL solvent-model parameter describing
- * the ratio of the electron density in the bulk solvent to the
- * electron density in the molecular solute.
- *
- * This is one of the two parameters (the other is
- * _refine.solvent_model_param_bsol) in Tronrud's method of
- * modelling the contribution of bulk solvent to the
- * scattering. The standard scale factor is modified according
- * to the expression
- *
- * k0 exp(-B0 * s^2^)[1-KSOL * exp(-BSOL * s^2^)]
- *
- * where k0 and B0 are the scale factors for the protein.
- *
- * Ref: Tronrud, D. E. (1997). Methods Enzymol. 277, 243-268.
+ * Assembly identifier for the container.
+ *
+ * Examples:
+ * 1, 5
+ *
*/
- readonly solvent_model_param_ksol?: Maybe<Scalars['Float']>;
+ readonly assembly_id: Scalars['String'];
+ /** Entry identifier for the container. */
+ readonly entry_id: Scalars['String'];
+ /**
+ * A unique identifier for each object in this assembly container formed by
+ * a dash separated concatenation of entry and assembly identifiers.
+ *
+ * Examples:
+ * 1KIP-1
+ *
+ */
+ readonly rcsb_id?: Maybe<Scalars['String']>;
};
-export type PdbxChemCompIdentifier = {
- /**
- * This data item is a pointer to _chem_comp.id in the CHEM_COMP
- * category.
- */
- readonly comp_id: Scalars['String'];
+export type RcsbAssemblyInfo = {
+ /** Entity identifier for the container. */
+ readonly assembly_id?: Maybe<Scalars['String']>;
+ /** The assembly non-hydrogen atomic coordinate count. */
+ readonly atom_count?: Maybe<Scalars['Int']>;
+ /** The assembly non-hydrogen branched entity atomic coordinate count. */
+ readonly branched_atom_count?: Maybe<Scalars['Int']>;
+ /** The number of distinct branched entities in the generated assembly. */
+ readonly branched_entity_count?: Maybe<Scalars['Int']>;
/**
- * This data item contains the identifier value for this
- * component.
+ * The number of branched instances in the generated assembly data set.
+ * This is the total count of branched entity instances generated in the assembly coordinate data.
*/
- readonly identifier?: Maybe<Scalars['String']>;
+ readonly branched_entity_instance_count?: Maybe<Scalars['Int']>;
/**
- * This data item contains the name of the program
- * or library used to compute the identifier.
- *
+ * The PDB entry accession code.
+ *
* Examples:
- * OPENEYE, DAYLIGHT, ACD, AUTONOM, PUBCHEM_CID, PUBCHEM_SID, OTHER, NONE
+ * 1KIP
+ *
*/
- readonly program: Scalars['String'];
+ readonly entry_id: Scalars['String'];
+ /** The assembly hydrogen atomic coordinate count. */
+ readonly hydrogen_atom_count?: Maybe<Scalars['Int']>;
/**
- * This data item contains the version of the program
- * or library used to compute the identifier.
+ * The number of modeled polymer monomers in the assembly coordinate data.
+ * This is the total count of monomers with reported coordinate data for all polymer
+ * entity instances in the generated assembly coordinate data.
*/
- readonly program_version: Scalars['String'];
+ readonly modeled_polymer_monomer_count?: Maybe<Scalars['Int']>;
/**
- * This data item contains the identifier type.
- *
+ * Nucleic acid polymer entity type categories describing the generated assembly.
+ *
* Allowable values:
- * CAS REGISTRY NUMBER, COMMON NAME, CONDENSED IUPAC CARB SYMBOL, CONDENSED IUPAC CARBOHYDRATE SYMBOL, IUPAC CARB SYMBOL, IUPAC CARBOHYDRATE SYMBOL, MDL Identifier, PUBCHEM Identifier, SNFG CARB SYMBOL, SNFG CARBOHYDRATE SYMBOL, SYNONYM, SYSTEMATIC NAME
+ * DNA (only), DNA/RNA (only), NA-hybrid (only), Other, RNA (only)
+ *
*/
- readonly type: Scalars['String'];
-};
-
-export type RcsbBranchedStructConn = {
- readonly connect_partner?: Maybe<RcsbBranchedStructConnConnectPartner>;
- readonly connect_target?: Maybe<RcsbBranchedStructConnConnectTarget>;
+ readonly na_polymer_entity_types?: Maybe<Scalars['String']>;
+ /** The assembly non-hydrogen non-polymer entity atomic coordinate count. */
+ readonly nonpolymer_atom_count?: Maybe<Scalars['Int']>;
+ /** The number of distinct non-polymer entities in the generated assembly exclusive of solvent. */
+ readonly nonpolymer_entity_count?: Maybe<Scalars['Int']>;
/**
- * The connection type.
- *
+ * The number of non-polymer instances in the generated assembly data set exclusive of solvent.
+ * This is the total count of non-polymer entity instances generated in the assembly coordinate data.
+ */
+ readonly nonpolymer_entity_instance_count?: Maybe<Scalars['Int']>;
+ /** The assembly non-hydrogen polymer entity atomic coordinate count. */
+ readonly polymer_atom_count?: Maybe<Scalars['Int']>;
+ /**
+ * Categories describing the polymer entity composition for the generated assembly.
+ *
* Allowable values:
- * covalent bond, hydrogen bond, ionic interaction, metal coordination, mismatched base pairs
+ * DNA, DNA/RNA, NA-hybrid, NA/oligosaccharide, RNA, heteromeric protein, homomeric protein, oligosaccharide, other, other type composition, other type pair, protein/NA, protein/NA/oligosaccharide, protein/oligosaccharide
+ *
*/
- readonly connect_type?: Maybe<Scalars['String']>;
- /** A description of special details of the connection. */
- readonly description?: Maybe<Scalars['String']>;
- /** Distance value for this contact. */
- readonly dist_value?: Maybe<Scalars['Float']>;
- /** The value of _rcsb_branched_struct_conn.id is an identifier for connection. */
- readonly id?: Maybe<Scalars['String']>;
+ readonly polymer_composition?: Maybe<Scalars['String']>;
+ /** The number of distinct polymer entities in the generated assembly. */
+ readonly polymer_entity_count?: Maybe<Scalars['Int']>;
+ /** The number of distinct DNA polymer entities in the generated assembly. */
+ readonly polymer_entity_count_DNA?: Maybe<Scalars['Int']>;
+ /** The number of distinct RNA polymer entities in the generated assembly. */
+ readonly polymer_entity_count_RNA?: Maybe<Scalars['Int']>;
+ /** The number of distinct nucleic acid polymer entities (DNA or RNA) in the generated assembly. */
+ readonly polymer_entity_count_nucleic_acid?: Maybe<Scalars['Int']>;
+ /** The number of distinct hybrid nucleic acid polymer entities in the generated assembly. */
+ readonly polymer_entity_count_nucleic_acid_hybrid?: Maybe<Scalars['Int']>;
+ /** The number of distinct protein polymer entities in the generated assembly. */
+ readonly polymer_entity_count_protein?: Maybe<Scalars['Int']>;
/**
- * The value of _rcsb_branched_struct_conn.id must uniquely identify a record in
- * the rcsb_branched_struct_conn list.
+ * The number of polymer instances in the generated assembly data set.
+ * This is the total count of polymer entity instances generated in the assembly coordinate data.
*/
- readonly ordinal_id: Scalars['Int'];
+ readonly polymer_entity_instance_count?: Maybe<Scalars['Int']>;
/**
- * The chemical or structural role of the interaction
- *
- * Allowable values:
- * C-Mannosylation, N-Glycosylation, O-Glycosylation
+ * The number of DNA polymer instances in the generated assembly data set.
+ * This is the total count of DNA polymer entity instances generated in the assembly coordinate data.
*/
- readonly role?: Maybe<Scalars['String']>;
+ readonly polymer_entity_instance_count_DNA?: Maybe<Scalars['Int']>;
/**
- * The chemical bond order associated with the specified atoms in
- * this contact.
- *
- * Allowable values:
- * doub, quad, sing, trip
+ * The number of RNA polymer instances in the generated assembly data set.
+ * This is the total count of RNA polymer entity instances generated in the assembly coordinate data.
*/
- readonly value_order?: Maybe<Scalars['String']>;
-};
-
-export type RcsbPolymerInstanceFeature = {
- /** Identifies the version of the feature assignment. */
- readonly assignment_version?: Maybe<Scalars['String']>;
- /** A description for the feature. */
- readonly description?: Maybe<Scalars['String']>;
- /** An identifier for the feature. */
- readonly feature_id?: Maybe<Scalars['String']>;
- readonly feature_positions?: Maybe<ReadonlyArray<Maybe<RcsbPolymerInstanceFeatureFeaturePositions>>>;
- /** A name for the feature. */
- readonly name?: Maybe<Scalars['String']>;
- /** Ordinal identifier for this category */
- readonly ordinal: Scalars['Int'];
+ readonly polymer_entity_instance_count_RNA?: Maybe<Scalars['Int']>;
/**
- * Code identifying the individual, organization or program that
- * assigned the feature.
+ * The number of nucleic acid polymer instances in the generated assembly data set.
+ * This is the total count of nucleic acid polymer entity instances generated in the assembly coordinate data.
*/
- readonly provenance_source?: Maybe<Scalars['String']>;
+ readonly polymer_entity_instance_count_nucleic_acid?: Maybe<Scalars['Int']>;
/**
- * Code residue coordinate system for the assigned feature.
- *
- * Allowable values:
- * NCBI, PDB entity, PDB entry, UniProt
+ * The number of hybrid nucleic acide polymer instances in the generated assembly data set.
+ * This is the total count of hybrid nucleic acid polymer entity instances generated in the assembly coordinate data.
*/
- readonly reference_scheme?: Maybe<Scalars['String']>;
+ readonly polymer_entity_instance_count_nucleic_acid_hybrid?: Maybe<Scalars['Int']>;
/**
- * A type or category of the feature.
- *
+ * The number of protein polymer instances in the generated assembly data set.
+ * This is the total count of protein polymer entity instances generated in the assembly coordinate data.
+ */
+ readonly polymer_entity_instance_count_protein?: Maybe<Scalars['Int']>;
+ /**
+ * The number of polymer monomers in sample entity instances comprising the assembly data set.
+ * This is the total count of monomers for all polymer entity instances
+ * in the generated assembly coordinate data.
+ */
+ readonly polymer_monomer_count?: Maybe<Scalars['Int']>;
+ /**
+ * Selected polymer entity type categories describing the generated assembly.
+ *
* Allowable values:
- * ANGLE_OUTLIER, BINDING_SITE, BOND_OUTLIER, CATH, CIS-PEPTIDE, HELIX_P, MOGUL_ANGLE_OUTLIER, MOGUL_BOND_OUTLIER, RAMACHANDRAN_OUTLIER, ROTAMER_OUTLIER, RSRCC_OUTLIER, RSRZ_OUTLIER, SCOP, SHEET, UNASSIGNED_SEC_STRUCT, UNOBSERVED_ATOM_XYZ, UNOBSERVED_RESIDUE_XYZ, ZERO_OCCUPANCY_ATOM_XYZ, ZERO_OCCUPANCY_RESIDUE_XYZ
+ * Nucleic acid (only), Other, Protein (only), Protein/NA
+ *
*/
- readonly type?: Maybe<Scalars['String']>;
+ readonly selected_polymer_entity_types?: Maybe<Scalars['String']>;
+ /** The assembly non-hydrogen solvent atomic coordinate count. */
+ readonly solvent_atom_count?: Maybe<Scalars['Int']>;
+ /** The number of distinct solvent entities in the generated assembly. */
+ readonly solvent_entity_count?: Maybe<Scalars['Int']>;
+ /**
+ * The number of solvent instances in the generated assembly data set.
+ * This is the total count of solvent entity instances generated in the assembly coordinate data.
+ */
+ readonly solvent_entity_instance_count?: Maybe<Scalars['Int']>;
+ /**
+ * The number of unmodeled polymer monomers in the assembly coordinate data. This is
+ * the total count of monomers with unreported coordinate data for all polymer
+ * entity instances in the generated assembly coordinate data.
+ */
+ readonly unmodeled_polymer_monomer_count?: Maybe<Scalars['Int']>;
};
-export type PdbxAuditRevisionCategory = {
+export type RcsbBindingAffinity = {
/**
- * The category updated in the pdbx_audit_revision_category record.
- *
+ * Ligand identifier.
+ *
* Examples:
- * audit_author, citation
+ * 0WE, SPE, CL
+ *
*/
- readonly category?: Maybe<Scalars['String']>;
+ readonly comp_id: Scalars['String'];
+ /** Link to external resource referencing the data. */
+ readonly link: Scalars['String'];
/**
- * The type of file that the pdbx_audit_revision_history record refers to.
- *
+ * The resource name for the related binding affinity reference.
+ *
* Allowable values:
- * Chemical component, NMR restraints, NMR shifts, Structure factors, Structure model
+ * PDBBind, Binding MOAD, BindingDB
+ *
*/
- readonly data_content_type: Scalars['String'];
+ readonly provenance_code: Scalars['String'];
/**
- * A unique identifier for the pdbx_audit_revision_category record.
- *
+ * Data point provided by BindingDB. Percent identity between PDB sequence and reference sequence.
+ *
* Examples:
- * 1
+ * null, null, null
+ *
*/
- readonly ordinal: Scalars['Int'];
+ readonly reference_sequence_identity?: Maybe<Scalars['Int']>;
/**
- * A pointer to _pdbx_audit_revision_history.ordinal
- *
+ * Binding affinity symbol indicating approximate or precise strength of the binding.
+ *
* Examples:
- * 1
+ * ~, =, >, <, >=, <=
+ *
*/
- readonly revision_ordinal: Scalars['Int'];
-};
-
-export type RcsbPolymerEntityContainerIdentifiers = {
- /** Instance identifiers corresponding to copies of the entity in this container. */
- readonly asym_ids?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
- /** Author instance identifiers corresponding to copies of the entity in this container. */
- readonly auth_asym_ids?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
- /** Unique list of monomer chemical component identifiers in the polymer entity in this container. */
- readonly chem_comp_monomers?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
- /** Unique list of non-standard monomer chemical component identifiers in the polymer entity in this container. */
- readonly chem_comp_nstd_monomers?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
- /** Entity identifier for the container. */
- readonly entity_id: Scalars['String'];
- /** Entry identifier for the container. */
- readonly entry_id: Scalars['String'];
- /** The BIRD identifier for the entity in this container. */
- readonly prd_id?: Maybe<Scalars['String']>;
+ readonly symbol?: Maybe<Scalars['String']>;
/**
- * A unique identifier for each object in this entity container formed by
- * an underscore separated concatenation of entry and entity identifiers.
+ * Binding affinity measurement given in one of the following types: The concentration constants: IC50: the concentration of ligand that reduces enzyme activity by 50%; EC50: the concentration of compound that generates a half-maximal response; The binding constant: Kd: dissociation constant; Ka: association constant; Ki: enzyme inhibition constant; The thermodynamic parameters: delta G: Gibbs free energy of binding (for association reaction); delta H: change in enthalpy associated with a chemical reaction; delta S: change in entropy associated with a chemical reaction.
+ *
+ * Allowable values:
+ * IC50, EC50, Kd, Ka, Ki, ΔG, ΔH, -TΔS
+ *
*/
- readonly rcsb_id?: Maybe<Scalars['String']>;
- readonly reference_sequence_identifiers?: Maybe<ReadonlyArray<Maybe<RcsbPolymerEntityContainerIdentifiersReferenceSequenceIdentifiers>>>;
- readonly uniprot_ids?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
-};
-
-export type CoreAssembly = {
- /** Get PDB entry that includes this assembly. */
- readonly entry?: Maybe<CoreEntry>;
- readonly pdbx_struct_assembly?: Maybe<PdbxStructAssembly>;
- readonly pdbx_struct_assembly_auth_evidence?: Maybe<ReadonlyArray<Maybe<PdbxStructAssemblyAuthEvidence>>>;
- readonly pdbx_struct_assembly_gen?: Maybe<ReadonlyArray<Maybe<PdbxStructAssemblyGen>>>;
- readonly pdbx_struct_assembly_prop?: Maybe<ReadonlyArray<Maybe<PdbxStructAssemblyProp>>>;
- readonly pdbx_struct_oper_list?: Maybe<ReadonlyArray<Maybe<PdbxStructOperList>>>;
- readonly rcsb_assembly_container_identifiers: RcsbAssemblyContainerIdentifiers;
- readonly rcsb_assembly_info?: Maybe<RcsbAssemblyInfo>;
+ readonly type: Scalars['String'];
/**
- * A unique identifier for each object in this assembly container formed by
- * a dash separated concatenation of entry and assembly identifiers.
+ * Binding affinity unit. Dissociation constant Kd is normally in molar units (or millimolar , micromolar, nanomolar, etc). Association constant Ka is normally expressed in inverse molar units (e.g. M-1).
+ *
+ * Examples:
+ * nM, kJ/mol
+ *
*/
- readonly rcsb_id: Scalars['String'];
- readonly rcsb_latest_revision?: Maybe<RcsbLatestRevision>;
- readonly rcsb_struct_symmetry?: Maybe<ReadonlyArray<Maybe<RcsbStructSymmetry>>>;
- readonly rcsb_struct_symmetry_lineage?: Maybe<ReadonlyArray<Maybe<RcsbStructSymmetryLineage>>>;
- /** The title and version of software package used for symmetry calculations. */
- readonly rcsb_struct_symmetry_provenance_code?: Maybe<Scalars['String']>;
+ readonly unit: Scalars['String'];
+ /** Binding affinity value between a ligand and its target molecule. */
+ readonly value: Scalars['Float'];
};
-export type Exptl = {
- /**
- * The total number of crystals used in the measurement of
- * intensities.
- */
- readonly crystals_number?: Maybe<Scalars['Int']>;
- /**
- * Any special information about the experimental work prior to the
- * intensity measurement. See also _exptl_crystal.preparation.
- */
- readonly details?: Maybe<Scalars['String']>;
+export type RcsbBirdCitation = {
/**
- * The method used in the experiment.
- *
- * Allowable values:
- * ELECTRON CRYSTALLOGRAPHY, ELECTRON MICROSCOPY, EPR, FIBER DIFFRACTION, FLUORESCENCE TRANSFER, INFRARED SPECTROSCOPY, NEUTRON DIFFRACTION, POWDER DIFFRACTION, SOLID-STATE NMR, SOLUTION NMR, SOLUTION SCATTERING, THEORETICAL MODEL, X-RAY DIFFRACTION
+ * The value of _rcsb_bird_citation.id must uniquely identify a record in the
+ * rcsb_bird_citation list.
+ *
+ * Examples:
+ * 1, 2
+ *
*/
- readonly method: Scalars['String'];
+ readonly id: Scalars['String'];
/**
- * A description of special aspects of the experimental method.
- *
+ * Abbreviated name of the cited journal as given in the
+ * Chemical Abstracts Service Source Index.
+ *
* Examples:
- * 29 structures, minimized average structure
+ * J.Mol.Biol., J. Mol. Biol.
+ *
*/
- readonly method_details?: Maybe<Scalars['String']>;
-};
-
-export type RcsbPolymerStructConnConnectTarget = {
+ readonly journal_abbrev?: Maybe<Scalars['String']>;
/**
- * A component of the identifier for the target of the structure
- * connection.
- *
- * This data item is a pointer to _atom_site.auth_asym_id in the
- * ATOM_SITE category.
+ * Volume number of the journal cited; relevant for journal
+ * articles.
+ *
+ * Examples:
+ * 174
+ *
*/
- readonly auth_asym_id?: Maybe<Scalars['String']>;
+ readonly journal_volume?: Maybe<Scalars['String']>;
/**
- * A component of the identifier for the target of the structure
- * connection.
- *
- * This data item is a pointer to _atom_site.auth_seq_id in the
- * ATOM_SITE category.
+ * The first page of the rcsb_bird_citation; relevant for journal
+ * articles, books and book chapters.
*/
- readonly auth_seq_id?: Maybe<Scalars['String']>;
+ readonly page_first?: Maybe<Scalars['String']>;
/**
- * A component of the identifier for the target of the structure
- * connection.
- *
- * This data item is a pointer to _atom_site.label_alt_id in the
- * ATOM_SITE category.
+ * The last page of the rcsb_bird_citation; relevant for journal
+ * articles, books and book chapters.
*/
- readonly label_alt_id?: Maybe<Scalars['String']>;
+ readonly page_last?: Maybe<Scalars['String']>;
/**
- * A component of the identifier for the target of the structure
- * connection.
- *
- * This data item is a pointer to _atom_site.label_asym_id in the
- * ATOM_SITE category.
+ * Document Object Identifier used by doi.org to uniquely
+ * specify bibliographic entry.
+ *
+ * Examples:
+ * 10.2345/S1384107697000225
+ *
*/
- readonly label_asym_id: Scalars['String'];
+ readonly pdbx_database_id_DOI?: Maybe<Scalars['String']>;
/**
- * A component of the identifier for the target of the structure
- * connection.
- *
- * This data item is a pointer to _atom_site.label_atom_id in the
- * ATOM_SITE category.
+ * Ascession number used by PubMed to categorize a specific
+ * bibliographic entry.
*/
- readonly label_atom_id?: Maybe<Scalars['String']>;
+ readonly pdbx_database_id_PubMed?: Maybe<Scalars['Int']>;
/**
- * A component of the identifier for the target of the structure
- * connection.
- *
- * This data item is a pointer to _atom_site.label_comp_id in the
- * ATOM_SITE category.
+ * Names of the authors of the citation; relevant for journal
+ * articles, books and book chapters. Names are separated by vertical bars.
+ *
+ * The family name(s), followed by a comma and including any
+ * dynastic components, precedes the first name(s) or initial(s).
*/
- readonly label_comp_id: Scalars['String'];
+ readonly rcsb_authors?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
/**
- * A component of the identifier for the target of the structure
- * connection.
- *
- * This data item is a pointer to _atom_site.connect_target_label_seq_id in the
- * ATOM_SITE category.
+ * The title of the rcsb_bird_citation; relevant for journal articles, books
+ * and book chapters.
+ *
+ * Examples:
+ * Structure of diferric duck ovotransferrin
+ * at 2.35 Angstroms resolution.
+ *
*/
- readonly label_seq_id?: Maybe<Scalars['Int']>;
+ readonly title?: Maybe<Scalars['String']>;
/**
- * Describes the symmetry operation that should be applied to the
- * atom set specified by _rcsb_polymer_struct_conn.label* to generate the
- * target of the structure connection.
- *
- * Examples:
- * 1_555, 7_645
+ * The year of the rcsb_bird_citation; relevant for journal articles, books
+ * and book chapters.
*/
- readonly symmetry?: Maybe<Scalars['String']>;
+ readonly year?: Maybe<Scalars['Int']>;
};
-export type RcsbPolymerEntityAlign = {
- readonly aligned_regions?: Maybe<ReadonlyArray<Maybe<RcsbPolymerEntityAlignAlignedRegions>>>;
+export type RcsbBranchedEntity = {
+ /** A description of special aspects of the branched entity. */
+ readonly details?: Maybe<Scalars['String']>;
/**
- * Code identifying the individual, organization or program that
- * assigned the reference sequence.
+ * Formula mass (KDa) of the branched entity.
+ *
+ * Examples:
+ * null, null
+ *
*/
- readonly provenance_source?: Maybe<Scalars['String']>;
- /** Reference sequence accession code. */
- readonly reference_database_accession?: Maybe<Scalars['String']>;
- /** Reference sequence isoform identifier. */
- readonly reference_database_isoform?: Maybe<Scalars['String']>;
+ readonly formula_weight?: Maybe<Scalars['Float']>;
/**
- * Reference sequence database name.
- *
- * Allowable values:
- * EMBL, GenBank, NDB, NORINE, PDB, PIR, PRF, RefSeq, UniProt
+ * A description of the branched entity.
+ *
+ * Examples:
+ * alpha-D-glucopyranose-(1-6)-beta-D-glucopyranose, beta-D-xylopyranose-(1-4)-beta-D-xylopyranose
+ *
*/
- readonly reference_database_name?: Maybe<Scalars['String']>;
+ readonly pdbx_description?: Maybe<Scalars['String']>;
+ /** The number of molecules of the branched entity in the entry. */
+ readonly pdbx_number_of_molecules?: Maybe<Scalars['Int']>;
};
-export type CorePolymerEntityInstance = {
- readonly pdbx_struct_special_symmetry?: Maybe<ReadonlyArray<Maybe<PdbxStructSpecialSymmetry>>>;
- /** Get polymer entity for this polymer entity instance. */
- readonly polymer_entity?: Maybe<CorePolymerEntity>;
+export type RcsbBranchedEntityAnnotation = {
+ /** An identifier for the annotation. */
+ readonly annotation_id?: Maybe<Scalars['String']>;
+ readonly annotation_lineage?: Maybe<ReadonlyArray<Maybe<RcsbBranchedEntityAnnotationAnnotationLineage>>>;
/**
- * A unique identifier for each object in this entity instance container formed by
- * an 'dot' (.) separated concatenation of entry and entity instance identifiers.
+ * Identifies the version of the annotation assignment.
+ *
+ * Examples:
+ * V4_0_2
+ *
*/
- readonly rcsb_id: Scalars['String'];
- readonly rcsb_latest_revision?: Maybe<RcsbLatestRevision>;
- readonly rcsb_polymer_entity_instance_container_identifiers?: Maybe<RcsbPolymerEntityInstanceContainerIdentifiers>;
- readonly rcsb_polymer_instance_annotation?: Maybe<ReadonlyArray<Maybe<RcsbPolymerInstanceAnnotation>>>;
- readonly rcsb_polymer_instance_feature?: Maybe<ReadonlyArray<Maybe<RcsbPolymerInstanceFeature>>>;
- readonly rcsb_polymer_instance_feature_summary?: Maybe<ReadonlyArray<Maybe<RcsbPolymerInstanceFeatureSummary>>>;
- readonly rcsb_polymer_struct_conn?: Maybe<ReadonlyArray<Maybe<RcsbPolymerStructConn>>>;
-};
-
-export type RcsbPolymerInstanceAnnotationAnnotationLineage = {
- /** Members of the annotation lineage as parent lineage depth (1-N) */
- readonly depth?: Maybe<Scalars['Int']>;
- /** Members of the annotation lineage as parent class identifiers. */
- readonly id?: Maybe<Scalars['String']>;
- /** Members of the annotation lineage as parent class names. */
+ readonly assignment_version?: Maybe<Scalars['String']>;
+ /** A description for the annotation. */
+ readonly description?: Maybe<Scalars['String']>;
+ /** A name for the annotation. */
readonly name?: Maybe<Scalars['String']>;
-};
-
-export type RcsbPolymerEntityRcsbEnzymeClassCombined = {
- /** The enzyme classification hierarchy depth (1-N). */
- readonly depth?: Maybe<Scalars['Int']>;
- /** Combined list of enzyme class assignments. */
- readonly ec?: Maybe<Scalars['String']>;
/**
- * Combined list of enzyme class associated provenance sources.
- *
- * Allowable values:
- * PDB Primary Data, UniProt
+ * Code identifying the individual, organization or program that
+ * assigned the annotation.
+ *
+ * Examples:
+ * PDB
+ *
*/
readonly provenance_source?: Maybe<Scalars['String']>;
-};
-
-export type RcsbPolymerEntityFeatureSummary = {
- /** The feature count. */
- readonly count?: Maybe<Scalars['Int']>;
- /** The fractional feature coverage relative to the full entity sequence. */
- readonly coverage?: Maybe<Scalars['Float']>;
- /** The maximum feature length. */
- readonly maximum_length?: Maybe<Scalars['Int']>;
- /** The maximum feature value. */
- readonly maximum_value?: Maybe<Scalars['Float']>;
- /** The minimum feature length. */
- readonly minimum_length?: Maybe<Scalars['Int']>;
- /** The minimum feature value. */
- readonly minimum_value?: Maybe<Scalars['Float']>;
- /**
- * Type or category of the feature.
- *
- * Allowable values:
- * artifact, modified_monomer, mutation
- */
+ /** A type or category of the annotation. */
readonly type?: Maybe<Scalars['String']>;
};
-export type RcsbStructSymmetryClusters = {
- /** Average RMSD between members of a given cluster. */
- readonly avg_rmsd?: Maybe<Scalars['Float']>;
- /** Subunits that belong to the cluster, identified by asym_id and optionally by assembly operator id(s). */
- readonly members: ReadonlyArray<Maybe<ClustersMembers>>;
-};
-
-export type RcsbChemCompAnnotationAnnotationLineage = {
+export type RcsbBranchedEntityAnnotationAnnotationLineage = {
/** Members of the annotation lineage as parent lineage depth (1-N) */
readonly depth?: Maybe<Scalars['Int']>;
/** Members of the annotation lineage as parent class identifiers. */
@@ -6534,2275 +7285,2663 @@ export type RcsbChemCompAnnotationAnnotationLineage = {
readonly name?: Maybe<Scalars['String']>;
};
-export type RcsbPfamContainerIdentifiers = {
- /** Accession number of Pfam entry. */
- readonly pfam_id?: Maybe<Scalars['String']>;
-};
-
-export type PdbxSgProject = {
- /**
- * The value identifies the full name of center.
- *
- * Allowable values:
- * Accelerated Technologies Center for Gene to 3D Structure, Assembly, Dynamics and Evolution of Cell-Cell and Cell-Matrix Adhesions, Atoms-to-Animals: The Immune Function Network, Bacterial targets at IGS-CNRS, France, Berkeley Structural Genomics Center, Center for Eukaryotic Structural Genomics, Center for High-Throughput Structural Biology, Center for Membrane Proteins of Infectious Diseases, Center for Structural Genomics of Infectious Diseases, Center for Structures of Membrane Proteins, Center for the X-ray Structure Determination of Human Transporters, Chaperone-Enabled Studies of Epigenetic Regulation Enzymes, Enzyme Discovery for Natural Product Biosynthesis, GPCR Network, Integrated Center for Structure and Function Innovation, Israel Structural Proteomics Center, Joint Center for Structural Genomics, Marseilles Structural Genomics Program @ AFMB, Medical Structural Genomics of Pathogenic Protozoa, Membrane Protein Structural Biology Consortium, Membrane Protein Structures by Solution NMR, Midwest Center for Macromolecular Research, Midwest Center for Structural Genomics, Mitochondrial Protein Partnership, Montreal-Kingston Bacterial Structural Genomics Initiative, Mycobacterium Tuberculosis Structural Proteomics Project, New York Consortium on Membrane Protein Structure, New York SGX Research Center for Structural Genomics, New York Structural GenomiX Research Consortium, New York Structural Genomics Research Consortium, Northeast Structural Genomics Consortium, Nucleocytoplasmic Transport: a Target for Cellular Control, Ontario Centre for Structural Proteomics, Oxford Protein Production Facility, Paris-Sud Yeast Structural Genomics, Partnership for Nuclear Receptor Signaling Code Biology, Partnership for Stem Cell Biology, Partnership for T-Cell Biology, Program for the Characterization of Secreted Effector Proteins, Protein Structure Factory, RIKEN Structural Genomics/Proteomics Initiative, Scottish Structural Proteomics Facility, Seattle Structural Genomics Center for Infectious Disease, South Africa Structural Targets Annotation Database, Southeast Collaboratory for Structural Genomics, Structural Genomics Consortium, Structural Genomics Consortium for Research on Gene Expression, Structural Genomics of Pathogenic Protozoa Consortium, Structural Proteomics in Europe, Structural Proteomics in Europe 2, Structure 2 Function Project, Structure, Dynamics and Activation Mechanisms of Chemokine Receptors, Structure-Function Analysis of Polymorphic CDI Toxin-Immunity Protein Complexes, Structure-Function Studies of Tight Junction Membrane Proteins, Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors, TB Structural Genomics Consortium, Transcontinental EM Initiative for Membrane Protein Structure, Transmembrane Protein Center
- */
- readonly full_name_of_center?: Maybe<Scalars['String']>;
+export type RcsbBranchedEntityContainerIdentifiers = {
+ /** Instance identifiers corresponding to copies of the entity in this container. */
+ readonly asym_ids?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
+ /** Author instance identifiers corresponding to copies of the entity in this container. */
+ readonly auth_asym_ids?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
+ /** Unique list of monomer chemical component identifiers in the entity in this container. */
+ readonly chem_comp_monomers?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
/**
- * A unique integer identifier for this center
- *
- * Allowable values:
- * 1, 2, 3, 4, 5, 6, 7, 8, 9, 10
+ * The chemical reference definition identifier for the entity in this container.
+ *
+ * Examples:
+ * PRD_000010
+ *
*/
- readonly id: Scalars['Int'];
+ readonly chem_ref_def_id?: Maybe<Scalars['String']>;
/**
- * The value identifies the full name of center.
- *
- * Allowable values:
- * ATCG3D, BIGS, BSGC, BSGI, CEBS, CELLMAT, CESG, CHSAM, CHTSB, CSGID, CSMP, GPCR, IFN, ISFI, ISPC, JCSG, MCMR, MCSG, MPID, MPP, MPSBC, MPSbyNMR, MSGP, MSGPP, MTBI, NESG, NHRs, NPCXstals, NYCOMPS, NYSGRC, NYSGXRC, NatPro, OCSP, OPPF, PCSEP, PSF, RSGI, S2F, SASTAD, SECSG, SGC, SGCGES, SGPP, SPINE, SPINE-2, SSGCID, SSPF, STEMCELL, TBSGC, TCELL, TEMIMPS, TJMP, TMPC, TransportPDB, UC4CDI, XMTB, YSG
+ * Entity identifier for the container.
+ *
+ * Examples:
+ * 1, 2
+ *
*/
- readonly initial_of_center?: Maybe<Scalars['String']>;
+ readonly entity_id: Scalars['String'];
/**
- * The value identifies the Structural Genomics project.
- *
- * Allowable values:
- * Enzyme Function Initiative, NIAID, National Institute of Allergy and Infectious Diseases, NPPSFA, National Project on Protein Structural and Functional Analyses, PSI, Protein Structure Initiative, PSI:Biology
+ * Entry identifier for the container.
+ *
+ * Examples:
+ * 1B5F, 2HYV
+ *
*/
- readonly project_name?: Maybe<Scalars['String']>;
-};
-
-export type RcsbPolymerEntityFeatureFeaturePositions = {
- /** An identifier for the monomer(s) corresponding to the feature assignment. */
- readonly beg_comp_id?: Maybe<Scalars['String']>;
- /** An identifier for the monomer at which this segment of the feature begins. */
- readonly beg_seq_id: Scalars['Int'];
- /** An identifier for the monomer at which this segment of the feature ends. */
- readonly end_seq_id?: Maybe<Scalars['Int']>;
- /** The value for the feature over this monomer segment. */
- readonly value?: Maybe<Scalars['Float']>;
-};
-
-export type RcsbAssemblyContainerIdentifiers = {
- /** Assembly identifier for the container. */
- readonly assembly_id: Scalars['String'];
- /** Entry identifier for the container. */
readonly entry_id: Scalars['String'];
/**
- * A unique identifier for each object in this assembly container formed by
- * a dash separated concatenation of entry and assembly identifiers.
- */
- readonly rcsb_id?: Maybe<Scalars['String']>;
-};
-
-export type RcsbPolymerStructConnConnectPartner = {
- /**
- * A component of the identifier for the partner in the structure
- * connection.
- *
- * This data item is a pointer to _atom_site.label_alt_id in the
- * ATOM_SITE category.
- */
- readonly label_alt_id?: Maybe<Scalars['String']>;
- /**
- * A component of the identifier for the partner in the structure
- * connection.
- *
- * This data item is a pointer to _atom_site.label_asym_id in the
- * ATOM_SITE category.
- */
- readonly label_asym_id: Scalars['String'];
- /**
- * A component of the identifier for the partner in the structure
- * connection.
- *
- * This data item is a pointer to _chem_comp_atom.atom_id in the
- * CHEM_COMP_ATOM category.
+ * The BIRD identifier for the entity in this container.
+ *
+ * Examples:
+ * PRD_000010
+ *
*/
- readonly label_atom_id?: Maybe<Scalars['String']>;
+ readonly prd_id?: Maybe<Scalars['String']>;
/**
- * A component of the identifier for the partner in the structure
- * connection.
- *
- * This data item is a pointer to _atom_site.label_comp_id in the
- * ATOM_SITE category.
+ * A unique identifier for each object in this entity container formed by
+ * an underscore separated concatenation of entry and entity identifiers.
+ *
+ * Examples:
+ * 2HYV_2
+ *
*/
- readonly label_comp_id: Scalars['String'];
+ readonly rcsb_id?: Maybe<Scalars['String']>;
+ readonly reference_identifiers?: Maybe<ReadonlyArray<Maybe<RcsbBranchedEntityContainerIdentifiersReferenceIdentifiers>>>;
+};
+
+export type RcsbBranchedEntityContainerIdentifiersReferenceIdentifiers = {
/**
- * A component of the identifier for the partner in the structure
- * connection.
- *
- * This data item is a pointer to _atom_site.label_seq_id in the
- * ATOM_SITE category.
+ * Source of the reference resource assignment
+ *
+ * Allowable values:
+ * PDB, RCSB
+ *
*/
- readonly label_seq_id?: Maybe<Scalars['Int']>;
+ readonly provenance_source?: Maybe<Scalars['String']>;
/**
- * Describes the symmetry operation that should be applied to the
- * atom set specified by _rcsb_polymer_struct_conn.connect_partner_label* to generate the
- * partner in the structure connection.
- *
+ * Reference resource accession code
+ *
* Examples:
- * 1_555, 7_645
+ * G07411ON, G42666HT
+ *
*/
- readonly symmetry?: Maybe<Scalars['String']>;
+ readonly resource_accession?: Maybe<Scalars['String']>;
+ /**
+ * Reference resource name
+ *
+ * Allowable values:
+ * GlyCosmos, GlyGen, GlyTouCan
+ *
+ */
+ readonly resource_name?: Maybe<Scalars['String']>;
};
-export type RcsbUniprotAnnotation = {
- /** An identifier for the annotation. */
- readonly annotation_id?: Maybe<Scalars['String']>;
- readonly annotation_lineage?: Maybe<ReadonlyArray<Maybe<RcsbUniprotAnnotationAnnotationLineage>>>;
- /** Identifies the version of the annotation assignment. */
+export type RcsbBranchedEntityFeature = {
+ readonly additional_properties?: Maybe<ReadonlyArray<Maybe<RcsbBranchedEntityFeatureAdditionalProperties>>>;
+ /**
+ * Identifies the version of the feature assignment.
+ *
+ * Examples:
+ * V4_0_2
+ *
+ */
readonly assignment_version?: Maybe<Scalars['String']>;
- /** A description for the annotation. */
+ /** A description for the feature. */
readonly description?: Maybe<Scalars['String']>;
- /** A name for the annotation. */
+ /** An identifier for the feature. */
+ readonly feature_id?: Maybe<Scalars['String']>;
+ readonly feature_positions?: Maybe<ReadonlyArray<Maybe<RcsbBranchedEntityFeatureFeaturePositions>>>;
+ /** A name for the feature. */
readonly name?: Maybe<Scalars['String']>;
/**
* Code identifying the individual, organization or program that
- * assigned the annotation.
+ * assigned the feature.
+ *
+ * Examples:
+ * PDB
+ *
*/
readonly provenance_source?: Maybe<Scalars['String']>;
/**
- * A type or category of the annotation.
- *
+ * Code residue coordinate system for the assigned feature.
+ *
* Allowable values:
- * disease, phenotype
+ * PDB entity
+ *
+ */
+ readonly reference_scheme?: Maybe<Scalars['String']>;
+ /**
+ * A type or category of the feature.
+ *
+ * Allowable values:
+ * mutation
+ *
*/
readonly type?: Maybe<Scalars['String']>;
};
-export type PdbxSolnScatter = {
+export type RcsbBranchedEntityFeatureAdditionalProperties = {
+ /** The additional property name. */
+ readonly name?: Maybe<Scalars['String']>;
+ /** The value(s) of the additional property. */
+ readonly values?: Maybe<ReadonlyArray<Maybe<Scalars['ObjectScalar']>>>;
+};
+
+export type RcsbBranchedEntityFeatureFeaturePositions = {
/**
- * The name of the buffer used for the sample in the solution scattering
- * experiment.
- *
+ * An identifier for the leading monomer corresponding to the feature assignment.
+ *
* Examples:
- * acetic acid
+ * NAG, MAN
+ *
*/
- readonly buffer_name?: Maybe<Scalars['String']>;
+ readonly beg_comp_id?: Maybe<Scalars['String']>;
+ /** An identifier for the leading monomer position of the feature. */
+ readonly beg_seq_id: Scalars['Int'];
+ /** An identifier for the leading monomer position of the feature. */
+ readonly end_seq_id?: Maybe<Scalars['Int']>;
/**
- * The concentration range (mg/mL) of the complex in the
- * sample used in the solution scattering experiment to
- * determine the mean radius of structural elongation.
- *
+ * The value for the feature at this monomer.
+ *
* Examples:
- * 0.7 - 14
+ * null, null
+ *
*/
- readonly concentration_range?: Maybe<Scalars['String']>;
+ readonly value?: Maybe<Scalars['Float']>;
+};
+
+export type RcsbBranchedEntityFeatureSummary = {
+ /** The feature count. */
+ readonly count?: Maybe<Scalars['Int']>;
/**
- * A list of the software used in the data analysis
- *
+ * The fractional feature coverage relative to the full branched entity.
+ *
* Examples:
- * SCTPL5 GNOM
+ * null, null
+ *
*/
- readonly data_analysis_software_list?: Maybe<Scalars['String']>;
+ readonly coverage?: Maybe<Scalars['Float']>;
+ /** The maximum feature length. */
+ readonly maximum_length?: Maybe<Scalars['Int']>;
/**
- * A list of the software used in the data reduction
- *
+ * The maximum feature value.
+ *
* Examples:
- * OTOKO
- */
- readonly data_reduction_software_list?: Maybe<Scalars['String']>;
- /**
- * The particular radiation detector. In general this will be a
- * manufacturer, description, model number or some combination of
- * these.
- */
- readonly detector_specific?: Maybe<Scalars['String']>;
- /** The general class of the radiation detector. */
- readonly detector_type?: Maybe<Scalars['String']>;
- /**
- * The value of _pdbx_soln_scatter.id must
- * uniquely identify the sample in the category PDBX_SOLN_SCATTER
- */
- readonly id: Scalars['String'];
- /**
- * The maximum mean radius of structural elongation of the sample.
- * In a given solute-solvent contrast, the radius of gyration
- * R_G is a measure of structural elongation if the internal
- * inhomogeneity of scattering densities has no effect. Guiner
- * analysis at low Q give the R_G and the forward scattering at
- * zero angle I(0).
- *
- * lnl(Q) = lnl(0) - R_G^2Q^2/3
- *
- * where
- * Q = 4(pi)sin(theta/lamda)
- * 2theta = scattering angle
- * lamda = wavelength
- *
- * The above expression is valid in a QR_G range for extended
- * rod-like particles. The relative I(0)/c values ( where
- * c = sample concentration) for sample measurements in a
- * constant buffer for a single sample data session, gives the
- * relative masses of the protein(s) studied when referenced
- * against a standard.
- *
- * see:
- * O.Glatter & O.Kratky, (1982). Editors of "Small angle
- * X-ray Scattering, Academic Press, New York.
- * O.Kratky. (1963). X-ray small angle scattering with
- * substances of biological interest in diluted solutions.
- * Prog. Biophys. Chem., 13, 105-173.
- * G.D.Wignall & F.S.Bates, (1987). The small-angle approximation
- * of X-ray and neutron scatter from rigid rods of non-uniform
- * cross section and finite length. J.Appl. Crystallog., 18, 452-460.
- *
- * If the structure is elongated, the mean radius of gyration
- * of the cross-sectional structure R_XS and the mean cross sectional
- * intensity at zero angle [I(Q).Q]_Q->0 is obtained from
- * ln[I(Q).Q] = ln[l(Q).(Q)]_Q->0 - ((R_XS)^2Q^2)/2
- */
- readonly max_mean_cross_sectional_radii_gyration?: Maybe<Scalars['Float']>;
- /**
- * The estimated standard deviation for the
- * minimum mean radius of structural elongation of the sample.
- * In a given solute-solvent contrast, the radius of gyration
- * R_G is a measure of structural elongation if the internal
- * inhomogeneity of scattering densities has no effect. Guiner
- * analysis at low Q give the R_G and the forward scattering at
- * zero angle I(0).
- *
- * lnl(Q) = lnl(0) - R_G^2Q^2/3
- *
- * where
- * Q = 4(pi)sin(theta/lamda)
- * 2theta = scattering angle
- * lamda = wavelength
- *
- * The above expression is valid in a QR_G range for extended
- * rod-like particles. The relative I(0)/c values ( where
- * c = sample concentration) for sample measurements in a
- * constant buffer for a single sample data session, gives the
- * relative masses of the protein(s) studied when referenced
- * against a standard.
- *
- * see:
- * O.Glatter & O.Kratky, (1982). Editors of "Small angle
- * X-ray Scattering, Academic Press, New York.
- * O.Kratky. (1963). X-ray small angle scattering with
- * substances of biological interest in diluted solutions.
- * Prog. Biophys. Chem., 13, 105-173.
- * G.D.Wignall & F.S.Bates, (1987). The small-angle approximation
- * of X-ray and neutron scatter from rigid rods of non-uniform
- * cross section and finite length. J.Appl. Crystallog., 18, 452-460.
- *
- * If the structure is elongated, the mean radius of gyration
- * of the cross-sectional structure R_XS and the mean cross sectional
- * intensity at zero angle [I(Q).Q]_Q->0 is obtained from
- * ln[I(Q).Q] = ln[l(Q).(Q)]_Q->0 - ((R_XS)^2Q^2)/2
+ * null, null
+ *
*/
- readonly max_mean_cross_sectional_radii_gyration_esd?: Maybe<Scalars['Float']>;
+ readonly maximum_value?: Maybe<Scalars['Float']>;
+ /** The minimum feature length. */
+ readonly minimum_length?: Maybe<Scalars['Int']>;
/**
- * The mean radius of structural elongation of the sample.
- * In a given solute-solvent contrast, the radius of gyration
- * R_G is a measure of structural elongation if the internal
- * inhomogeneity of scattering densities has no effect. Guiner
- * analysis at low Q gives the R_G and the forward scattering at
- * zero angle I(0).
- *
- * lnl(Q) = lnl(0) - R_G^2Q^2/3
- *
- * where
- * Q = 4(pi)sin(theta/lamda)
- * 2theta = scattering angle
- * lamda = wavelength
- *
- * The above expression is valid in a QR_G range for extended
- * rod-like particles. The relative I(0)/c values ( where
- * c = sample concentration) for sample measurements in a
- * constant buffer for a single sample data session, gives the
- * relative masses of the protein(s) studied when referenced
- * against a standard.
- *
- * see: O.Glatter & O.Kratky, (1982). Editors of "Small angle
- * X-ray Scattering, Academic Press, New York.
- * O.Kratky. (1963). X-ray small angle scattering with
- * substances of biological interest in diluted solutions.
- * Prog. Biophys. Chem., 13, 105-173.
- *
- * G.D.Wignall & F.S.Bates, (1987). The small-angle approximation
- * of X-ray and neutron scatter from rigid rods of non-uniform
- * cross section and finite length. J.Appl. Crystallog., 18, 452-460.
- *
- * If the structure is elongated, the mean radius of gyration
- * of the cross-sectional structure R_XS and the mean cross sectional
- * intensity at zero angle [I(Q).Q]_Q->0 is obtained from
- *
- * ln[I(Q).Q] = ln[l(Q).(Q)]_Q->0 - ((R_XS)^2Q^2)/2
+ * The minimum feature value.
+ *
+ * Examples:
+ * null, null
+ *
*/
- readonly mean_guiner_radius?: Maybe<Scalars['Float']>;
+ readonly minimum_value?: Maybe<Scalars['Float']>;
/**
- * The estimated standard deviation for the
- * mean radius of structural elongation of the sample.
- * In a given solute-solvent contrast, the radius of gyration
- * R_G is a measure of structural elongation if the internal
- * inhomogeneity of scattering densities has no effect. Guiner
- * analysis at low Q give the R_G and the forward scattering at
- * zero angle I(0).
- *
- * lnl(Q) = lnl(0) - R_G^2Q^2/3
- *
- * where
- * Q = 4(pi)sin(theta/lamda)
- * 2theta = scattering angle
- * lamda = wavelength
- *
- * The above expression is valid in a QR_G range for extended
- * rod-like particles. The relative I(0)/c values ( where
- * c = sample concentration) for sample measurements in a
- * constant buffer for a single sample data session, gives the
- * relative masses of the protein(s) studied when referenced
- * against a standard.
- *
- * see:
- * O.Glatter & O.Kratky, (1982). Editors of "Small angle
- * X-ray Scattering, Academic Press, New York.
- * O.Kratky. (1963). X-ray small angle scattering with
- * substances of biological interest in diluted solutions.
- * Prog. Biophys. Chem., 13, 105-173.
- * G.D.Wignall & F.S.Bates, (1987). The small-angle approximation
- * of X-ray and neutron scatter from rigid rods of non-uniform
- * cross section and finite length. J.Appl. Crystallog., 18, 452-460.
- *
- * If the structure is elongated, the mean radius of gyration
- * of the cross-sectional structure R_XS and the mean cross sectional
- * intensity at zero angle [I(Q).Q]_Q->0 is obtained from
- * ln[I(Q).Q] = ln[l(Q).(Q)]_Q->0 - ((R_XS)^2Q^2)/2
+ * Type or category of the feature.
+ *
+ * Allowable values:
+ * mutation
+ *
*/
- readonly mean_guiner_radius_esd?: Maybe<Scalars['Float']>;
+ readonly type?: Maybe<Scalars['String']>;
+};
+
+export type RcsbBranchedEntityInstanceContainerIdentifiers = {
+ /** Instance identifier for this container. */
+ readonly asym_id: Scalars['String'];
+ /** Author instance identifier for this container. */
+ readonly auth_asym_id?: Maybe<Scalars['String']>;
+ /** Entity identifier for the container. */
+ readonly entity_id?: Maybe<Scalars['String']>;
+ /** Entry identifier for the container. */
+ readonly entry_id: Scalars['String'];
/**
- * The minimum mean radius of structural elongation of the sample.
- * In a given solute-solvent contrast, the radius of gyration
- * R_G is a measure of structural elongation if the internal
- * inhomogeneity of scattering densities has no effect. Guiner
- * analysis at low Q give the R_G and the forward scattering at
- * zero angle I(0).
- *
- * lnl(Q) = lnl(0) - R_G^2Q^2/3
- *
- * where
- * Q = 4(pi)sin(theta/lamda)
- * 2theta = scattering angle
- * lamda = wavelength
- *
- * The above expression is valid in a QR_G range for extended
- * rod-like particles. The relative I(0)/c values ( where
- * c = sample concentration) for sample measurements in a
- * constant buffer for a single sample data session, gives the
- * relative masses of the protein(s) studied when referenced
- * against a standard.
- *
- * see:
- * O.Glatter & O.Kratky, (1982). Editors of "Small angle
- * X-ray Scattering, Academic Press, New York.
- * O.Kratky. (1963). X-ray small angle scattering with
- * substances of biological interest in diluted solutions.
- * Prog. Biophys. Chem., 13, 105-173.
- * G.D.Wignall & F.S.Bates, (1987). The small-angle approximation
- * of X-ray and neutron scatter from rigid rods of non-uniform
- * cross section and finite length. J.Appl. Crystallog., 18, 452-460.
- *
- * If the structure is elongated, the mean radius of gyration
- * of the cross-sectional structure R_XS and the mean cross sectional
- * intensity at zero angle [I(Q).Q]_Q->0 is obtained from
- * ln[I(Q).Q] = ln[l(Q).(Q)]_Q->0 - ((R_XS)^2Q^2)/2
+ * A unique identifier for each object in this entity instance container formed by
+ * an 'dot' (.) separated concatenation of entry and entity instance identifiers.
+ *
+ * Examples:
+ * 1KIP.A
+ *
*/
- readonly min_mean_cross_sectional_radii_gyration?: Maybe<Scalars['Float']>;
+ readonly rcsb_id?: Maybe<Scalars['String']>;
+};
+
+export type RcsbBranchedEntityKeywords = {
+ /** Keywords describing this branched entity. */
+ readonly text?: Maybe<Scalars['String']>;
+};
+
+export type RcsbBranchedEntityNameCom = {
/**
- * The estimated standard deviation for the
- * minimum mean radius of structural elongation of the sample.
- * In a given solute-solvent contrast, the radius of gyration
- * R_G is a measure of structural elongation if the internal
- * inhomogeneity of scattering densities has no effect. Guiner
- * analysis at low Q give the R_G and the forward scattering at
- * zero angle I(0).
- *
- * lnl(Q) = lnl(0) - R_G^2Q^2/3
- *
- * where
- * Q = 4(pi)sin(theta/lamda)
- * 2theta = scattering angle
- * lamda = wavelength
- *
- * The above expression is valid in a QR_G range for extended
- * rod-like particles. The relative I(0)/c values ( where
- * c = sample concentration) for sample measurements in a
- * constant buffer for a single sample data session, gives the
- * relative masses of the protein(s) studied when referenced
- * against a standard.
- *
- * see:
- * O.Glatter & O.Kratky, (1982). Editors of "Small angle
- * X-ray Scattering, Academic Press, New York.
- * O.Kratky. (1963). X-ray small angle scattering with
- * substances of biological interest in diluted solutions.
- * Prog. Biophys. Chem., 13, 105-173.
- * G.D.Wignall & F.S.Bates, (1987). The small-angle approximation
- * of X-ray and neutron scatter from rigid rods of non-uniform
- * cross section and finite length. J.Appl. Crystallog., 18, 452-460.
- *
- * If the structure is elongated, the mean radius of gyration
- * of the cross-sectional structure R_XS and the mean cross sectional
- * intensity at zero angle [I(Q).Q]_Q->0 is obtained from
- *
- * ln[I(Q).Q] = ln[l(Q).(Q)]_Q->0 - ((R_XS)^2Q^2)/2
+ * A common name for the branched entity.
+ *
+ * Examples:
+ * HIV protease monomer, hemoglobin alpha chain
+ *
*/
- readonly min_mean_cross_sectional_radii_gyration_esd?: Maybe<Scalars['Float']>;
- /** The number of time frame solution scattering images used. */
- readonly num_time_frames?: Maybe<Scalars['Int']>;
+ readonly name?: Maybe<Scalars['String']>;
+};
+
+export type RcsbBranchedEntityNameSys = {
+ /** The systematic name for the branched entity. */
+ readonly name: Scalars['String'];
+ /** The system used to generate the systematic name of the branched entity. */
+ readonly system?: Maybe<Scalars['String']>;
+};
+
+export type RcsbBranchedInstanceAnnotation = {
+ /** An identifier for the annotation. */
+ readonly annotation_id?: Maybe<Scalars['String']>;
+ readonly annotation_lineage?: Maybe<ReadonlyArray<Maybe<RcsbBranchedInstanceAnnotationAnnotationLineage>>>;
/**
- * The length (or range) of the protein sample under study.
- * If the solution structure is approximated as an elongated elliptical
- * cyclinder the the length L is determined from,
- *
- * L = sqrt [12( (R_G)^2 - (R_XS)^2 ) ]
- *
- * The length should also be given by
- *
- * L = pi I(0) / [ I(Q).Q]_Q->0
+ * Identifies the version of the annotation assignment.
+ *
+ * Examples:
+ * V4_0_2
+ *
*/
- readonly protein_length?: Maybe<Scalars['String']>;
- /** The pH value of the buffered sample. */
- readonly sample_pH?: Maybe<Scalars['Float']>;
- /** The beamline name used for the experiment */
- readonly source_beamline?: Maybe<Scalars['String']>;
- /** The instrumentation used on the beamline */
- readonly source_beamline_instrument?: Maybe<Scalars['String']>;
+ readonly assignment_version?: Maybe<Scalars['String']>;
/**
- * The general class of the radiation source.
- *
+ * Chemical component identifier.
+ *
* Examples:
- * neutron source, synchrotron
+ * ATP
+ *
*/
- readonly source_class?: Maybe<Scalars['String']>;
- /** The make, model, name or beamline of the source of radiation. */
- readonly source_type?: Maybe<Scalars['String']>;
+ readonly comp_id?: Maybe<Scalars['String']>;
+ /** A description for the annotation. */
+ readonly description?: Maybe<Scalars['String']>;
+ /** A name for the annotation. */
+ readonly name?: Maybe<Scalars['String']>;
+ /** Ordinal identifier for this category */
+ readonly ordinal: Scalars['Int'];
/**
- * The temperature in kelvins at which the experiment
- * was conducted
+ * Code identifying the individual, organization or program that
+ * assigned the annotation.
+ *
+ * Examples:
+ * PDB
+ *
*/
- readonly temperature?: Maybe<Scalars['Float']>;
+ readonly provenance_source?: Maybe<Scalars['String']>;
/**
- * The type of solution scattering experiment carried out
- *
+ * A type or category of the annotation.
+ *
* Allowable values:
- * modelling, neutron, x-ray
+ * CATH, SCOP
+ *
*/
readonly type?: Maybe<Scalars['String']>;
};
-export type RcsbPolymerEntityRcsbMacromolecularNamesCombined = {
- /** Combined list of macromolecular names. */
+export type RcsbBranchedInstanceAnnotationAnnotationLineage = {
+ /** Members of the annotation lineage as parent lineage depth (1-N) */
+ readonly depth?: Maybe<Scalars['Int']>;
+ /** Members of the annotation lineage as parent class identifiers. */
+ readonly id?: Maybe<Scalars['String']>;
+ /** Members of the annotation lineage as parent class names. */
readonly name?: Maybe<Scalars['String']>;
+};
+
+export type RcsbBranchedInstanceFeature = {
+ readonly additional_properties?: Maybe<ReadonlyArray<Maybe<RcsbBranchedInstanceFeatureAdditionalProperties>>>;
/**
- * Combined list of macromolecular names associated provenance code.
- *
- * ECO (https://github.com/evidenceontology/evidenceontology)
+ * Identifies the version of the feature assignment.
+ *
+ * Examples:
+ * V4_0_2
+ *
*/
- readonly provenance_code?: Maybe<Scalars['String']>;
+ readonly assignment_version?: Maybe<Scalars['String']>;
+ /** A description for the feature. */
+ readonly description?: Maybe<Scalars['String']>;
+ /** An identifier for the feature. */
+ readonly feature_id?: Maybe<Scalars['String']>;
+ readonly feature_positions?: Maybe<ReadonlyArray<Maybe<RcsbBranchedInstanceFeatureFeaturePositions>>>;
+ readonly feature_value?: Maybe<ReadonlyArray<Maybe<RcsbBranchedInstanceFeatureFeatureValue>>>;
+ /** A name for the feature. */
+ readonly name?: Maybe<Scalars['String']>;
+ /** Ordinal identifier for this category */
+ readonly ordinal: Scalars['Int'];
/**
- * Combined list of macromolecular names associated name source.
- *
- * Allowable values:
- * PDB Preferred Name, PDB Synonym
+ * Code identifying the individual, organization or program that
+ * assigned the feature.
+ *
+ * Examples:
+ * PDB
+ *
*/
readonly provenance_source?: Maybe<Scalars['String']>;
+ /**
+ * Code residue coordinate system for the assigned feature.
+ *
+ * Allowable values:
+ * PDB entity, PDB entry
+ *
+ */
+ readonly reference_scheme?: Maybe<Scalars['String']>;
+ /**
+ * A type or category of the feature.
+ *
+ * Allowable values:
+ * BINDING_SITE, CATH, ECOD, MOGUL_ANGLE_OUTLIER, MOGUL_BOND_OUTLIER, RSCC_OUTLIER, RSRZ_OUTLIER, SCOP, STEREO_OUTLIER, UNOBSERVED_ATOM_XYZ, UNOBSERVED_RESIDUE_XYZ, ZERO_OCCUPANCY_ATOM_XYZ, ZERO_OCCUPANCY_RESIDUE_XYZ
+ *
+ */
+ readonly type?: Maybe<Scalars['String']>;
};
-export type EmVitrification = {
+export type RcsbBranchedInstanceFeatureAdditionalProperties = {
/**
- * The temperature (in degrees Kelvin) of the sample just prior to vitrification.
- *
+ * The additional property name.
+ *
* Examples:
- * 298
+ * bond_distance, bond_angle
+ *
*/
- readonly chamber_temperature?: Maybe<Scalars['Float']>;
+ readonly name?: Maybe<Scalars['String']>;
+ /** The value(s) of the additional property. */
+ readonly values?: Maybe<ReadonlyArray<Maybe<Scalars['ObjectScalar']>>>;
+};
+
+export type RcsbBranchedInstanceFeatureFeaturePositions = {
/**
- * This is the name of the cryogen.
- *
- * Allowable values:
- * ETHANE, ETHANE-PROPANE, FREON 12, FREON 22, HELIUM, METHANE, NITROGEN, OTHER, PROPANE
+ * An identifier for the monomer(s) corresponding to the feature assignment.
+ *
+ * Examples:
+ * NAG, MAN
+ *
*/
- readonly cryogen_name?: Maybe<Scalars['String']>;
+ readonly beg_comp_id?: Maybe<Scalars['String']>;
+ /** An identifier for the leading monomer feature position. */
+ readonly beg_seq_id: Scalars['Int'];
+ /** An identifier for the terminal monomer feature position. */
+ readonly end_seq_id?: Maybe<Scalars['Int']>;
/**
- * Any additional details relating to vitrification.
- *
+ * The value of the feature at the monomer position.
+ *
* Examples:
- * Vitrification carried out in argon atmosphere.
+ * null, null
+ *
+ */
+ readonly value?: Maybe<Scalars['Float']>;
+ /** The value(s) of the feature at the monomer position. */
+ readonly values?: Maybe<ReadonlyArray<Maybe<Scalars['Float']>>>;
+};
+
+export type RcsbBranchedInstanceFeatureFeatureValue = {
+ /**
+ * The chemical component identifier for the instance of the feature value.
+ *
+ * Examples:
+ * ATP,, STN
+ *
+ */
+ readonly comp_id?: Maybe<Scalars['String']>;
+ /**
+ * Specific details about the feature.
+ *
+ * Examples:
+ * C1,C2, C1,C2,C3
+ *
*/
readonly details?: Maybe<Scalars['String']>;
/**
- * The humidity (%) in the vicinity of the vitrification process.
- *
+ * The reference value of the feature.
+ *
* Examples:
- * 90
+ * null, null
+ *
*/
- readonly humidity?: Maybe<Scalars['Float']>;
+ readonly reference?: Maybe<Scalars['Float']>;
/**
- * The value of _em_vitrification.id must uniquely identify
- * the vitrification procedure.
+ * The reported value of the feature.
+ *
+ * Examples:
+ * null, null
+ *
*/
- readonly id: Scalars['String'];
+ readonly reported?: Maybe<Scalars['Float']>;
/**
- * The type of instrument used in the vitrification process.
- *
+ * The estimated uncertainty of the reported feature value.
+ *
+ * Examples:
+ * null, null
+ *
+ */
+ readonly uncertainty_estimate?: Maybe<Scalars['Float']>;
+ /**
+ * The type of estimated uncertainty for the reported feature value.
+ *
* Allowable values:
- * EMS-002 RAPID IMMERSION FREEZER, FEI VITROBOT MARK I, FEI VITROBOT MARK II, FEI VITROBOT MARK III, FEI VITROBOT MARK IV, GATAN CRYOPLUNGE 3, HOMEMADE PLUNGER, LEICA EM CPC, LEICA EM GP, LEICA KF80, LEICA PLUNGER, REICHERT-JUNG PLUNGER, SPOTITON, ZEISS PLUNGE FREEZER CRYOBOX
+ * Z-Score
+ *
*/
- readonly instrument?: Maybe<Scalars['String']>;
+ readonly uncertainty_estimate_type?: Maybe<Scalars['String']>;
+};
+
+export type RcsbBranchedInstanceFeatureSummary = {
+ /** The feature count. */
+ readonly count?: Maybe<Scalars['Int']>;
/**
- * The procedure for vitrification.
- *
+ * The fractional feature coverage relative to the full branched entity.
+ *
* Examples:
- * plunge freezing
+ * null, null
+ *
*/
- readonly method?: Maybe<Scalars['String']>;
- /** This data item is a pointer to _em_specimen.id */
- readonly specimen_id: Scalars['String'];
+ readonly coverage?: Maybe<Scalars['Float']>;
+ /** The maximum feature length. */
+ readonly maximum_length?: Maybe<Scalars['Int']>;
/**
- * The vitrification temperature (in degrees Kelvin), e.g.,
- * temperature of the plunge instrument cryogen bath.
- *
+ * The maximum feature value.
+ *
* Examples:
- * 90
+ * null, null
+ *
*/
- readonly temp?: Maybe<Scalars['Float']>;
+ readonly maximum_value?: Maybe<Scalars['Float']>;
+ /** The minimum feature length. */
+ readonly minimum_length?: Maybe<Scalars['Int']>;
/**
- * The length of time after an event effecting the sample that
- * vitrification was induced and a description of the event.
- *
+ * The minimum feature value.
+ *
* Examples:
- * plunge 30 msec after spraying with effector
+ * null, null
+ *
*/
- readonly time_resolved_state?: Maybe<Scalars['String']>;
+ readonly minimum_value?: Maybe<Scalars['Float']>;
+ /**
+ * Type or category of the feature.
+ *
+ * Allowable values:
+ * BINDING_SITE, CATH, MOGUL_ANGLE_OUTLIER, MOGUL_BOND_OUTLIER, RSCC_OUTLIER, RSRZ_OUTLIER, SCOP, STEREO_OUTLIER, UNOBSERVED_ATOM_XYZ, UNOBSERVED_RESIDUE_XYZ, ZERO_OCCUPANCY_ATOM_XYZ, ZERO_OCCUPANCY_RESIDUE_XYZ
+ *
+ */
+ readonly type?: Maybe<Scalars['String']>;
};
-export type RefineHist = {
+export type RcsbBranchedStructConn = {
+ readonly connect_partner?: Maybe<RcsbBranchedStructConnConnectPartner>;
+ readonly connect_target?: Maybe<RcsbBranchedStructConnConnectTarget>;
/**
- * The value of _refine_hist.cycle_id must uniquely identify a
- * record in the REFINE_HIST list.
- *
- * Note that this item need not be a number; it can be any unique
- * identifier.
+ * The connection type.
+ *
+ * Allowable values:
+ * covalent bond, hydrogen bond, ionic interaction, metal coordination, mismatched base pairs
+ *
+ */
+ readonly connect_type?: Maybe<Scalars['String']>;
+ /**
+ * A description of special details of the connection.
+ *
+ * Examples:
+ * Watson-Crick base pair
+ *
+ */
+ readonly description?: Maybe<Scalars['String']>;
+ /** Distance value for this contact. */
+ readonly dist_value?: Maybe<Scalars['Float']>;
+ /** The value of _rcsb_branched_struct_conn.id is an identifier for connection. */
+ readonly id?: Maybe<Scalars['String']>;
+ /**
+ * The value of _rcsb_branched_struct_conn.id must uniquely identify a record in
+ * the rcsb_branched_struct_conn list.
+ */
+ readonly ordinal_id: Scalars['Int'];
+ /**
+ * The chemical or structural role of the interaction
+ *
+ * Allowable values:
+ * C-Mannosylation, N-Glycosylation, O-Glycosylation
+ *
+ */
+ readonly role?: Maybe<Scalars['String']>;
+ /**
+ * The chemical bond order associated with the specified atoms in
+ * this contact.
+ *
+ * Allowable values:
+ * doub, quad, sing, trip
+ *
+ */
+ readonly value_order?: Maybe<Scalars['String']>;
+};
+
+export type RcsbBranchedStructConnConnectPartner = {
+ /**
+ * A component of the identifier for the partner in the structure
+ * connection.
+ *
+ * This data item is a pointer to _atom_site.label_alt_id in the
+ * ATOM_SITE category.
*/
- readonly cycle_id: Scalars['String'];
+ readonly label_alt_id?: Maybe<Scalars['String']>;
/**
- * The lowest value for the interplanar spacings for the
- * reflection data for this cycle of refinement. This is called
- * the highest resolution.
+ * A component of the identifier for the partner in the structure
+ * connection.
+ *
+ * This data item is a pointer to _atom_site.label_asym_id in the
+ * ATOM_SITE category.
*/
- readonly d_res_high?: Maybe<Scalars['Float']>;
+ readonly label_asym_id: Scalars['String'];
/**
- * The highest value for the interplanar spacings for the
- * reflection data for this cycle of refinement. This is
- * called the lowest resolution.
+ * A component of the identifier for the partner in the structure
+ * connection.
+ *
+ * This data item is a pointer to _chem_comp_atom.atom_id in the
+ * CHEM_COMP_ATOM category.
*/
- readonly d_res_low?: Maybe<Scalars['Float']>;
+ readonly label_atom_id?: Maybe<Scalars['String']>;
/**
- * The number of solvent atoms that were included in the model at
- * this cycle of the refinement.
+ * A component of the identifier for the partner in the structure
+ * connection.
+ *
+ * This data item is a pointer to _atom_site.label_comp_id in the
+ * ATOM_SITE category.
*/
- readonly number_atoms_solvent?: Maybe<Scalars['Int']>;
+ readonly label_comp_id: Scalars['String'];
/**
- * The total number of atoms that were included in the model at
- * this cycle of the refinement.
+ * A component of the identifier for the partner in the structure
+ * connection.
+ *
+ * This data item is a pointer to _atom_site.label_seq_id in the
+ * ATOM_SITE category.
*/
- readonly number_atoms_total?: Maybe<Scalars['Int']>;
- /** Mean isotropic B-value for ligand molecules included in refinement. */
- readonly pdbx_B_iso_mean_ligand?: Maybe<Scalars['Float']>;
- /** Mean isotropic B-value for solvent molecules included in refinement. */
- readonly pdbx_B_iso_mean_solvent?: Maybe<Scalars['Float']>;
- /** Number of ligand atoms included in refinement */
- readonly pdbx_number_atoms_ligand?: Maybe<Scalars['Int']>;
- /** Number of nucleic atoms included in refinement */
- readonly pdbx_number_atoms_nucleic_acid?: Maybe<Scalars['Int']>;
- /** Number of protein atoms included in refinement */
- readonly pdbx_number_atoms_protein?: Maybe<Scalars['Int']>;
- /** Total number of polymer residues included in refinement. */
- readonly pdbx_number_residues_total?: Maybe<Scalars['Int']>;
+ readonly label_seq_id?: Maybe<Scalars['Int']>;
/**
- * This data item uniquely identifies a refinement within an entry.
- * _refine_hist.pdbx_refine_id can be used to distinguish the results
- * of joint refinements.
+ * Describes the symmetry operation that should be applied to the
+ * atom set specified by _rcsb_branched_struct_conn.connect_partner_label* to generate the
+ * partner in the structure connection.
+ *
+ * Examples:
+ * 1_555, 7_645
+ *
*/
- readonly pdbx_refine_id: Scalars['String'];
+ readonly symmetry?: Maybe<Scalars['String']>;
};
-export type PdbxVrptSummary = {
- /**
- * String for B_factor_type either "PARTIAL" or "FULL".
- *
- * Allowable values:
- * FULL, PARTIAL
- */
- readonly B_factor_type?: Maybe<Scalars['String']>;
- /**
- * REFMAC scaling parameter as reported in log output line starting 'bulk solvent: scale'.
- * Example: X-ray entry specific, obtained in the eds step from REFMAC calculation.
- */
- readonly Babinet_b?: Maybe<Scalars['Float']>;
+export type RcsbBranchedStructConnConnectTarget = {
/**
- * REFMAC scaling parameter as reported in log output line starting 'bulk solvent: scale'.
- * Example: X-ray entry specific, obtained in the eds step from REFMAC calculation.
+ * A component of the identifier for the target of the structure
+ * connection.
+ *
+ * This data item is a pointer to _atom_site.auth_asym_id in the
+ * ATOM_SITE category.
*/
- readonly Babinet_k?: Maybe<Scalars['Float']>;
+ readonly auth_asym_id?: Maybe<Scalars['String']>;
/**
- * The string "yes".
- *
- * Allowable values:
- * yes
+ * A component of the identifier for the target of the structure
+ * connection.
+ *
+ * This data item is a pointer to _atom_site.auth_seq_id in the
+ * ATOM_SITE category.
*/
- readonly CA_ONLY?: Maybe<Scalars['String']>;
+ readonly auth_seq_id?: Maybe<Scalars['String']>;
/**
- * The overall R-factor from a DCC recalculation of an electron density map.
- * Example: Currently value is rounded to 2 decimal places.
- * X-ray entry specific, obtained from the DCC program.
+ * A component of the identifier for the target of the structure
+ * connection.
+ *
+ * This data item is a pointer to _atom_site.label_alt_id in the
+ * ATOM_SITE category.
*/
- readonly DCC_R?: Maybe<Scalars['Float']>;
- /** Either a decimal number or the string "NotAvailable". */
- readonly DCC_Rfree?: Maybe<Scalars['Float']>;
+ readonly label_alt_id?: Maybe<Scalars['String']>;
/**
- * The pdbx_vrpt_software used by DCC to perform the recaluclation of the electron density maps.
- *  Currently one of "CNS", "REFMAC" or "PHENIX".
- * Example: X-ray entry specific, obtained from the DCC program.
+ * A component of the identifier for the target of the structure
+ * connection.
+ *
+ * This data item is a pointer to _atom_site.label_asym_id in the
+ * ATOM_SITE category.
*/
- readonly DCC_refinement_program?: Maybe<Scalars['String']>;
+ readonly label_asym_id: Scalars['String'];
/**
- * The overall R factor from the EDS REFMAC calculation (no free set is used in this).
- * Example: Currently value is rounded to 2 decimal places.
- * X-ray entry specific, obtained in the eds step from REFMAC calculation.
+ * A component of the identifier for the target of the structure
+ * connection.
+ *
+ * This data item is a pointer to _atom_site.label_atom_id in the
+ * ATOM_SITE category.
*/
- readonly EDS_R?: Maybe<Scalars['Float']>;
+ readonly label_atom_id?: Maybe<Scalars['String']>;
/**
- * The data high resolution diffraction limit, in Angstroms, found in the input structure factor file.
- * Example: X-ray entry specific, obtained in the eds step.
+ * A component of the identifier for the target of the structure
+ * connection.
+ *
+ * This data item is a pointer to _atom_site.label_comp_id in the
+ * ATOM_SITE category.
*/
- readonly EDS_resolution?: Maybe<Scalars['Float']>;
+ readonly label_comp_id: Scalars['String'];
/**
- * The data low resolution diffraction limit, in Angstroms, found in the input structure factor file.
- * Example: X-ray entry specific, obtained in the eds step.
+ * A component of the identifier for the target of the structure
+ * connection.
+ *
+ * This data item is a pointer to _atom_site.connect_target_label_seq_id in the
+ * ATOM_SITE category.
*/
- readonly EDS_resolution_low?: Maybe<Scalars['Float']>;
+ readonly label_seq_id?: Maybe<Scalars['Int']>;
/**
- * Date in yyyy-mm-dd format when map was deposited to the EMDB.
- * Reports produced by the validation server or during the initial deposition process should not have this item.
- * If there is a difficulty parsing the item then "unknown" will be given.
+ * Describes the symmetry operation that should be applied to the
+ * atom set specified by _rcsb_branched_struct_conn.label* to generate the
+ * target of the structure connection.
+ *
+ * Examples:
+ * 1_555, 7_645
+ *
*/
- readonly EMDB_deposition_date?: Maybe<Scalars['Date']>;
- /** Either a decimal number or the string "NotAvailable". */
- readonly EMDB_resolution?: Maybe<Scalars['Float']>;
+ readonly symmetry?: Maybe<Scalars['String']>;
+};
+
+export type RcsbChemCompAnnotation = {
+ /** An identifier for the annotation. */
+ readonly annotation_id?: Maybe<Scalars['String']>;
+ readonly annotation_lineage?: Maybe<ReadonlyArray<Maybe<RcsbChemCompAnnotationAnnotationLineage>>>;
/**
- * Fo,Fc correlation: The difference between the observed structure factors (Fo) and the
- * calculated structure factors (Fc) measures the correlation between the PDB_model_num and the i
- * experimental data.
- * Example: X-ray entry specific, obtained in the eds step from REFMAC calculation.
+ * Identifies the version of the annotation assignment.
+ *
+ * Examples:
+ * V4_0_2
+ *
*/
- readonly Fo_Fc_correlation?: Maybe<Scalars['Float']>;
+ readonly assignment_version?: Maybe<Scalars['String']>;
+ /** A description for the annotation. */
+ readonly description?: Maybe<Scalars['String']>;
+ /** A name for the annotation. */
+ readonly name?: Maybe<Scalars['String']>;
/**
- * Each reflection has an intensity (I) and an uncertainty in measurement
- * (sigma(I)), so I/sigma(I) is the signal-to-noise ratio. This
- * ratio decreases at higher resolution. <I/sigma(I)> is the mean of individual I/sigma(I)
- * values. Value for outer resolution shell is given in parentheses. In case
- * structure factor amplitudes are deposited, Xtriage estimates the intensities
- * first and then calculates this metric. When intensities are available in the
- * deposited file, these are converted to amplitudes and then back to intensity
- * estimate before calculating the metric.
- * Example X-ray entry specific, calculated by Phenix Xtriage program.
+ * Code identifying the individual, organization or program that
+ * assigned the annotation.
+ *
+ * Examples:
+ * RESID, UniProt, PDB
+ *
*/
- readonly I_over_sigma?: Maybe<Scalars['String']>;
- /** Either a decimal number or the string "NotAvailable". */
- readonly PDB_R?: Maybe<Scalars['Float']>;
- /** Either a decimal number or the string "NotAvailable". */
- readonly PDB_Rfree?: Maybe<Scalars['Float']>;
+ readonly provenance_source?: Maybe<Scalars['String']>;
/**
- * Date in yyyy-mm-dd format when structure was deposited to the PDB.
- * Obtained from mmCIF table _database_PDB_rev item _database_PDB_rev.date_original
- * Reports produced by the validation server or during the initial deposition process should not have this item.
- * If there is a difficulty parsing the item then "unknown" will be given.
+ * A type or category of the annotation.
+ *
+ * Allowable values:
+ * ATC, Carbohydrate Anomer, Carbohydrate Isomer, Carbohydrate Primary Carbonyl Group, Carbohydrate Ring, Generating Enzyme, Modification Type, PSI-MOD
+ *
*/
- readonly PDB_deposition_date?: Maybe<Scalars['Date']>;
- /** Either a decimal number or the string "NotAvailable". */
- readonly PDB_resolution?: Maybe<Scalars['Float']>;
- /** Either a decimal number or the string "NotAvailable". */
- readonly PDB_resolution_low?: Maybe<Scalars['Float']>;
+ readonly type?: Maybe<Scalars['String']>;
+};
+
+export type RcsbChemCompAnnotationAnnotationLineage = {
+ /** Members of the annotation lineage as parent lineage depth (1-N) */
+ readonly depth?: Maybe<Scalars['Int']>;
+ /** Members of the annotation lineage as parent class identifiers. */
+ readonly id?: Maybe<Scalars['String']>;
+ /** Members of the annotation lineage as parent class names. */
+ readonly name?: Maybe<Scalars['String']>;
+};
+
+export type RcsbChemCompContainerIdentifiers = {
/**
- * Date in yyyy-mm-dd format when the structure was last revised by PDB.
- * Obtained from mmCIF table _database_PDB_rev item _database_PDB_rev.date
- * Reports produced by the validation server or during the initial depositon process should not have this item.
- * If there is a difficulty parsing the item then "unknown" will be given.
+ * The Anatomical Therapeutic Chemical (ATC) Classification System identifiers corresponding
+ * to the chemical component.
*/
- readonly PDB_revision_date?: Maybe<Scalars['Date']>;
+ readonly atc_codes?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
/**
- * The last highest number that appears in mmCIF item _database_PDB_rev.num.
- * Data items in the DATABASE_PDB_REV category record details about the history of the data block as archived by the Protein Data Bank (PDB).
- * If the input mmCIF coordinate file lacks the information then a value of -1 is supplied.
+ * The chemical component identifier.
+ *
+ * Examples:
+ * ATP, STI
+ *
*/
- readonly PDB_revision_number?: Maybe<Scalars['Float']>;
+ readonly comp_id: Scalars['String'];
/**
- * The MolProbity conformer-match quality parameter for RNA structures.
- * Low values are worse.
- * Example: Specific to structures that contain RNA polymers.
+ * The DrugBank identifier corresponding to the chemical component.
+ *
+ * Examples:
+ * DB00781, DB15263
+ *
*/
- readonly RNA_suiteness?: Maybe<Scalars['Float']>;
+ readonly drugbank_id?: Maybe<Scalars['String']>;
/**
- * Result of absolute likelihood based Wilson scaling,
- * The anisotropic B value of the data is determined using a likelihood based approach.
- * The resulting B tensor is reported, the 3 diagonal values are given first, followed
- * by the 3 off diagonal values.
- * A large spread in (especially the diagonal) values indicates anisotropy.
- * Example: X-ray entry specific, calculated by Phenix Xtriage program.
+ * The BIRD definition identifier.
+ *
+ * Examples:
+ * PRD_000010
+ *
*/
- readonly Wilson_B_aniso?: Maybe<Scalars['String']>;
+ readonly prd_id?: Maybe<Scalars['String']>;
/**
- * An estimate of the overall B-value of the structure, calculated from the diffraction data.
- * Units Angstroms squared.
- * It serves as an indicator of the degree of order in the crystal and the value is usually
- * not hugely different from the average B-value calculated from the model.
- * Example: X-ray entry specific, calculated by Phenix Xtriage program.
+ * A unique identifier for the chemical definition in this container.
+ *
+ * Examples:
+ * ATP, PRD_000010
+ *
*/
- readonly Wilson_B_estimate?: Maybe<Scalars['Float']>;
+ readonly rcsb_id?: Maybe<Scalars['String']>;
+ /** The list of subcomponents contained in this component. */
+ readonly subcomponent_ids?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
+};
+
+export type RcsbChemCompDescriptor = {
/**
- * Structures are judged in comparison to previously deposited PDB entries.
- * The comparison is carried out by calculation of the percentile rank, i.e. the percentage of entries
- * that are equal or poorer than this structure in terms of a quality indicator.
- * Percentile ranks range from 0 (the worst) to 100 (the best).
+ * Standard IUPAC International Chemical Identifier (InChI) descriptor for the chemical component.
+ *
+ * InChI, the IUPAC International Chemical Identifier,
+ * by Stephen R Heller, Alan McNaught, Igor Pletnev, Stephen Stein and Dmitrii Tchekhovskoi,
+ * Journal of Cheminformatics, 2015, 7:23;
+ *
+ * Examples:
+ * InChI=1S/C3H6FO6P/c4-1-2(3(5)6)10-11(7,8)9/h2H,1H2,(H,5,6)(H2,7,8,9)/t2-/m0/s1
+ *
*/
- readonly absolute_percentile_DCC_Rfree?: Maybe<Scalars['Float']>;
+ readonly InChI?: Maybe<Scalars['String']>;
/**
- * Structures are judged in comparison to previously deposited PDB entries.
- * The comparison is carried out by calculation of the percentile rank, i.e. the percentage of entries
- * that are equal or poorer than this structure in terms of a quality indicator.
- * Percentile ranks range from 0 (the worst) to 100 (the best).
+ * Standard IUPAC International Chemical Identifier (InChI) descriptor key
+ * for the chemical component
+ *
+ * InChI, the IUPAC International Chemical Identifier,
+ * by Stephen R Heller, Alan McNaught, Igor Pletnev, Stephen Stein and Dmitrii Tchekhovskoi,
+ * Journal of Cheminformatics, 2015, 7:23
+ *
+ * Examples:
+ * BNOCDEBUFVJMQI-REOHCLBHSA-N
+ *
*/
- readonly absolute_percentile_RNA_suiteness?: Maybe<Scalars['Float']>;
+ readonly InChIKey?: Maybe<Scalars['String']>;
/**
- * Structures are judged in comparison to previously deposited PDB entries.
- * The comparison is carried out by calculation of the percentile rank, i.e. the percentage of entries
- * that are equal or poorer than this structure in terms of a quality indicator.
- * Percentile ranks range from 0 (the worst) to 100 (the best).
+ * Simplified molecular-input line-entry system (SMILES) descriptor for the chemical component.
+ *
+ * Weininger D (February 1988). "SMILES, a chemical language and information system. 1.
+ * Introduction to methodology and encoding rules". Journal of Chemical Information and Modeling. 28 (1): 31-6.
+ *
+ * Weininger D, Weininger A, Weininger JL (May 1989).
+ * "SMILES. 2. Algorithm for generation of unique SMILES notation",
+ * Journal of Chemical Information and Modeling. 29 (2): 97-101.
+ *
+ * Examples:
+ * OC(=O)[CH](CF)O[P](O)(O)=O
+ *
*/
- readonly absolute_percentile_clashscore?: Maybe<Scalars['Float']>;
+ readonly SMILES?: Maybe<Scalars['String']>;
/**
- * Structures are judged in comparison to previously deposited PDB entries.
- * The comparison is carried out by calculation of the percentile rank, i.e. the percentage of entries
- * that are equal or poorer than this structure in terms of a quality indicator.
- * Percentile ranks range from 0 (the worst) to 100 (the best).
+ * Simplified molecular-input line-entry system (SMILES) descriptor for the chemical
+ * component including stereochemical features.
+ *
+ * Weininger D (February 1988). "SMILES, a chemical language and information system. 1.
+ * Introduction to methodology and encoding rules".
+ * Journal of Chemical Information and Modeling. 28 (1): 31-6.
+ *
+ * Weininger D, Weininger A, Weininger JL (May 1989).
+ * "SMILES. 2. Algorithm for generation of unique SMILES notation".
+ * Journal of Chemical Information and Modeling. 29 (2): 97-101.
+ *
+ * Examples:
+ * OC(=O)[C@H](CF)O[P](O)(O)=O
+ *
*/
- readonly absolute_percentile_percent_RSRZ_outliers?: Maybe<Scalars['Float']>;
+ readonly SMILES_stereo?: Maybe<Scalars['String']>;
+ /** The chemical component identifier. */
+ readonly comp_id: Scalars['String'];
+};
+
+export type RcsbChemCompInfo = {
+ /** Chemical component total atom count */
+ readonly atom_count?: Maybe<Scalars['Int']>;
+ /** Chemical component chiral atom count */
+ readonly atom_count_chiral?: Maybe<Scalars['Int']>;
+ /** Chemical component heavy atom count */
+ readonly atom_count_heavy?: Maybe<Scalars['Int']>;
+ /** Chemical component total bond count */
+ readonly bond_count?: Maybe<Scalars['Int']>;
+ /** Chemical component aromatic bond count */
+ readonly bond_count_aromatic?: Maybe<Scalars['Int']>;
+ /** The chemical component identifier. */
+ readonly comp_id: Scalars['String'];
/**
- * Structures are judged in comparison to previously deposited PDB entries.
- * The comparison is carried out by calculation of the percentile rank, i.e. the percentage of entries
- * that are equal or poorer than this structure in terms of a quality indicator.
- * Percentile ranks range from 0 (the worst) to 100 (the best).
+ * The date the chemical definition was first deposited in the PDB repository.
+ *
+ * Examples:
+ * 2016-09-11
+ *
*/
- readonly absolute_percentile_percent_ramachandran_outliers?: Maybe<Scalars['Float']>;
+ readonly initial_deposition_date?: Maybe<Scalars['Date']>;
/**
- * Structures are judged in comparison to previously deposited PDB entries.
- * The comparison is carried out by calculation of the percentile rank, i.e. the percentage of entries
- * that are equal or poorer than this structure in terms of a quality indicator.
- * Percentile ranks range from 0 (the worst) to 100 (the best).
+ * The initial date the chemical definition was released in the PDB repository.
+ *
+ * Examples:
+ * 2016-09-11
+ *
*/
- readonly absolute_percentile_percent_rotamer_outliers?: Maybe<Scalars['Float']>;
+ readonly initial_release_date?: Maybe<Scalars['Date']>;
/**
- * The number of acentric reflections that Xtriage identifies as outliers on the basis
- * of Wilson statistics. Note that if pseudo translational symmetry is present,
- * a large number of 'outliers' will be present.
- * Example: X-ray entry specific, calculated by Phenix Xtriage program.
+ * The release status of the chemical definition.
+ *
+ * Allowable values:
+ * DEL, HOLD, HPUB, OBS, REF_ONLY, REL
+ *
*/
- readonly acentric_outliers?: Maybe<Scalars['Int']>;
+ readonly release_status?: Maybe<Scalars['String']>;
/**
- * The overall root mean square of the Z-score for deviations of bond angles in comparison to
- * "standard geometry" made using the MolProbity dangle program.
- * Standard geometry parameters are taken from Engh and Huber (2001) and Parkinson et al. (1996).
- * This value is for all chains in the structure.
+ * The date of last revision of the chemical definition.
+ *
+ * Examples:
+ * 2016-10-12
+ *
*/
- readonly angles_RMSZ?: Maybe<Scalars['Float']>;
- /** The proportion of all non hydrogen atoms within density. */
- readonly atom_inclusion_all_atoms?: Maybe<Scalars['Float']>;
- /** The proportion of backbone atoms within density. */
- readonly atom_inclusion_backbone?: Maybe<Scalars['Float']>;
+ readonly revision_date?: Maybe<Scalars['Date']>;
+};
+
+export type RcsbChemCompRelated = {
/**
- * The steps that were attempted by the validation pipeline software.
- * A step typically involves running a 3rd party validation tool, for instance "mogul"
- * Each step that was successfully completed will result in a pdbx_vrpt_software element in the pdbx_vrpt_sotfware_notused list.
+ * The value of _rcsb_chem_comp_related.comp_id is a reference to
+ * a chemical component definition.
*/
- readonly attempted_validation_steps?: Maybe<Scalars['String']>;
- /** The resolution from the intersection of the author provided fsc and the indicator curve halfbit. */
- readonly author_provided_fsc_resolution_by_cutoff_halfbit?: Maybe<Scalars['Float']>;
- /** The resolution from the intersection of the author provided fsc and the indicator curve onebit. */
- readonly author_provided_fsc_resolution_by_cutoff_onebit?: Maybe<Scalars['Float']>;
- /** The resolution from the intersection of the author provided fsc and the indicator curve 0.143. */
- readonly author_provided_fsc_resolution_by_cutoff_pt_143?: Maybe<Scalars['Float']>;
- /** The resolution from the intersection of the author provided fsc and the indicator curve 0.333. */
- readonly author_provided_fsc_resolution_by_cutoff_pt_333?: Maybe<Scalars['Float']>;
- /** The resolution from the intersection of the author provided fsc and the indicator curve 0.5. */
- readonly author_provided_fsc_resolution_by_cutoff_pt_5?: Maybe<Scalars['Float']>;
- /** The resolution from the intersection of the author provided fsc and the indicator curve threesigma. */
- readonly author_provided_fsc_resolution_by_cutoff_threesigma?: Maybe<Scalars['Float']>;
+ readonly comp_id: Scalars['String'];
/**
- * The overall root mean square of the Z-score for deviations of bond lengths in comparison to
- * "standard geometry" made using the MolProbity dangle program.
- * Standard geometry parameters are taken from Engh and Huber (2001) and Parkinson et al. (1996).
- * This value is for all chains in the structure.
+ * The value of _rcsb_chem_comp_related.ordinal distinguishes
+ * related examples for each chemical component.
*/
- readonly bonds_RMSZ?: Maybe<Scalars['Float']>;
+ readonly ordinal: Scalars['Int'];
/**
- * REFMAC scaling parameter as reported in log output line starting
- * 'Partial structure 1: scale.'
- * Example: X-ray entry specific, obtained in the eds step from REFMAC calculation.
+ * The method used to establish the resource correspondence.
+ *
+ * Allowable values:
+ * assigned by DrugBank resource, assigned by PDB, assigned by PubChem resource, matching ChEMBL ID in Pharos, matching InChIKey in DrugBank, matching InChIKey in PubChem, matching InChIKey-prefix in DrugBank, matching by RESID resource
+ *
*/
- readonly bulk_solvent_b?: Maybe<Scalars['Float']>;
+ readonly related_mapping_method?: Maybe<Scalars['String']>;
/**
- * REFMAC scaling parameter as reported in log output line starting
- * 'Partial structure 1: scale.'
- * Example: X-ray entry specific, obtained in the eds step from REFMAC calculation.
+ * The resource identifier code for the related chemical reference.
+ *
+ * Examples:
+ * 124832
+ *
*/
- readonly bulk_solvent_k?: Maybe<Scalars['Float']>;
- /** The resolution from the intersection of the fsc curve generated by from the provided halfmaps and the indicator curve halfbit. */
- readonly calculated_fsc_resolution_by_cutoff_halfbit?: Maybe<Scalars['Float']>;
- /** The resolution from the intersection of the fsc curve generated by from the provided halfmaps and the indicator curve onebit. */
- readonly calculated_fsc_resolution_by_cutoff_onebit?: Maybe<Scalars['Float']>;
- /** The resolution from the intersection of the fsc curve generated by from the provided halfmaps and the indicator curve 0.143. */
- readonly calculated_fsc_resolution_by_cutoff_pt_143?: Maybe<Scalars['Float']>;
- /** The resolution from the intersection of the fsc curve generated by from the provided halfmaps and the indicator curve 0.333. */
- readonly calculated_fsc_resolution_by_cutoff_pt_333?: Maybe<Scalars['Float']>;
- /** The resolution from the intersection of the fsc curve generated by from the provided halfmaps and the indicator curve 0.5. */
- readonly calculated_fsc_resolution_by_cutoff_pt_5?: Maybe<Scalars['Float']>;
- /** The resolution from the intersection of the fsc curve generated by from the provided halfmaps and the indicator curve threesigma. */
- readonly calculated_fsc_resolution_by_cutoff_threesigma?: Maybe<Scalars['Float']>;
+ readonly resource_accession_code?: Maybe<Scalars['String']>;
/**
- * The version of CCP4 suite pdbx_vrpt_sotfware_notused used in the analysis.
- * Example: X-ray entry specific, obtained from the eds step.
+ * The resource name for the related chemical reference.
+ *
+ * Allowable values:
+ * CAS, CCDC/CSD, ChEBI, ChEMBL, DrugBank, Pharos, PubChem, RESID
+ *
*/
- readonly ccp4version?: Maybe<Scalars['String']>;
+ readonly resource_name?: Maybe<Scalars['String']>;
+};
+
+export type RcsbChemCompSynonyms = {
+ /** The chemical component to which this synonym applies. */
+ readonly comp_id: Scalars['String'];
/**
- * The number of centric reflections that Xtriage identifies as outliers.
- * Example: X-ray entry specific, calculated by Phenix Xtriage program.
+ * The synonym of this particular chemical component.
+ *
+ * Examples:
+ * Ursonic acid, Talotrexin, 4-oxodecanedioic acid
+ *
*/
- readonly centric_outliers?: Maybe<Scalars['Float']>;
+ readonly name?: Maybe<Scalars['String']>;
/**
- * Overall completeness of the chemical shift assignments for the well-defined
- * regions of the structure.
+ * This data item is an ordinal index for the
+ * RCSB_CHEM_COMP_SYNONYMS category.
*/
- readonly chemical_shift_completeness?: Maybe<Scalars['Float']>;
+ readonly ordinal: Scalars['Int'];
/**
- * Overall completeness of the chemical shift assignments for the full
- * macromolecule or complex as suggested by the molecular description of an entry
- * (whether some portion of it is modelled or not).
+ * The provenance of this synonym.
+ *
+ * Allowable values:
+ * ACDLabs, Author, ChEBI, ChEMBL, DrugBank, GMML, Lexichem, OpenEye OEToolkits, OpenEye/Lexichem, PDB Reference Data, PDB Reference Data (Preferred), PDB-CARE, PubChem, RESID
+ *
*/
- readonly chemical_shift_completeness_full_length?: Maybe<Scalars['Float']>;
+ readonly provenance_source?: Maybe<Scalars['String']>;
/**
- * The filename for the input chemical shifts file given to the validation pipeline.
- * Not reported for runs at the annotation or release stage.
+ * This data item contains the synonym type.
+ *
+ * Allowable values:
+ * Brand Name, Common Name, Condensed IUPAC Carbohydrate Symbol, IUPAC Carbohydrate Symbol, Preferred Common Name, Preferred Name, Preferred Synonym, SNFG Carbohydrate Symbol, Synonym, Systematic Name
+ *
*/
- readonly chemical_shifts_input_filename?: Maybe<Scalars['String']>;
+ readonly type?: Maybe<Scalars['String']>;
+};
+
+export type RcsbChemCompTarget = {
/**
- * This score is derived from the number of pairs of atoms in the PDB_model_num that are unusually close to each other.
- * It is calculated by the MolProbity pdbx_vrpt_software and expressed as the number or such clashes per thousand atoms.
- * For structures determined by NMR the clashscore value here will only consider label_atom_id pairs in the
- * well-defined (core) residues from ensemble analysis.
+ * The value of _rcsb_chem_comp_target.comp_id is a reference to
+ * a chemical component definition.
*/
- readonly clashscore?: Maybe<Scalars['Float']>;
- /** Only given for structures determined by NMR. The MolProbity pdbx_vrpt_clashes score for all label_atom_id pairs. */
- readonly clashscore_full_length?: Maybe<Scalars['Float']>;
- /** The recommended contour level for the primary map of this deposition. */
- readonly contour_level_primary_map?: Maybe<Scalars['String']>;
+ readonly comp_id: Scalars['String'];
+ /** The type of target interaction. */
+ readonly interaction_type?: Maybe<Scalars['String']>;
+ /** The chemical component target name. */
+ readonly name?: Maybe<Scalars['String']>;
/**
- * The filename for the input mmCIF coordinate file given to the validation pipeline.
- * Not reported for runs at the annotation or release stage.
+ * The value of _rcsb_chem_comp_target.ordinal distinguishes
+ * related examples for each chemical component.
*/
- readonly coordinates_input_filename?: Maybe<Scalars['String']>;
+ readonly ordinal: Scalars['Int'];
/**
- * Diagnostic message from the wrapper of Cyrange software which identifies the
- * well-defined cores (domains) of NMR protein structures.
+ * A code indicating the provenance of the target interaction assignment
+ *
+ * Allowable values:
+ * DrugBank, PDB Primary Data
+ *
*/
- readonly cyrange_error?: Maybe<Scalars['String']>;
- /** Total number of well-defined cores (domains) identified by Cyrange */
- readonly cyrange_number_of_domains?: Maybe<Scalars['Int']>;
- /** Reference for the Cyrange software. */
- readonly cyrange_version?: Maybe<Scalars['String']>;
+ readonly provenance_source?: Maybe<Scalars['String']>;
/**
- * The ratio (Bmax ‑ Bmin) / Bmean where Bmax, Bmin and Bmean are computed from the B-values
- * associated with the principal axes of the anisotropic thermal ellipsoid.
- * This ratio is usually less than 0.5; for only 1% of PDB entries it is more than 1.0 (Read et al., 2011).
- * Example: X-ray entry specific, obtained from the Xtriage program.
+ * The reference identifier code for the target interaction reference.
+ *
+ * Examples:
+ * Q9HD40
+ *
*/
- readonly data_anisotropy?: Maybe<Scalars['Float']>;
- /** A percentage, Normally percent proportion of the total number. Between 0% and 100%. */
- readonly data_completeness?: Maybe<Scalars['Float']>;
+ readonly reference_database_accession_code?: Maybe<Scalars['String']>;
/**
- * An identifier for the map
- * For released or annotated structures this will be the EMDB ID EMD-\d{4-5} eg "EMD-1001", "EMD-12325"
+ * The reference database name for the target interaction.
+ *
+ * Allowable values:
+ * UniProt
+ *
*/
- readonly emdb_id?: Maybe<Scalars['String']>;
+ readonly reference_database_name?: Maybe<Scalars['String']>;
+ /** The mechanism of action of the chemical component - target interaction. */
+ readonly target_actions?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
+};
+
+export type RcsbClusterFlexibility = {
+ /** Average RMSD refer to average pairwise RMSD (Root Mean Square Deviation of C-alpha atoms) between structures in the cluster (95% sequence identity) where a given entity belongs. */
+ readonly avg_rmsd?: Maybe<Scalars['Float']>;
+ /** Structural flexibility in the cluster (95% sequence identity) where a given entity belongs. */
+ readonly label?: Maybe<Scalars['String']>;
+ /** Link to the associated PDBFlex database entry. */
+ readonly link?: Maybe<Scalars['String']>;
+ /** Maximal RMSD refer to maximal pairwise RMSD (Root Mean Square Deviation of C-alpha atoms) between structures in the cluster (95% sequence identity) where a given entity belongs. */
+ readonly max_rmsd?: Maybe<Scalars['Float']>;
+ /** Allowable values: PDBFlex. */
+ readonly provenance_code?: Maybe<Scalars['String']>;
+};
+
+export type RcsbClusterMembership = {
+ /** Identifier for a cluster at the specified level of sequence identity within the cluster data set. */
+ readonly cluster_id?: Maybe<Scalars['Int']>;
+ /** Sequence identity expressed as an integer percent value. */
+ readonly identity?: Maybe<Scalars['Int']>;
+};
+
+export type RcsbEntityHostOrganism = {
/**
- * The resolution bin limit in Angstroms for PDB depositions used in the comparison when calculating
- * the attribute "relative-percentile-DCC_Rfree".
- * Note that the "high_resol_relative_percentile_DCC_Rfree" value is numerically smaller than the
- * corresponding low-* value.
- * Example: X-ray entry specific, produced by the percentiles step of the validation pipeline software.
+ * The beginning polymer sequence position for the polymer section corresponding
+ * to this host organism.
+ *
+ * A reference to the sequence position in the entity_poly category.
*/
- readonly high_resol_relative_percentile_DCC_Rfree?: Maybe<Scalars['Float']>;
+ readonly beg_seq_num?: Maybe<Scalars['Int']>;
+ /** The common name of the host organism */
+ readonly common_name?: Maybe<Scalars['String']>;
/**
- * The resolution bin limit in Angstroms for PDB depositions used in the comparison when calculating
- * the attribute "relative-percentile-RNAsuiteness".
- * Note that the "high_resol_relative_percentile_RNA_suiteness" value is numerically smaller than the
- * corresponding low value.
- * Example: Specific to entries that contain RNA polymers (and have a RNA_suiteness attribute),
- * and have been determined by X-ray crystallography.
- * Produced by the percentiles step of the validation pipeline software.
+ * The ending polymer sequence position for the polymer section corresponding
+ * to this host organism.
+ *
+ * A reference to the sequence position in the entity_poly category.
*/
- readonly high_resol_relative_percentile_RNA_suiteness?: Maybe<Scalars['Float']>;
+ readonly end_seq_num?: Maybe<Scalars['Int']>;
/**
- * The resolution bin limit in Angstroms for PDB depositions used in the comparison when calculating
- * the attribute "relative-percentile-clashscore".
- * Note that the "high_resol_relative_percentile_clashscore" value is numerically smaller than the
- * corresponding low value.
- * Example: Specific to that have a clashscore attribute and have been determined by X-ray crystallography.
- * Produced by the percentiles step of the validation pipeline software.
+ * Common names associated with this taxonomy code obtained from NCBI Taxonomy Database.
+ *
+ * These names correspond to the taxonomy identifier assigned by the PDB depositor.
+ *
+ * References:
+ *
+ * Sayers EW, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V,
+ * Church DM, DiCuccio M, Edgar R, Federhen S, Feolo M, Geer LY,
+ * Helmberg W, Kapustin Y, Landsman D, Lipman DJ, Madden TL, Maglott DR,
+ * Miller V, Mizrachi I, Ostell J, Pruitt KD, Schuler GD, Sequeira E,
+ * Sherry ST, Shumway M, Sirotkin K, Souvorov A, Starchenko G,
+ * Tatusova TA, Wagner L, Yaschenko E, Ye J (2009). Database resources
+ * of the National Center for Biotechnology Information. Nucleic Acids
+ * Res. 2009 Jan;37(Database issue):D5-15. Epub 2008 Oct 21.
+ *
+ * Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW (2009).
+ * GenBank. Nucleic Acids Res. 2009 Jan;37(Database issue):D26-31.
+ * Epub 2008 Oct 21.
*/
- readonly high_resol_relative_percentile_clashscore?: Maybe<Scalars['Float']>;
+ readonly ncbi_common_names?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
/**
- * The resolution bin limit in Angstroms for PDB depositions used in the comparison when calculating
- * the attribute "relative-percentile-percent-RSRZ-outliers".
- * Note that the "high_resol_relative_percentile_percent_RSRZ_outliers" value is numerically smaller than the
- * corresponding low-* value.
- * Example: X-ray entry specific, produced by the percentiles step of the validation pipeline software.
+ * The parent scientific name in the NCBI taxonomy hierarchy (depth=1) associated with this taxonomy code.
+ *
+ * References:
+ *
+ * Sayers EW, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V,
+ * Church DM, DiCuccio M, Edgar R, Federhen S, Feolo M, Geer LY,
+ * Helmberg W, Kapustin Y, Landsman D, Lipman DJ, Madden TL, Maglott DR,
+ * Miller V, Mizrachi I, Ostell J, Pruitt KD, Schuler GD, Sequeira E,
+ * Sherry ST, Shumway M, Sirotkin K, Souvorov A, Starchenko G,
+ * Tatusova TA, Wagner L, Yaschenko E, Ye J (2009). Database resources
+ * of the National Center for Biotechnology Information. Nucleic Acids
+ * Res. 2009 Jan;37(Database issue):D5-15. Epub 2008 Oct 21.
+ *
+ * Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW (2009).
+ * GenBank. Nucleic Acids Res. 2009 Jan;37(Database issue):D26-31.
+ * Epub 2008 Oct 21.
*/
- readonly high_resol_relative_percentile_percent_RSRZ_outliers?: Maybe<Scalars['Float']>;
+ readonly ncbi_parent_scientific_name?: Maybe<Scalars['String']>;
/**
- * The resolution bin limit in Angstroms for PDB depositions used in the comparison when calculating
- * the attribute "relative-percentile-percent-rama-outliers".
- * Note that the "high_resol_relative_percentile_percent_ramachandran_outliers" value is numerically smaller than the
- * corresponding low value.
- * Example: Specific to structures that have a percent_ramachandran_outliers attribute and have been determined by X-ray crystallography.
- * Produced by the percentiles step of the validation pipeline software.
+ * The scientific name associated with this taxonomy code aggregated by the NCBI Taxonomy Database.
+ *
+ * This name corresponds to the taxonomy identifier assigned by the PDB depositor.
+ *
+ *
+ * References:
+ *
+ * Sayers EW, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V,
+ * Church DM, DiCuccio M, Edgar R, Federhen S, Feolo M, Geer LY,
+ * Helmberg W, Kapustin Y, Landsman D, Lipman DJ, Madden TL, Maglott DR,
+ * Miller V, Mizrachi I, Ostell J, Pruitt KD, Schuler GD, Sequeira E,
+ * Sherry ST, Shumway M, Sirotkin K, Souvorov A, Starchenko G,
+ * Tatusova TA, Wagner L, Yaschenko E, Ye J (2009). Database resources
+ * of the National Center for Biotechnology Information. Nucleic Acids
+ * Res. 2009 Jan;37(Database issue):D5-15. Epub 2008 Oct 21.
+ *
+ * Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW (2009).
+ * GenBank. Nucleic Acids Res. 2009 Jan;37(Database issue):D26-31.
+ * Epub 2008 Oct 21.
*/
- readonly high_resol_relative_percentile_percent_ramachandran_outliers?: Maybe<Scalars['Float']>;
+ readonly ncbi_scientific_name?: Maybe<Scalars['String']>;
/**
- * The resolution bin limit in Angstroms for PDB depositions used in the comparison when calculating
- * the attribute "relative-percentile-percent-rota-outliers".
- * Note that the "high_resol_relative_percentile_percent_rotamer_outliers" value is numerically smaller than the
- * corresponding low value.
- * Example: Specific to that have a percent_rotamer_outliers attribute and have been determined by X-ray crystallography.
- * Produced by the percentiles step of the validation pipeline software.
+ * NCBI Taxonomy identifier for the host organism.
+ *
+ *
+ * Reference:
+ *
+ * Wheeler DL, Chappey C, Lash AE, Leipe DD, Madden TL, Schuler GD,
+ * Tatusova TA, Rapp BA (2000). Database resources of the National
+ * Center for Biotechnology Information. Nucleic Acids Res 2000 Jan
+ * 1;28(1):10-4
+ *
+ * Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Rapp BA,
+ * Wheeler DL (2000). GenBank. Nucleic Acids Res 2000 Jan 1;28(1):15-18.
*/
- readonly high_resol_relative_percentile_percent_rotamer_outliers?: Maybe<Scalars['Float']>;
+ readonly ncbi_taxonomy_id?: Maybe<Scalars['Int']>;
+ /** An identifier for an entity segment. */
+ readonly pdbx_src_id: Scalars['String'];
/**
- * The string "yes".
- *
+ * A code indicating the provenance of the host organism.
+ *
* Allowable values:
- * yes
+ * PDB Primary Data
+ *
*/
- readonly ligands_for_buster_report?: Maybe<Scalars['String']>;
+ readonly provenance_source?: Maybe<Scalars['String']>;
+ /** The scientific name of the host organism */
+ readonly scientific_name?: Maybe<Scalars['String']>;
+ readonly taxonomy_lineage?: Maybe<ReadonlyArray<Maybe<RcsbEntityHostOrganismTaxonomyLineage>>>;
+};
+
+export type RcsbEntityHostOrganismTaxonomyLineage = {
+ /** Members of the NCBI Taxonomy lineage as parent taxonomy lineage depth (1-N) */
+ readonly depth?: Maybe<Scalars['Int']>;
/**
- * The resolution bin limit in Angstroms for PDB depositions used in the comparison when calculating
- * the attribute "relative-percentile-DCC_Rfree".
- * Note that the "low_resol_relative_percentile_DCC_Rfree" value is numerically greater than the
- * corresponding high value.
- * Example: X-ray entry specific, produced by the percentiles step of the validation pipeline software.
+ * Members of the NCBI Taxonomy lineage as parent taxonomy idcodes.
+ *
+ * Examples:
+ * 469008, 10469
+ *
*/
- readonly low_resol_relative_percentile_DCC_Rfree?: Maybe<Scalars['Float']>;
+ readonly id?: Maybe<Scalars['String']>;
/**
- * The resolution bin limit in Angstroms for PDB depositions used in the comparison when calculating
- * the attribute "relative-percentile-RNAsuiteness".
- * Note that the "low_resol_relative_percentile_RNA_suiteness" value is numerically greater than the
- * corresponding high value.
- * Example: Specific to entries that contain RNA polymers (and have a RNA_suiteness attribute),
- * and have been determined by X-ray crystallography.
- * Produced by the percentiles step of the validation pipeline software.
+ * Members of the NCBI Taxonomy lineage as parent taxonomy names.
+ *
+ * Examples:
+ * Escherichia coli BL21(DE3), Baculovirus
+ *
*/
- readonly low_resol_relative_percentile_RNA_suiteness?: Maybe<Scalars['Float']>;
+ readonly name?: Maybe<Scalars['String']>;
+};
+
+export type RcsbEntitySourceOrganism = {
/**
- * The resolution bin limit in Angstroms for PDB depositions used in the comparison when calculating
- * the attribute "relative-percentile-clashscore".
- * Note that the "low_resol_relative_percentile_clashscore" value is numerically greater than the
- * corresponding high value.
- * Example: Specific to that have a clashscore attribute and have been determined by X-ray crystallography.
- * Produced by the percentiles step of the validation pipeline software.
+ * The beginning polymer sequence position for the polymer section corresponding
+ * to this source.
+ *
+ * A reference to the sequence position in the entity_poly category.
*/
- readonly low_resol_relative_percentile_clashscore?: Maybe<Scalars['Float']>;
+ readonly beg_seq_num?: Maybe<Scalars['Int']>;
+ /** The common name for the source organism assigned by the PDB depositor. */
+ readonly common_name?: Maybe<Scalars['String']>;
/**
- * The resolution bin limit in Angstroms for PDB depositions used in the comparison when calculating
- * the attribute "relative-percentile-percent-RSRZ-outliers".
- * Note that the "low_resol_relative_percentile_percent_RSRZ_outliers" value is numerically greater than the
- * corresponding high value.
- * Example: X-ray entry specific, produced by the percentiles step of the validation pipeline software.
+ * The ending polymer sequence position for the polymer section corresponding
+ * to this source.
+ *
+ * A reference to the sequence position in the entity_poly category.
*/
- readonly low_resol_relative_percentile_percent_RSRZ_outliers?: Maybe<Scalars['Float']>;
+ readonly end_seq_num?: Maybe<Scalars['Int']>;
/**
- * The resolution bin limit in Angstroms for PDB depositions used in the comparison when calculating
- * the attribute "relative-percentile-percent-rama-outliers".
- * Note that the "low_resol_relative_percentile_percent_ramachandran_outliers" value is numerically greater than the
- * corresponding high value.
- * Example: Specific to that have a percent_ramachandran_outliers attribute and have been determined by X-ray crystallography.
- * Produced by the percentiles step of the validation pipeline software.
+ * Common names associated with this taxonomy code aggregated by the NCBI Taxonomy Database.
+ *
+ * These name correspond to the taxonomy identifier assigned by the PDB depositor.
+ *
+ * References:
+ *
+ * Sayers EW, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V,
+ * Church DM, DiCuccio M, Edgar R, Federhen S, Feolo M, Geer LY,
+ * Helmberg W, Kapustin Y, Landsman D, Lipman DJ, Madden TL, Maglott DR,
+ * Miller V, Mizrachi I, Ostell J, Pruitt KD, Schuler GD, Sequeira E,
+ * Sherry ST, Shumway M, Sirotkin K, Souvorov A, Starchenko G,
+ * Tatusova TA, Wagner L, Yaschenko E, Ye J (2009). Database resources
+ * of the National Center for Biotechnology Information. Nucleic Acids
+ * Res. 2009 Jan;37(Database issue):D5-15. Epub 2008 Oct 21.
+ *
+ * Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW (2009).
+ * GenBank. Nucleic Acids Res. 2009 Jan;37(Database issue):D26-31.
+ * Epub 2008 Oct 21.
*/
- readonly low_resol_relative_percentile_percent_ramachandran_outliers?: Maybe<Scalars['Float']>;
+ readonly ncbi_common_names?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
/**
- * The resolution bin limit in Angstroms for PDB depositions used in the comparison when calculating
- * the attribute "relative-percentile-percent-rota-outliers".
- * Note that the "low_resol_relative_percentile_percent_rotamer_outliers" value is numerically greater than the
- * corresponding high value.
- * Example: Specific to that have a percent_rotamer_outliers attribute and have been determined by X-ray crystallography.
- * Produced by the percentiles step of the validation pipeline software.
+ * A parent scientific name in the NCBI taxonomy hierarchy of the source organism assigned by the PDB depositor.
+ * For cellular organism this corresponds to a superkingdom (e.g., Archaea, Bacteria, Eukaryota). For viruses this
+ * corresponds to a clade (e.g. Adnaviria, Bicaudaviridae, Clavaviridae). For other and unclassified entries this
+ * corresponds to the first level of any taxonomic rank below the root level.
+ *
+ * References:
+ *
+ * Sayers EW, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V,
+ * Church DM, DiCuccio M, Edgar R, Federhen S, Feolo M, Geer LY,
+ * Helmberg W, Kapustin Y, Landsman D, Lipman DJ, Madden TL, Maglott DR,
+ * Miller V, Mizrachi I, Ostell J, Pruitt KD, Schuler GD, Sequeira E,
+ * Sherry ST, Shumway M, Sirotkin K, Souvorov A, Starchenko G,
+ * Tatusova TA, Wagner L, Yaschenko E, Ye J (2009). Database resources
+ * of the National Center for Biotechnology Information. Nucleic Acids
+ * Res. 2009 Jan;37(Database issue):D5-15. Epub 2008 Oct 21.
+ *
+ * Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW (2009).
+ * GenBank. Nucleic Acids Res. 2009 Jan;37(Database issue):D26-31.
+ * Epub 2008 Oct 21.
+ *
+ * Examples:
+ * Archaea, Bacteria, Eukaryota, Adnaviria, Bicaudaviridae, Clavaviridae, Duplodnaviria
+ *
*/
- readonly low_resol_relative_percentile_percent_rotamer_outliers?: Maybe<Scalars['Float']>;
+ readonly ncbi_parent_scientific_name?: Maybe<Scalars['String']>;
/**
- * For each Cyrange well-defined core ("cyrange_domain") the id of the PDB_model_num which is most
- * similar to other models as measured by pairwise RMSDs over the domain.
- * For the whole entry ("Entry"), the medoid PDB_model_num of the largest core is taken as an overall
- * representative of the structure.
+ * The scientific name associated with this taxonomy code aggregated by the NCBI Taxonomy Database.
+ *
+ * This name corresponds to the taxonomy identifier assigned by the PDB depositor.
+ *
+ *
+ * References:
+ *
+ * Sayers EW, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V,
+ * Church DM, DiCuccio M, Edgar R, Federhen S, Feolo M, Geer LY,
+ * Helmberg W, Kapustin Y, Landsman D, Lipman DJ, Madden TL, Maglott DR,
+ * Miller V, Mizrachi I, Ostell J, Pruitt KD, Schuler GD, Sequeira E,
+ * Sherry ST, Shumway M, Sirotkin K, Souvorov A, Starchenko G,
+ * Tatusova TA, Wagner L, Yaschenko E, Ye J (2009). Database resources
+ * of the National Center for Biotechnology Information. Nucleic Acids
+ * Res. 2009 Jan;37(Database issue):D5-15. Epub 2008 Oct 21.
+ *
+ * Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW (2009).
+ * GenBank. Nucleic Acids Res. 2009 Jan;37(Database issue):D26-31.
+ * Epub 2008 Oct 21.
*/
- readonly medoid_model?: Maybe<Scalars['Int']>;
+ readonly ncbi_scientific_name?: Maybe<Scalars['String']>;
/**
- * A flag indicating if all models in the NMR ensemble contain the exact
- * same atoms ("True") or if the models differ in this respect ("False").
+ * NCBI Taxonomy identifier for the gene source organism assigned by the PDB depositor.
+ *
+ * Reference:
+ *
+ * Wheeler DL, Chappey C, Lash AE, Leipe DD, Madden TL, Schuler GD,
+ * Tatusova TA, Rapp BA (2000). Database resources of the National
+ * Center for Biotechnology Information. Nucleic Acids Res 2000 Jan
+ * 1;28(1):10-4
+ *
+ * Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Rapp BA,
+ * Wheeler DL (2000). GenBank. Nucleic Acids Res 2000 Jan 1;28(1):15-18.
*/
- readonly nmr_models_consistency_flag?: Maybe<Scalars['String']>;
- /** Diagnostic message from the wrapper of NMRClust software which clusters NMR models. */
- readonly nmrclust_error?: Maybe<Scalars['String']>;
- /** Total number of clusters in the NMR ensemble identified by NMRClust. */
- readonly nmrclust_number_of_clusters?: Maybe<Scalars['Int']>;
+ readonly ncbi_taxonomy_id?: Maybe<Scalars['Int']>;
+ /** An identifier for the entity segment. */
+ readonly pdbx_src_id: Scalars['String'];
/**
- * Number of models analysed by NMRClust - should in almost all cases be the
- * same as the number of models in the NMR ensemble.
+ * A code indicating the provenance of the source organism details for the entity
+ *
+ * Allowable values:
+ * PDB Primary Data
+ *
*/
- readonly nmrclust_number_of_models?: Maybe<Scalars['Int']>;
- /** Number of models that do not belong to any cluster as deemed by NMRClust. */
- readonly nmrclust_number_of_outliers?: Maybe<Scalars['Int']>;
- /** Overall representative PDB_model_num of the NMR ensemble as identified by NMRClust. */
- readonly nmrclust_representative_model?: Maybe<Scalars['Int']>;
- /** Reference for the NMRClust software. */
- readonly nmrclust_version?: Maybe<Scalars['String']>;
+ readonly provenance_source?: Maybe<Scalars['String']>;
+ readonly rcsb_gene_name?: Maybe<ReadonlyArray<Maybe<RcsbEntitySourceOrganismRcsbGeneName>>>;
+ /** The scientific name of the source organism assigned by the PDB depositor. */
+ readonly scientific_name?: Maybe<Scalars['String']>;
/**
- * The string "yes".
- *
+ * The source type for the entity
+ *
* Allowable values:
- * yes
+ * genetically engineered, natural, synthetic
+ *
*/
- readonly no_ligands_for_buster_report?: Maybe<Scalars['String']>;
+ readonly source_type?: Maybe<Scalars['String']>;
+ readonly taxonomy_lineage?: Maybe<ReadonlyArray<Maybe<RcsbEntitySourceOrganismTaxonomyLineage>>>;
+};
+
+export type RcsbEntitySourceOrganismRcsbGeneName = {
/**
- * The string "yes".
- *
+ * A code indicating the provenance of the source organism details for the entity
+ *
* Allowable values:
- * yes
+ * PDB Primary Data, UniProt
+ *
*/
- readonly no_ligands_for_mogul?: Maybe<Scalars['String']>;
+ readonly provenance_source?: Maybe<Scalars['String']>;
/**
- * Will be set to "true" if no property was found to do percentile analysis on.
- * Please note that currently due to a bug that this attribute is "true" erronously for NMR structures.
+ * Gene name.
+ *
+ * Examples:
+ * lacA, hemH
+ *
*/
- readonly no_percentile_property?: Maybe<Scalars['String']>;
+ readonly value?: Maybe<Scalars['String']>;
+};
+
+export type RcsbEntitySourceOrganismTaxonomyLineage = {
+ /** Members of the NCBI Taxonomy lineage as parent taxonomy lineage depth (1-N) */
+ readonly depth?: Maybe<Scalars['Int']>;
/**
- * This is the number of hydrogen atoms added and optimized by the MolProbity reduce pdbx_vrpt_software as part of the
- * all-atom clashscore.
+ * Members of the NCBI Taxonomy lineage as parent taxonomy idcodes.
+ *
+ * Examples:
+ * 9606, 10090
+ *
*/
- readonly num_H_reduce?: Maybe<Scalars['Float']>;
+ readonly id?: Maybe<Scalars['String']>;
/**
- * The number of PDB depositions used in the comparison when calculating the attribute
- * "absolute-percentile-DCC_Rfree".
- * Example: X-ray entry specific, produced by the percentiles step of the validation pipeline software.
+ * Memebers of the NCBI Taxonomy lineage as parent taxonomy names.
+ *
+ * Examples:
+ * Homo sapiens, Mus musculus
+ *
*/
- readonly num_PDBids_absolute_percentile_DCC_Rfree?: Maybe<Scalars['Int']>;
+ readonly name?: Maybe<Scalars['String']>;
+};
+
+export type RcsbEntryContainerIdentifiers = {
+ /** List of identifiers for assemblies generated from the entry. */
+ readonly assembly_ids?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
+ /** List of identifiers for the branched entity constituents for the entry. */
+ readonly branched_entity_ids?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
/**
- * The number of PDB depositions used in the comparison when calculating the attribute
- * "absolute-percentile-RNAsuiteness".
- * Example: Specific to entries that contain RNA polymers (and have a RNA_suiteness attribute).
- * Produced by the percentiles step of the validation pipeline software.
+ * List of EMDB identifiers for the 3D electron microscopy density maps
+ * used in the production of the structure model.
*/
- readonly num_PDBids_absolute_percentile_RNA_suiteness?: Maybe<Scalars['Int']>;
+ readonly emdb_ids?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
+ /** List of identifiers or the entity constituents for the entry. */
+ readonly entity_ids?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
/**
- * The number of PDB depositions used in the comparison when calculating the attribute
- * "absolute-percentile-clashscore"
- * Example: Produced by the percentiles step of the validation pipeline software.
+ * Entry identifier for the container.
+ *
+ * Examples:
+ * 1KIP, 4HHB
+ *
*/
- readonly num_PDBids_absolute_percentile_clashscore?: Maybe<Scalars['Int']>;
+ readonly entry_id: Scalars['String'];
+ /** List of PDB model identifiers for the entry. */
+ readonly model_ids?: Maybe<ReadonlyArray<Maybe<Scalars['Int']>>>;
+ /** List of identifiers for the non-polymer entity constituents for the entry. */
+ readonly non_polymer_entity_ids?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
+ /** List of identifiers for the polymer entity constituents for the entry. */
+ readonly polymer_entity_ids?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
+ /** Unique integer value assigned to each PubMed record. */
+ readonly pubmed_id?: Maybe<Scalars['Int']>;
/**
- * The number of PDB depositions used in the comparison when calculating the attribute
- * "absolute-percentile-percent-RSRZ-outliers".
- * Example: X-ray entry specific, produced by the percentiles step of the validation pipeline software.
+ * A unique identifier for each object in this entry container.
+ *
+ * Examples:
+ * 1KIP
+ *
*/
- readonly num_PDBids_absolute_percentile_percent_RSRZ_outliers?: Maybe<Scalars['Int']>;
+ readonly rcsb_id?: Maybe<Scalars['String']>;
/**
- * The number of PDB depositions used in the comparison when calculating the attribute
- * "absolute-percentile-percent-rama-outliers"
- * Example: Produced by the percentiles step of the validation pipeline software.
+ * List of EMDB identifiers for the 3D electron microscopy density maps
+ * related to the structure model.
*/
- readonly num_PDBids_absolute_percentile_percent_ramachandran_outliers?: Maybe<Scalars['Int']>;
+ readonly related_emdb_ids?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
+ /** List of identifiers for the solvent/water entity constituents for the entry. */
+ readonly water_entity_ids?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
+};
+
+export type RcsbEntryInfo = {
+ /** The number of assemblies defined for this entry including the deposited assembly. */
+ readonly assembly_count?: Maybe<Scalars['Int']>;
+ /** The number of distinct branched entities in the structure entry. */
+ readonly branched_entity_count?: Maybe<Scalars['Int']>;
/**
- * The number of PDB depositions used in the comparison when calculating the attribute
- * "absolute-percentile-percent-rota-outliers"
- * Example: Produced by the percentiles step of the validation pipeline software.
+ * The maximum molecular mass (KDa) of a branched entity in the deposited structure entry.
+ *
+ * Examples:
+ * null, null
+ *
*/
- readonly num_PDBids_absolute_percentile_percent_rotamer_outliers?: Maybe<Scalars['Int']>;
+ readonly branched_molecular_weight_maximum?: Maybe<Scalars['Float']>;
/**
- * The number of PDB depositions used in the comparison when calculating the attribute
- * "relative-percentile-DCC_Rfree".
- * Example: X-ray entry specific, produced by the percentiles step of the validation pipeline software.
+ * The minimum molecular mass (KDa) of a branched entity in the deposited structure entry.
+ *
+ * Examples:
+ * null, null
+ *
*/
- readonly num_PDBids_relative_percentile_DCC_Rfree?: Maybe<Scalars['Int']>;
+ readonly branched_molecular_weight_minimum?: Maybe<Scalars['Float']>;
+ /** The number of cis-peptide linkages per deposited structure model. */
+ readonly cis_peptide_count?: Maybe<Scalars['Int']>;
+ /** The number of heavy atom coordinates records per deposited structure model. */
+ readonly deposited_atom_count?: Maybe<Scalars['Int']>;
+ /** The number of hydrogen atom coordinates records per deposited structure model. */
+ readonly deposited_hydrogen_atom_count?: Maybe<Scalars['Int']>;
+ /** The number of model structures deposited. */
+ readonly deposited_model_count?: Maybe<Scalars['Int']>;
/**
- * The number of PDB depositions used in the comparison when calculating the attribute
- * "relative-percentile-RNAsuiteness".
- * Example: Specific to entries that contain RNA polymers (and have a RNA_suiteness attribute).
- * Produced by the percentiles step of the validation pipeline software.
+ * The number of modeled polymer monomers in the deposited coordinate data.
+ * This is the total count of monomers with reported coordinate data for all polymer
+ * entity instances in the deposited coordinate data.
*/
- readonly num_PDBids_relative_percentile_RNA_suiteness?: Maybe<Scalars['Int']>;
+ readonly deposited_modeled_polymer_monomer_count?: Maybe<Scalars['Int']>;
/**
- * The number of PDB depositions used in the comparison when calculating the attribute
- * "relative-percentile-clashscore"
- * Example: Produced by the percentiles step of the validation pipeline software.
+ * The number of non-polymer instances in the deposited data set.
+ * This is the total count of non-polymer entity instances reported
+ * per deposited structure model.
*/
- readonly num_PDBids_relative_percentile_clashscore?: Maybe<Scalars['Int']>;
+ readonly deposited_nonpolymer_entity_instance_count?: Maybe<Scalars['Int']>;
/**
- * The number of PDB depositions used in the comparison when calculating the attribute
- * "relative-percentile-percent-RSRZ-outliers".
- * Example: X-ray entry specific, produced by the percentiles step of the validation pipeline software.
+ * The number of polymer instances in the deposited data set.
+ * This is the total count of polymer entity instances reported
+ * per deposited structure model.
*/
- readonly num_PDBids_relative_percentile_percent_RSRZ_outliers?: Maybe<Scalars['Int']>;
+ readonly deposited_polymer_entity_instance_count?: Maybe<Scalars['Int']>;
/**
- * The number of PDB depositions used in the comparison when calculating the attribute
- * "relative-percentile-percent-rama-outliers"
- * Example: Produced by the percentiles step of the validation pipeline software.
+ * The number of polymer monomers in sample entity instances in the deposited data set.
+ * This is the total count of monomers for all polymer entity instances reported
+ * per deposited structure model.
*/
- readonly num_PDBids_relative_percentile_percent_ramachandran_outliers?: Maybe<Scalars['Int']>;
+ readonly deposited_polymer_monomer_count?: Maybe<Scalars['Int']>;
+ /** The number of heavy solvent atom coordinates records per deposited structure model. */
+ readonly deposited_solvent_atom_count?: Maybe<Scalars['Int']>;
/**
- * The number of PDB depositions used in the comparison when calculating the attribute
- * "relative-percentile-percent-rota-outliers"
- * Example: Produced by the percentiles step of the validation pipeline software.
+ * The number of unmodeled polymer monomers in the deposited coordinate data. This is
+ * the total count of monomers with unreported coordinate data for all polymer
+ * entity instances per deposited structure model.
*/
- readonly num_PDBids_relative_percentile_percent_rotamer_outliers?: Maybe<Scalars['Int']>;
+ readonly deposited_unmodeled_polymer_monomer_count?: Maybe<Scalars['Int']>;
+ /** The maximum radiation wavelength in angstroms. */
+ readonly diffrn_radiation_wavelength_maximum?: Maybe<Scalars['Float']>;
+ /** The minimum radiation wavelength in angstroms. */
+ readonly diffrn_radiation_wavelength_minimum?: Maybe<Scalars['Float']>;
+ readonly diffrn_resolution_high?: Maybe<RcsbEntryInfoDiffrnResolutionHigh>;
+ /** The number of disulfide bonds per deposited structure model. */
+ readonly disulfide_bond_count?: Maybe<Scalars['Int']>;
+ /** The number of distinct polymer, non-polymer, branched molecular, and solvent entities per deposited structure model. */
+ readonly entity_count?: Maybe<Scalars['Int']>;
/**
- * The number of bond angless compared to "standard geometry" made using the MolProbity dangle program.
- * Standard geometry parameters are taken from Engh and Huber (2001) and Parkinson et al. (1996).
- * This value is for all chains in the structure.
+ * The category of experimental method(s) used to determine the structure entry.
+ *
+ * Allowable values:
+ * EM, Multiple methods, NMR, Neutron, Other, X-ray
+ *
*/
- readonly num_angles_RMSZ?: Maybe<Scalars['Int']>;
+ readonly experimental_method?: Maybe<Scalars['String']>;
+ /** The number of experimental methods contributing data to the structure determination. */
+ readonly experimental_method_count?: Maybe<Scalars['Int']>;
+ /** The number of intermolecular covalent bonds. */
+ readonly inter_mol_covalent_bond_count?: Maybe<Scalars['Int']>;
+ /** The number of intermolecular metalic bonds. */
+ readonly inter_mol_metalic_bond_count?: Maybe<Scalars['Int']>;
/**
- * The number of bond lengths compared to "standard geometry" made using the MolProbity dangle program.
- * Standard geometry parameters are taken from Engh and Huber (2001) and Parkinson et al. (1996).
- * This value is for all chains in the structure.
+ * The molecular mass (KDa) of polymer and non-polymer entities (exclusive of solvent) in the deposited structure entry.
+ *
+ * Examples:
+ * null, null
+ *
*/
- readonly num_bonds_RMSZ?: Maybe<Scalars['Int']>;
+ readonly molecular_weight?: Maybe<Scalars['Float']>;
/**
- * The number of reflections in the free set as defined in the input structure factor file supplied to the validation pipeline.
- * example: X-ray entry specific, obtained from the DCC program.
+ * Nucleic acid polymer entity type categories describing the entry.
+ *
+ * Allowable values:
+ * DNA (only), DNA/RNA (only), NA-hybrid (only), Other, RNA (only)
+ *
*/
- readonly num_free_reflections?: Maybe<Scalars['Int']>;
+ readonly na_polymer_entity_types?: Maybe<Scalars['String']>;
+ /** Bound nonpolymer components in this entry. */
+ readonly nonpolymer_bound_components?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
+ /** The number of distinct non-polymer entities in the structure entry exclusive of solvent. */
+ readonly nonpolymer_entity_count?: Maybe<Scalars['Int']>;
/**
- * The number of Miller Indices reported by the Xtriage program. This should be the same as the
- * number of _refln in the input structure factor file.
- * Example: X-ray entry specific, calculated by Phenix Xtriage program.
+ * The maximum molecular mass (KDa) of a non-polymer entity in the deposited structure entry.
+ *
+ * Examples:
+ * null, null
+ *
*/
- readonly num_miller_indices?: Maybe<Scalars['Int']>;
- /** Reference for the PANAV software. */
- readonly panav_version?: Maybe<Scalars['String']>;
- /** A percentage, Normally percent proportion of the total number. Between 0% and 100%. */
- readonly percent_RSRZ_outliers?: Maybe<Scalars['Float']>;
- /** A percentage, Normally percent proportion of the total number. Between 0% and 100%. */
- readonly percent_free_reflections?: Maybe<Scalars['Float']>;
- /** A percentage, Normally percent proportion of the total number. Between 0% and 100%. */
- readonly percent_ramachandran_outliers?: Maybe<Scalars['Float']>;
- /** A percentage, Normally percent proportion of the total number. Between 0% and 100%. */
- readonly percent_ramachandran_outliers_full_length?: Maybe<Scalars['Float']>;
- /** A percentage, Normally percent proportion of the total number. Between 0% and 100%. */
- readonly percent_rotamer_outliers?: Maybe<Scalars['Float']>;
- /** A percentage, Normally percent proportion of the total number. Between 0% and 100%. */
- readonly percent_rotamer_outliers_full_length?: Maybe<Scalars['Float']>;
+ readonly nonpolymer_molecular_weight_maximum?: Maybe<Scalars['Float']>;
/**
- * The percentile bins that this structure would contribute to in a recalculation of
- * percentile. The string is a comma separated list.
- * Example: An X-ray entry with a resolution of 1.8 Angstroms,
- * that would contribute to bins all structures, what ever bin 1.8 Angstrom resolution is in and
- * the all xray bin.
- * Example #2: An EM entry that would contribute to all and em structures bins.
- * Example #3: A NMR entry hat would contribute to all and nmr structures bins.
+ * The minimum molecular mass (KDa) of a non-polymer entity in the deposited structure entry.
+ *
+ * Examples:
+ * null, null
+ *
*/
- readonly percentilebins?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
+ readonly nonpolymer_molecular_weight_minimum?: Maybe<Scalars['Float']>;
/**
- * Comma separated list of the _entity.id's for the molecular entities that are present in the structure
- * and have _entity_poly.type indicating that they are protein, RNA or DNA: that is in the list
- * 'polypeptide(L)', 'polypeptide(D)', 'polyribonucleotide, 'polydeoxyribonucleotide' or
- * 'polydeoxyribonucleotide/polyribonucleotide hybrid'.
- * Normally the entity.id's are integer numbers but not necessarily so.
- * Example
+ * Categories describing the polymer entity composition for the entry.
+ *
+ * Allowable values:
+ * DNA, DNA/RNA, NA-hybrid, NA/oligosaccharide, RNA, heteromeric protein, homomeric protein, oligosaccharide, other, other type composition, other type pair, protein/NA, protein/NA/oligosaccharide, protein/oligosaccharide
+ *
*/
- readonly protein_DNA_RNA_entities?: Maybe<Scalars['String']>;
- /** Version and reference of the RCI software */
- readonly rci_version?: Maybe<Scalars['String']>;
+ readonly polymer_composition?: Maybe<Scalars['String']>;
+ /** The number of distinct polymer entities in the structure entry. */
+ readonly polymer_entity_count?: Maybe<Scalars['Int']>;
+ /** The number of distinct DNA polymer entities. */
+ readonly polymer_entity_count_DNA?: Maybe<Scalars['Int']>;
+ /** The number of distinct RNA polymer entities. */
+ readonly polymer_entity_count_RNA?: Maybe<Scalars['Int']>;
+ /** The number of distinct nucleic acid polymer entities (DNA or RNA). */
+ readonly polymer_entity_count_nucleic_acid?: Maybe<Scalars['Int']>;
+ /** The number of distinct hybrid nucleic acid polymer entities. */
+ readonly polymer_entity_count_nucleic_acid_hybrid?: Maybe<Scalars['Int']>;
+ /** The number of distinct protein polymer entities. */
+ readonly polymer_entity_count_protein?: Maybe<Scalars['Int']>;
+ /** The number of distinct taxonomies represented among the polymer entities in the entry. */
+ readonly polymer_entity_taxonomy_count?: Maybe<Scalars['Int']>;
/**
- * The filename for the input mmCIF format reflection file given to the validation pipeline.
- * Not reported for runs at the annotation or release stage.
+ * The maximum molecular mass (KDa) of a polymer entity in the deposited structure entry.
+ *
+ * Examples:
+ * null, null
+ *
*/
- readonly reflections_input_filename?: Maybe<Scalars['String']>;
+ readonly polymer_molecular_weight_maximum?: Maybe<Scalars['Float']>;
/**
- * Version of the REFMAC pdbx_vrpt_software used in the EDS step.
- * Example: X-ray entry specific, obtained in the eds step from REFMAC calculation.
+ * The minimum molecular mass (KDa) of a polymer entity in the deposited structure entry.
+ *
+ * Examples:
+ * null, null
+ *
*/
- readonly refmac_version?: Maybe<Scalars['String']>;
+ readonly polymer_molecular_weight_minimum?: Maybe<Scalars['Float']>;
+ /** The maximum monomer count of a polymer entity per deposited structure model. */
+ readonly polymer_monomer_count_maximum?: Maybe<Scalars['Int']>;
+ /** The minimum monomer count of a polymer entity per deposited structure model. */
+ readonly polymer_monomer_count_minimum?: Maybe<Scalars['Int']>;
+ /** Combined estimates of experimental resolution contributing to the refined structural model. */
+ readonly resolution_combined?: Maybe<ReadonlyArray<Maybe<Scalars['Float']>>>;
/**
- * Structures are judged in comparison to previously deposited PDB entries.
- * The comparison is carried out by calculation of the percentile rank, i.e. the percentage of entries
- * that are equal or poorer than this structure in terms of a quality indicator.
- * Percentile ranks range from 0 (the worst) to 100 (the best).
+ * Selected polymer entity type categories describing the entry.
+ *
+ * Allowable values:
+ * Nucleic acid (only), Oligosaccharide (only), Other, Protein (only), Protein/NA, Protein/Oligosaccharide
+ *
*/
- readonly relative_percentile_DCC_Rfree?: Maybe<Scalars['Float']>;
+ readonly selected_polymer_entity_types?: Maybe<Scalars['String']>;
+ /** Combined list of software programs names reported in connection with the production of this entry. */
+ readonly software_programs_combined?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
+ /** The number of distinct solvent entities per deposited structure model. */
+ readonly solvent_entity_count?: Maybe<Scalars['Int']>;
+};
+
+export type RcsbEntryInfoDiffrnResolutionHigh = {
/**
- * Structures are judged in comparison to previously deposited PDB entries.
- * The comparison is carried out by calculation of the percentile rank, i.e. the percentage of entries
- * that are equal or poorer than this structure in terms of a quality indicator.
- * Percentile ranks range from 0 (the worst) to 100 (the best).
+ * The provenence source for the high resolution limit of data collection.
+ *
+ * Allowable values:
+ * Depositor assigned, From refinement resolution cutoff, From the high resolution shell
+ *
*/
- readonly relative_percentile_RNA_suiteness?: Maybe<Scalars['Float']>;
+ readonly provenance_source?: Maybe<Scalars['String']>;
+ /** The high resolution limit of data collection. */
+ readonly value?: Maybe<Scalars['Float']>;
+};
+
+export type RcsbExternalReferences = {
+ /** ID (accession) from external resource linked to this entry. */
+ readonly id: Scalars['String'];
+ /** Link to this entry in external resource. */
+ readonly link: Scalars['String'];
/**
- * Structures are judged in comparison to previously deposited PDB entries.
- * The comparison is carried out by calculation of the percentile rank, i.e. the percentage of entries
- * that are equal or poorer than this structure in terms of a quality indicator.
- * Percentile ranks range from 0 (the worst) to 100 (the best).
+ * Internal identifier for external resource.
+ *
+ * Allowable values:
+ * OLDERADO, BMRB, NDB, SB GRID, PROTEIN DIFFRACTION, EM DATA RESOURCE
+ *
*/
- readonly relative_percentile_clashscore?: Maybe<Scalars['Float']>;
+ readonly type: Scalars['String'];
+};
+
+export type RcsbGenomicLineage = {
+ /** Classification hierarchy depth. */
+ readonly depth?: Maybe<Scalars['Int']>;
/**
- * Structures are judged in comparison to previously deposited PDB entries.
- * The comparison is carried out by calculation of the percentile rank, i.e. the percentage of entries
- * that are equal or poorer than this structure in terms of a quality indicator.
- * Percentile ranks range from 0 (the worst) to 100 (the best).
+ * Automatically assigned ID that uniquely identifies taxonomy, chromosome or gene in the Genome Location Browser.
+ *
+ * Examples:
+ * 9606, 568815441, 414325
+ *
*/
- readonly relative_percentile_percent_RSRZ_outliers?: Maybe<Scalars['Float']>;
+ readonly id?: Maybe<Scalars['String']>;
/**
- * Structures are judged in comparison to previously deposited PDB entries.
- * The comparison is carried out by calculation of the percentile rank, i.e. the percentage of entries
- * that are equal or poorer than this structure in terms of a quality indicator.
- * Percentile ranks range from 0 (the worst) to 100 (the best).
+ * A human-readable term name.
+ *
+ * Examples:
+ * Homo sapiens, 8, defensin beta 103A
+ *
*/
- readonly relative_percentile_percent_ramachandran_outliers?: Maybe<Scalars['Float']>;
+ readonly name?: Maybe<Scalars['String']>;
+};
+
+export type RcsbLatestRevision = {
+ /** The major version number of the latest revision. */
+ readonly major_revision?: Maybe<Scalars['Int']>;
+ /** The minor version number of the latest revision. */
+ readonly minor_revision?: Maybe<Scalars['Int']>;
+ /** The release date of the latest revision item. */
+ readonly revision_date?: Maybe<Scalars['Date']>;
+};
+
+export type RcsbLigandNeighbors = {
+ /** Alternate conformer identifier for the target instance. */
+ readonly alt_id?: Maybe<Scalars['String']>;
/**
- * Structures are judged in comparison to previously deposited PDB entries.
- * The comparison is carried out by calculation of the percentile rank, i.e. the percentage of entries
- * that are equal or poorer than this structure in terms of a quality indicator.
- * Percentile ranks range from 0 (the worst) to 100 (the best).
+ * The atom identifier for the target instance.
+ *
+ * Examples:
+ * O1, N1, C1
+ *
*/
- readonly relative_percentile_percent_rotamer_outliers?: Maybe<Scalars['Float']>;
+ readonly atom_id?: Maybe<Scalars['String']>;
+ /** The author residue index for the target instance. */
+ readonly auth_seq_id?: Maybe<Scalars['Int']>;
+ /** Component identifier for the target instance. */
+ readonly comp_id?: Maybe<Scalars['String']>;
+ /** Distance value for this ligand interaction. */
+ readonly distance?: Maybe<Scalars['Float']>;
+ /** Alternate conformer identifier for the ligand interaction. */
+ readonly ligand_alt_id?: Maybe<Scalars['String']>;
/**
- * The date, time and time-zone that the validation XML file was created.
- * The string will be formatted like "Feb 7, 2017 -- 12:32 pm GMT".
+ * The entity instance identifier for the ligand interaction.
+ *
+ * Examples:
+ * A, B
+ *
*/
- readonly report_creation_date?: Maybe<Scalars['String']>;
+ readonly ligand_asym_id?: Maybe<Scalars['String']>;
/**
- * The data high resolution diffraction limit, in Angstroms, obtained from cif item
- * _reflns.d_resolution_high.
- * X-ray entry specific.
+ * The atom identifier for the ligand interaction.
+ *
+ * Examples:
+ * OG, OE1, CD1
+ *
*/
- readonly resol_high_from_reflectionsfile?: Maybe<Scalars['Float']>;
+ readonly ligand_atom_id?: Maybe<Scalars['String']>;
/**
- * The data low resolution diffraction limit, in Angstroms, obtained from cif item
- * _reflns.d_resolution_low.
- * X-ray entry specific.
+ * The chemical component identifier for the ligand interaction.
+ *
+ * Examples:
+ * ASN, TRP, SER
+ *
*/
- readonly resol_low_from_reflectionsfile?: Maybe<Scalars['Float']>;
+ readonly ligand_comp_id?: Maybe<Scalars['String']>;
/**
- * This is a comma separated list of the residue types whose bond lengths and bond angles have
- * not been checked against "standard geometry" using the MolProbity dangle program.
- * Standard geometry parameters are taken from Engh and Huber (2001) and Parkinson et al. (1996)
+ * The entity identifier for the ligand of interaction.
+ *
+ * Examples:
+ * 1, 2
+ *
*/
- readonly restypes_notchecked_for_bond_angle_geometry?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
+ readonly ligand_entity_id?: Maybe<Scalars['String']>;
/**
- * Version of the software for chemical shift outlier detection - currently
- * same as revision number of the validation pipeline.
+ * A flag to indicate the nature of the ligand interaction is covalent or metal-coordination.
+ *
+ * Allowable values:
+ * N, Y
+ *
*/
- readonly shiftchecker_version?: Maybe<Scalars['String']>;
+ readonly ligand_is_bound?: Maybe<Scalars['String']>;
+ /** Model identifier for the ligand interaction. */
+ readonly ligand_model_id?: Maybe<Scalars['Int']>;
+ /** The sequence position for the target instance. */
+ readonly seq_id?: Maybe<Scalars['Int']>;
+};
+
+export type RcsbMembraneLineage = {
+ /** Hierarchy depth. */
+ readonly depth?: Maybe<Scalars['Int']>;
/**
- * A sentence giving the result of Xtriage’s analysis on translational NCS.
- * Example: largest off-origin peak in the Patterson function is 8.82% of the height of the origin peak. No significant pseudotranslation is detected."
- * X-ray entry specific, obtained from the Xtriage program.
+ * Automatically assigned ID for membrane classification term in the Membrane Protein Browser.
+ *
+ * Examples:
+ * MONOTOPIC MEMBRANE PROTEINS.Oxidases.Monoamine Oxidase A
+ *
*/
- readonly trans_NSC?: Maybe<Scalars['String']>;
+ readonly id?: Maybe<Scalars['String']>;
+ /** Membrane protein classification term. */
+ readonly name?: Maybe<Scalars['String']>;
+};
+
+export type RcsbNonpolymerEntity = {
+ /** A description of special aspects of the entity. */
+ readonly details?: Maybe<Scalars['String']>;
+ /** Formula mass (KDa) of the entity. */
+ readonly formula_weight?: Maybe<Scalars['Float']>;
+ /** A description of the nonpolymer entity. */
+ readonly pdbx_description?: Maybe<Scalars['String']>;
+ /** The number of molecules of the nonpolymer entity in the entry. */
+ readonly pdbx_number_of_molecules?: Maybe<Scalars['Int']>;
+};
+
+export type RcsbNonpolymerEntityAnnotation = {
+ /** An identifier for the annotation. */
+ readonly annotation_id?: Maybe<Scalars['String']>;
+ readonly annotation_lineage?: Maybe<ReadonlyArray<Maybe<RcsbNonpolymerEntityAnnotationAnnotationLineage>>>;
/**
- * Padilla and Yeates twinning parameter <|L|>.
- * Theoretical values is 0.5 in the untwinned case, and 0.375 in the perfectly twinned case.
- * Example: X-ray entry specific, obtained from the Xtriage program.
+ * Identifies the version of the annotation assignment.
+ *
+ * Examples:
+ * V4_0_2
+ *
*/
- readonly twin_L?: Maybe<Scalars['Float']>;
+ readonly assignment_version?: Maybe<Scalars['String']>;
/**
- * Padilla and Yeates twinning parameter <|L**2|>.
- * Theoretical values is 0.333 in the untwinned case, and 0.2 in the perfectly twinned case.
- * Example: X-ray entry specific, obtained from the Xtriage program.
+ * Non-polymer(ligand) chemical component identifier for the entity.
+ *
+ * Examples:
+ * GTP, STN
+ *
*/
- readonly twin_L2?: Maybe<Scalars['Float']>;
+ readonly comp_id?: Maybe<Scalars['String']>;
+ /** A description for the annotation. */
+ readonly description?: Maybe<Scalars['String']>;
+ /** A name for the annotation. */
+ readonly name?: Maybe<Scalars['String']>;
/**
- * Estimated twinning fraction for operators as identified by Xtriage. A semicolon separated
- * list of operators with fractions is givens
- * Example: X-ray entry specific, obtained from the Xtriage program.
+ * Code identifying the individual, organization or program that
+ * assigned the annotation.
+ *
+ * Examples:
+ * PDB
+ *
*/
- readonly twin_fraction?: Maybe<Scalars['String']>;
+ readonly provenance_source?: Maybe<Scalars['String']>;
/**
- * The mmCIF item names of the _refln columns used as input to the Xtriage program.
- * Example X-ray entry specific, calculated by Phenix Xtriage program.
+ * A type or category of the annotation.
+ *
+ * Allowable values:
+ * SUBJECT_OF_INVESTIGATION
+ *
*/
- readonly xtriage_input_columns?: Maybe<Scalars['String']>;
+ readonly type?: Maybe<Scalars['String']>;
};
-export type RcsbUniprotContainerIdentifiersReferenceSequenceIdentifiers = {
- /** Reference database accession code */
- readonly database_accession?: Maybe<Scalars['String']>;
- /** Reference database identifier for the sequence isoform */
- readonly database_isoform?: Maybe<Scalars['String']>;
- /** Reference database name */
- readonly database_name?: Maybe<Scalars['String']>;
- /** Source of the reference database assignment */
- readonly provenance_source?: Maybe<Scalars['String']>;
+export type RcsbNonpolymerEntityAnnotationAnnotationLineage = {
+ /** Members of the annotation lineage as parent lineage depth (1-N) */
+ readonly depth?: Maybe<Scalars['Int']>;
+ /** Members of the annotation lineage as parent class identifiers. */
+ readonly id?: Maybe<Scalars['String']>;
+ /** Members of the annotation lineage as parent class names. */
+ readonly name?: Maybe<Scalars['String']>;
};
-export type RcsbEntitySourceOrganismRcsbGeneName = {
+export type RcsbNonpolymerEntityContainerIdentifiers = {
+ /** Instance identifiers corresponding to copies of the entity in this container. */
+ readonly asym_ids?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
+ /** Author instance identifiers corresponding to copies of the entity in this container. */
+ readonly auth_asym_ids?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
/**
- * A code indicating the provenance of the source organism details for the entity
- *
- * Allowable values:
- * PDB Primary Data, UniProt
+ * The chemical reference definition identifier for the entity in this container.
+ *
+ * Examples:
+ * PRD_000010
+ *
*/
- readonly provenance_source?: Maybe<Scalars['String']>;
- /** Gene name. */
- readonly value?: Maybe<Scalars['String']>;
-};
-
-export type RcsbPolymerStructConn = {
- readonly connect_partner?: Maybe<RcsbPolymerStructConnConnectPartner>;
- readonly connect_target?: Maybe<RcsbPolymerStructConnConnectTarget>;
+ readonly chem_ref_def_id?: Maybe<Scalars['String']>;
/**
- * The connection type.
- *
- * Allowable values:
- * covalent bond, covalent modification of a nucleotide base, covalent modification of a nucleotide phosphate, covalent modification of a nucleotide sugar, covalent residue modification, disulfide bridge, hydrogen bond, ionic interaction, metal coordination, mismatched base pairs
+ * Entity identifier for the container.
+ *
+ * Examples:
+ * 1, 2
+ *
*/
- readonly connect_type?: Maybe<Scalars['String']>;
- /** A description of special details of the connection. */
- readonly description?: Maybe<Scalars['String']>;
- /** Distance value for this contact. */
- readonly dist_value?: Maybe<Scalars['Float']>;
+ readonly entity_id: Scalars['String'];
/**
- * The value of _rcsb_polymer_struct_conn.id is an identifier for connection.
- *
- * Note that this item need not be a number; it can be any unique
- * identifier.
+ * Entry identifier for the container.
+ *
+ * Examples:
+ * 4HHB, 1KIP
+ *
*/
- readonly id?: Maybe<Scalars['String']>;
+ readonly entry_id: Scalars['String'];
/**
- * The value of _rcsb_polymer_struct_conn.id must uniquely identify a record in
- * the rcsb_polymer_struct_conn list.
+ * Non-polymer(ligand) chemical component identifier for the entity in this container.
+ *
+ * Examples:
+ * GTP, STN
+ *
*/
- readonly ordinal_id: Scalars['Int'];
+ readonly nonpolymer_comp_id?: Maybe<Scalars['String']>;
/**
- * The chemical or structural role of the interaction
- *
+ * The BIRD identifier for the entity in this container.
+ *
+ * Examples:
+ * PRD_000010
+ *
+ */
+ readonly prd_id?: Maybe<Scalars['String']>;
+ /**
+ * A unique identifier for each object in this entity container formed by
+ * an underscore separated concatenation of entry and entity identifiers.
+ *
+ * Examples:
+ * 6EL3_1
+ *
+ */
+ readonly rcsb_id?: Maybe<Scalars['String']>;
+ /**
+ * Source of the reference database assignment
+ *
* Allowable values:
- * C-Mannosylation, N-Glycosylation, O-Glycosylation, S-Glycosylation
+ * PDB, RCSB
+ *
*/
- readonly role?: Maybe<Scalars['String']>;
+ readonly reference_chemical_identifiers_provenance_source?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
+ /** Reference resource accession code */
+ readonly reference_chemical_identifiers_resource_accession?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
/**
- * The chemical bond order associated with the specified atoms in
- * this contact.
- *
+ * Reference resource name
+ *
* Allowable values:
- * doub, quad, sing, trip
+ * ChEBI, ChEMBL, DrugBank, PubChem
+ *
*/
- readonly value_order?: Maybe<Scalars['String']>;
+ readonly reference_chemical_identifiers_resource_name?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
};
-export type EmHelicalEntity = {
- /**
- * The angular rotation per helical subunit in degrees.
- *
- * Examples:
- * -34.616000
- */
- readonly angular_rotation_per_subunit?: Maybe<Scalars['Float']>;
+export type RcsbNonpolymerEntityFeature = {
+ readonly additional_properties?: Maybe<ReadonlyArray<Maybe<RcsbNonpolymerEntityFeatureAdditionalProperties>>>;
/**
- * The axial rise per subunit in the helical assembly.
- *
+ * Identifies the version of the feature assignment.
+ *
* Examples:
- * 17.400000
+ * V4_0_2
+ *
*/
- readonly axial_rise_per_subunit?: Maybe<Scalars['Float']>;
+ readonly assignment_version?: Maybe<Scalars['String']>;
/**
- * Symmetry of the helical axis, either cyclic (Cn) or dihedral (Dn), where n>=1.
- *
+ * Non-polymer(ligand) chemical component identifier for the entity.
+ *
* Examples:
- * C1, D2, C7
+ * GTP, STN
+ *
*/
- readonly axial_symmetry?: Maybe<Scalars['String']>;
+ readonly comp_id?: Maybe<Scalars['String']>;
+ /** A description for the feature. */
+ readonly description?: Maybe<Scalars['String']>;
+ /** An identifier for the feature. */
+ readonly feature_id?: Maybe<Scalars['String']>;
+ /** A name for the feature. */
+ readonly name?: Maybe<Scalars['String']>;
/**
- * Any other details regarding the helical assembly
- *
+ * Code identifying the individual, organization or program that
+ * assigned the feature.
+ *
* Examples:
- * Dihedral symmetry
- */
- readonly details?: Maybe<Scalars['String']>;
- /**
- * The value of _em_helical_entity.id must uniquely identify
- * a set of the filament parameters for this assembly component.
+ * PDB
+ *
*/
- readonly id: Scalars['String'];
+ readonly provenance_source?: Maybe<Scalars['String']>;
/**
- * The value of _em_helical_entity.reconstruction_id identifies a particular reconstruction.
- *
- * This data item is a pointer to _em_image_processing.id.
+ * A type or category of the feature.
+ *
+ * Allowable values:
+ * SUBJECT_OF_INVESTIGATION
+ *
*/
- readonly image_processing_id: Scalars['String'];
+ readonly type?: Maybe<Scalars['String']>;
+ /** The feature value. */
+ readonly value?: Maybe<Scalars['Float']>;
};
-export type CoreEntityAlignmentsCoreEntityIdentifiers = {
- readonly entity_id: Scalars['String'];
- readonly entry_id: Scalars['String'];
+export type RcsbNonpolymerEntityFeatureAdditionalProperties = {
+ /** The additional property name. */
+ readonly name?: Maybe<Scalars['String']>;
+ /** The value(s) of the additional property. */
+ readonly values?: Maybe<ReadonlyArray<Maybe<Scalars['ObjectScalar']>>>;
};
-export type PdbxStructAssembly = {
+export type RcsbNonpolymerEntityFeatureSummary = {
/**
- * A description of special aspects of the macromolecular assembly.
- *
+ * Non-polymer(ligand) chemical component identifier for the entity.
+ *
* Examples:
- * The icosahedral virus particle.
- */
- readonly details?: Maybe<Scalars['String']>;
- /**
- * The value of _pdbx_struct_assembly.id must uniquely identify a record in
- * the PDBX_STRUCT_ASSEMBLY list.
- */
- readonly id: Scalars['String'];
- /**
- * Provides details of the method used to determine or
- * compute the assembly.
+ * GTP, STN
+ *
*/
- readonly method_details?: Maybe<Scalars['String']>;
- /** The number of polymer molecules in the assembly. */
- readonly oligomeric_count?: Maybe<Scalars['Int']>;
+ readonly comp_id?: Maybe<Scalars['String']>;
+ /** The feature count. */
+ readonly count?: Maybe<Scalars['Int']>;
+ /** The maximum feature length. */
+ readonly maximum_length?: Maybe<Scalars['Int']>;
/**
- * Provides the details of the oligomeric state of the assembly.
- *
+ * The maximum feature value.
+ *
* Examples:
- * monomer, octameric, tetradecameric, eicosameric, 21-meric, 60-meric, 180-meric, helical
+ * null, null
+ *
*/
- readonly oligomeric_details?: Maybe<Scalars['String']>;
+ readonly maximum_value?: Maybe<Scalars['Float']>;
+ /** The minimum feature length. */
+ readonly minimum_length?: Maybe<Scalars['Int']>;
/**
- * Candidate macromolecular assembly.
- *
- * Excludes the following cases classified in pdbx_struct_asembly.details:
- *
- * 'crystal asymmetric unit', 'crystal asymmetric unit, crystal frame', 'helical asymmetric unit',
- * 'helical asymmetric unit, std helical frame','icosahedral 23 hexamer', 'icosahedral asymmetric unit',
- * 'icosahedral asymmetric unit, std point frame','icosahedral pentamer', 'pentasymmetron capsid unit',
- * 'point asymmetric unit', 'point asymmetric unit, std point frame','trisymmetron capsid unit',
- * and 'deposited_coordinates'.
- *
- * Allowable values:
- * N, Y
+ * The minimum feature value.
+ *
+ * Examples:
+ * null, null
+ *
*/
- readonly rcsb_candidate_assembly?: Maybe<Scalars['String']>;
+ readonly minimum_value?: Maybe<Scalars['Float']>;
/**
- * A filtered description of the macromolecular assembly.
- *
+ * Type or category of the feature.
+ *
* Allowable values:
- * author_and_software_defined_assembly, author_defined_assembly, software_defined_assembly
+ * SUBJECT_OF_INVESTIGATION
+ *
*/
- readonly rcsb_details?: Maybe<Scalars['String']>;
+ readonly type?: Maybe<Scalars['String']>;
};
-export type RcsbBranchedEntityContainerIdentifiers = {
- /** Instance identifiers corresponding to copies of the entity in this container. */
- readonly asym_ids?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
- /** Author instance identifiers corresponding to copies of the entity in this container. */
- readonly auth_asym_ids?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
- /** Unique list of monomer chemical component identifiers in the entity in this container. */
- readonly chem_comp_monomers?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
+export type RcsbNonpolymerEntityInstanceContainerIdentifiers = {
+ /** Instance identifier for this container. */
+ readonly asym_id: Scalars['String'];
+ /** Author instance identifier for this container. */
+ readonly auth_asym_id?: Maybe<Scalars['String']>;
+ /** Residue number for non-polymer entity instance. */
+ readonly auth_seq_id?: Maybe<Scalars['String']>;
+ /** Component identifier for non-polymer entity instance. */
+ readonly comp_id?: Maybe<Scalars['String']>;
/** Entity identifier for the container. */
- readonly entity_id: Scalars['String'];
+ readonly entity_id?: Maybe<Scalars['String']>;
/** Entry identifier for the container. */
readonly entry_id: Scalars['String'];
- /** The BIRD identifier for the entity in this container. */
- readonly prd_id?: Maybe<Scalars['String']>;
/**
- * A unique identifier for each object in this entity container formed by
- * an underscore separated concatenation of entry and entity identifiers.
+ * A unique identifier for each object in this entity instance container formed by
+ * an 'dot' (.) separated concatenation of entry and entity instance identifiers.
+ *
+ * Examples:
+ * 1KIP.A
+ *
*/
readonly rcsb_id?: Maybe<Scalars['String']>;
};
-export type RcsbRepositoryHoldingsCurrentEntryContainerIdentifiers = {
- /** The assembly id codes. */
- readonly assembly_ids?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
- /** The PDB entry accession code. */
- readonly entry_id: Scalars['String'];
- /** The RCSB entry identifier. */
- readonly rcsb_id?: Maybe<Scalars['String']>;
- /** Identifier for the current data exchange status record. */
- readonly update_id?: Maybe<Scalars['String']>;
+export type RcsbNonpolymerEntityKeywords = {
+ /** Keywords describing this non-polymer entity. */
+ readonly text?: Maybe<Scalars['String']>;
};
-export type CorePubmed = {
- /** Unique integer value assigned to each PubMed record. */
- readonly rcsb_id?: Maybe<Scalars['String']>;
- /** A concise, accurate and factual mini-version of the paper contents. */
- readonly rcsb_pubmed_abstract_text?: Maybe<Scalars['String']>;
- readonly rcsb_pubmed_affiliation_info?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
- /** Unique integer value assigned to each PubMed Central record. */
- readonly rcsb_pubmed_central_id?: Maybe<Scalars['String']>;
- readonly rcsb_pubmed_container_identifiers: RcsbPubmedContainerIdentifiers;
- /** Persistent identifier used to provide a link to an article location on the Internet. */
- readonly rcsb_pubmed_doi?: Maybe<Scalars['String']>;
- readonly rcsb_pubmed_mesh_descriptors?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
- readonly rcsb_pubmed_mesh_descriptors_lineage?: Maybe<ReadonlyArray<Maybe<RcsbPubmedMeshDescriptorsLineage>>>;
+export type RcsbNonpolymerEntityNameCom = {
+ /** A common name for the nonpolymer entity. */
+ readonly name: Scalars['String'];
};
-export type ChemComp = {
+export type RcsbNonpolymerInstanceAnnotation = {
+ /** An identifier for the annotation. */
+ readonly annotation_id?: Maybe<Scalars['String']>;
+ readonly annotation_lineage?: Maybe<ReadonlyArray<Maybe<RcsbNonpolymerInstanceAnnotationAnnotationLineage>>>;
/**
- * The formula for the chemical component. Formulae are written
- * according to the following rules:
- *
- * (1) Only recognized element symbols may be used.
- *
- * (2) Each element symbol is followed by a 'count' number. A count
- * of '1' may be omitted.
- *
- * (3) A space or parenthesis must separate each cluster of
- * (element symbol + count), but in general parentheses are
- * not used.
- *
- * (4) The order of elements depends on whether carbon is
- * present or not. If carbon is present, the order should be:
- * C, then H, then the other elements in alphabetical order
- * of their symbol. If carbon is not present, the elements
- * are listed purely in alphabetic order of their symbol. This
- * is the 'Hill' system used by Chemical Abstracts.
- *
+ * Identifies the version of the annotation assignment.
+ *
* Examples:
- * C18 H19 N7 O8 S
+ * V4_0_2
+ *
*/
- readonly formula?: Maybe<Scalars['String']>;
- /** Formula mass of the chemical component. */
- readonly formula_weight?: Maybe<Scalars['Float']>;
+ readonly assignment_version?: Maybe<Scalars['String']>;
/**
- * The value of _chem_comp.id must uniquely identify each item in
- * the CHEM_COMP list.
- *
- * For protein polymer entities, this is the three-letter code for
- * the amino acid.
- *
- * For nucleic acid polymer entities, this is the one-letter code
- * for the base.
- *
+ * Chemical component identifier.
+ *
* Examples:
- * ALA, VAL, DG, C
+ * ATP
+ *
*/
- readonly id: Scalars['String'];
+ readonly comp_id?: Maybe<Scalars['String']>;
+ /** A description for the annotation. */
+ readonly description?: Maybe<Scalars['String']>;
+ /** A name for the annotation. */
+ readonly name?: Maybe<Scalars['String']>;
+ /** Ordinal identifier for this category */
+ readonly ordinal: Scalars['Int'];
/**
- * The identifier for the parent component of the nonstandard
- * component. May be be a comma separated list if this component
- * is derived from multiple components.
- *
- * Items in this indirectly point to _chem_comp.id in
- * the CHEM_COMP category.
+ * Code identifying the individual, organization or program that
+ * assigned the annotation.
+ *
+ * Examples:
+ * PDB
+ *
*/
- readonly mon_nstd_parent_comp_id?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
+ readonly provenance_source?: Maybe<Scalars['String']>;
/**
- * The full name of the component.
- *
- * Examples:
- * alanine, valine, adenine, cytosine
+ * A type or category of the annotation.
+ *
+ * Allowable values:
+ * HAS_COVALENT_LINKAGE, HAS_METAL_COORDINATION_LINKAGE
+ *
*/
+ readonly type?: Maybe<Scalars['String']>;
+};
+
+export type RcsbNonpolymerInstanceAnnotationAnnotationLineage = {
+ /** Members of the annotation lineage as parent lineage depth (1-N) */
+ readonly depth?: Maybe<Scalars['Int']>;
+ /** Members of the annotation lineage as parent class identifiers. */
+ readonly id?: Maybe<Scalars['String']>;
+ /** Members of the annotation lineage as parent class names. */
readonly name?: Maybe<Scalars['String']>;
+};
+
+export type RcsbNonpolymerInstanceFeature = {
+ readonly additional_properties?: Maybe<ReadonlyArray<Maybe<RcsbNonpolymerInstanceFeatureAdditionalProperties>>>;
/**
- * For standard polymer components, the one-letter code for
- * the component. For non-standard polymer components, the
- * one-letter code for parent component if this exists;
- * otherwise, the one-letter code should be given as 'X'.
- *
- * Components that derived from multiple parents components
- * are described by a sequence of one-letter-codes.
- *
+ * Identifies the version of the feature assignment.
+ *
* Examples:
- * A, B, R, N, D, C, Q, E, Z, G, H, I, L, K, M, F, P, S, T, W, Y, V, U, O, X
- */
- readonly one_letter_code?: Maybe<Scalars['String']>;
- /**
- * A preliminary classification used by PDB to indicate
- * that the chemistry of this component while described
- * as clearly as possible is still ambiguous. Software
- * tools may not be able to process this component
- * definition.
+ * V4_0_2
+ *
*/
- readonly pdbx_ambiguous_flag?: Maybe<Scalars['String']>;
+ readonly assignment_version?: Maybe<Scalars['String']>;
+ /** Component identifier for non-polymer entity instance. */
+ readonly comp_id?: Maybe<Scalars['String']>;
+ /** A description for the feature. */
+ readonly description?: Maybe<Scalars['String']>;
+ /** An identifier for the feature. */
+ readonly feature_id?: Maybe<Scalars['String']>;
+ readonly feature_value?: Maybe<ReadonlyArray<Maybe<RcsbNonpolymerInstanceFeatureFeatureValue>>>;
+ /** A name for the feature. */
+ readonly name?: Maybe<Scalars['String']>;
+ /** Ordinal identifier for this category */
+ readonly ordinal: Scalars['Int'];
/**
- * The net integer charge assigned to this component. This is the
- * formal charge assignment normally found in chemical diagrams.
+ * Code identifying the individual, organization or program that
+ * assigned the feature.
+ *
+ * Examples:
+ * PDB
+ *
*/
- readonly pdbx_formal_charge?: Maybe<Scalars['Int']>;
- /** Date component was added to database. */
- readonly pdbx_initial_date?: Maybe<Scalars['Date']>;
- /** Date component was last modified. */
- readonly pdbx_modified_date?: Maybe<Scalars['Date']>;
+ readonly provenance_source?: Maybe<Scalars['String']>;
/**
- * This data item identifies the deposition site that processed
- * this chemical component defintion.
- *
+ * A type or category of the feature.
+ *
* Allowable values:
- * EBI, PDBC, PDBE, PDBJ, RCSB
+ * HAS_COVALENT_LINKAGE, HAS_METAL_COORDINATION_LINKAGE, MOGUL_ANGLE_OUTLIER, MOGUL_BOND_OUTLIER, RSCC_OUTLIER, RSRZ_OUTLIER, STEREO_OUTLIER
+ *
*/
- readonly pdbx_processing_site?: Maybe<Scalars['String']>;
+ readonly type?: Maybe<Scalars['String']>;
+};
+
+export type RcsbNonpolymerInstanceFeatureAdditionalProperties = {
/**
- * This data item holds the current release status for the component.
- *
- * Allowable values:
- * DEL, HOLD, HPUB, OBS, REF_ONLY, REL
+ * The additional property name.
+ *
+ * Examples:
+ * bond_distance, bond_angle
+ *
*/
- readonly pdbx_release_status?: Maybe<Scalars['String']>;
+ readonly name?: Maybe<Scalars['String']>;
+ /** The value(s) of the additional property. */
+ readonly values?: Maybe<ReadonlyArray<Maybe<Scalars['ObjectScalar']>>>;
+};
+
+export type RcsbNonpolymerInstanceFeatureFeatureValue = {
/**
- * Identifies the _chem_comp.id of the component that
- * has replaced this component.
- *
+ * The chemical component identifier for the instance of the feature value.
+ *
* Examples:
- * q11, tvx
+ * ATP,, STN
+ *
*/
- readonly pdbx_replaced_by?: Maybe<Scalars['String']>;
+ readonly comp_id?: Maybe<Scalars['String']>;
/**
- * Identifies the _chem_comp.id's of the components
- * which have been replaced by this component.
- * Multiple id codes should be separated by commas.
- *
+ * Specific details about the feature.
+ *
* Examples:
- * q11, tvx,atv
+ * C1,C2, C1,C2,C3
+ *
*/
- readonly pdbx_replaces?: Maybe<Scalars['String']>;
+ readonly details?: Maybe<Scalars['String']>;
/**
- * The list of subcomponents contained in this component.
- *
+ * The reference value of the feature.
+ *
* Examples:
- * TSM DPH HIS CHF EMR
+ * null, null
+ *
*/
- readonly pdbx_subcomponent_list?: Maybe<Scalars['String']>;
+ readonly reference?: Maybe<Scalars['Float']>;
/**
- * For standard polymer components, the common three-letter code for
- * the component. Non-standard polymer components and non-polymer
- * components are also assigned three-letter-codes.
- *
- * For ambiguous polymer components three-letter code should
- * be given as 'UNK'. Ambiguous ions are assigned the code 'UNX'.
- * Ambiguous non-polymer components are assigned the code 'UNL'.
- *
+ * The reported value of the feature.
+ *
* Examples:
- * ALA, ARG, ASN, ASP, ASX, CYS, GLN, GLU, GLY, GLX, HIS, ILE, LEU, LYS, MET, PHE, PRO, SER, THR, TRP, TYR, VAL, 1MA, 5MC, OMC, 1MG, 2MG, M2G, 7MG, 0MG, H2U, 5MU, PSU, ACE, FOR, HOH, UNK
+ * null, null
+ *
*/
- readonly three_letter_code?: Maybe<Scalars['String']>;
+ readonly reported?: Maybe<Scalars['Float']>;
/**
- * For standard polymer components, the type of the monomer.
- * Note that monomers that will form polymers are of three types:
- * linking monomers, monomers with some type of N-terminal (or 5')
- * cap and monomers with some type of C-terminal (or 3') cap.
- *
- * Allowable values:
- * D-beta-peptide, C-gamma linking, D-gamma-peptide, C-delta linking, D-peptide COOH carboxy terminus, D-peptide NH3 amino terminus, D-peptide linking, D-saccharide, D-saccharide, alpha linking, D-saccharide, beta linking, DNA OH 3 prime terminus, DNA OH 5 prime terminus, DNA linking, L-DNA linking, L-RNA linking, L-beta-peptide, C-gamma linking, L-gamma-peptide, C-delta linking, L-peptide COOH carboxy terminus, L-peptide NH3 amino terminus, L-peptide linking, L-saccharide, L-saccharide, alpha linking, L-saccharide, beta linking, RNA OH 3 prime terminus, RNA OH 5 prime terminus, RNA linking, non-polymer, other, peptide linking, peptide-like, saccharide
+ * The estimated uncertainty of the reported feature value.
+ *
+ * Examples:
+ * null, null
+ *
*/
- readonly type?: Maybe<Scalars['String']>;
-};
-
-export type RcsbUniprotExternalReference = {
- readonly provenance_source?: Maybe<Scalars['String']>;
- readonly reference_id?: Maybe<Scalars['String']>;
+ readonly uncertainty_estimate?: Maybe<Scalars['Float']>;
/**
+ * The type of estimated uncertainty for the reported feature value.
+ *
* Allowable values:
- * IMPC, GTEX, PHAROS
+ * Z-Score
+ *
*/
- readonly reference_name?: Maybe<Scalars['String']>;
+ readonly uncertainty_estimate_type?: Maybe<Scalars['String']>;
};
-export type PdbxReferenceEntityPoly = {
- /** The database code for this source information */
- readonly db_code?: Maybe<Scalars['String']>;
- /** The database name for this source information */
- readonly db_name?: Maybe<Scalars['String']>;
+export type RcsbNonpolymerInstanceFeatureSummary = {
+ /** Component identifier for non-polymer entity instance. */
+ readonly comp_id?: Maybe<Scalars['String']>;
+ /** The feature count. */
+ readonly count?: Maybe<Scalars['Int']>;
+ /** The maximum feature length. */
+ readonly maximum_length?: Maybe<Scalars['Int']>;
/**
- * The value of _pdbx_reference_entity_poly.prd_id is a reference
- * _pdbx_reference_entity_list.prd_id in the PDBX_REFERENCE_ENTITY_LIST category.
+ * The maximum feature value.
+ *
+ * Examples:
+ * null, null
+ *
*/
- readonly prd_id: Scalars['String'];
+ readonly maximum_value?: Maybe<Scalars['Float']>;
+ /** The minimum feature length. */
+ readonly minimum_length?: Maybe<Scalars['Int']>;
/**
- * The value of _pdbx_reference_entity_poly.ref_entity_id is a reference
- * to _pdbx_reference_entity_list.ref_entity_id in PDBX_REFERENCE_ENTITY_LIST category.
+ * The minimum feature value.
+ *
+ * Examples:
+ * null, null
+ *
*/
- readonly ref_entity_id: Scalars['String'];
+ readonly minimum_value?: Maybe<Scalars['Float']>;
/**
- * The type of the polymer.
- *
+ * Type or category of the feature.
+ *
* Allowable values:
- * nucleic-acid-like, oligosaccharide, peptide-like, polysaccharide-like
+ * HAS_COVALENT_LINKAGE, HAS_METAL_COORDINATION_LINKAGE, MOGUL_ANGLE_OUTLIER, MOGUL_BOND_OUTLIER, RSCC_OUTLIER, RSRZ_OUTLIER, STEREO_OUTLIER
+ *
*/
readonly type?: Maybe<Scalars['String']>;
};
-export type CurrentEntry = {
- /** The RCSB entry identifier. */
- readonly rcsb_id: Scalars['String'];
- readonly rcsb_repository_holdings_current?: Maybe<RcsbRepositoryHoldingsCurrent>;
- readonly rcsb_repository_holdings_current_entry_container_identifiers?: Maybe<RcsbRepositoryHoldingsCurrentEntryContainerIdentifiers>;
-};
-
-export type RcsbStructSymmetry = {
- readonly clusters: ReadonlyArray<Maybe<RcsbStructSymmetryClusters>>;
+export type RcsbNonpolymerInstanceValidationScore = {
/**
- * The granularity at which the symmetry calculation is performed. In 'Global Symmetry' all polymeric subunits in assembly are used. In 'Local Symmetry' only a subset of polymeric subunits is considered. In 'Pseudo Symmetry' the threshold for subunits similarity is relaxed.
- *
- * Allowable values:
- * Global Symmetry, Pseudo Symmetry, Local Symmetry
+ * The real space correlation coefficient (RSCC) for the non-polymer entity instance.
+ *
+ * Examples:
+ * null, null
+ *
*/
- readonly kind: Scalars['String'];
+ readonly RSCC?: Maybe<Scalars['Float']>;
/**
- * Oligomeric state refers to a composition of polymeric subunits in quaternary structure. Quaternary structure may be composed either exclusively of several copies of identical subunits, in which case they are termed homo-oligomers, or alternatively by at least one copy of different subunits (hetero-oligomers). Quaternary structure composed of a single subunit is denoted as 'Monomer'.
- *
+ * The real space R-value (RSR) for the non-polymer entity instance.
+ *
* Examples:
- * Monomer, Homo 2-mer, Hetero 3-mer
+ * null, null
+ *
*/
- readonly oligomeric_state: Scalars['String'];
- /** The orientation of the principal rotation (symmetry) axis. */
- readonly rotation_axes?: Maybe<ReadonlyArray<Maybe<RcsbStructSymmetryRotationAxes>>>;
- /** Each type of different subunits is assigned a latter. The number of equivalent subunits is added as a coefficient after each letter (except 1 which is not added explicitly). */
- readonly stoichiometry: ReadonlyArray<Maybe<Scalars['String']>>;
+ readonly RSR?: Maybe<Scalars['Float']>;
+ /** Alternate conformer identifier for the non-polymer entity instance. */
+ readonly alt_id?: Maybe<Scalars['String']>;
/**
- * Symmetry symbol refers to point group or helical symmetry of identical polymeric subunits in Schönflies notation. Contains point group symbol (e.g., C2, C5, D2, T, O, I) or H for helical symmetry.
- *
+ * The average heavy atom occupancy for coordinate records for the non-polymer entity instance.
+ *
* Examples:
- * C1, D3, H
+ * null, null
+ *
*/
- readonly symbol: Scalars['String'];
+ readonly average_occupancy?: Maybe<Scalars['Float']>;
/**
- * Symmetry type refers to point group or helical symmetry of identical polymeric subunits. Contains point group types (e.g. Cyclic, Dihedral) or Helical for helical symmetry.
- *
+ * The reported fraction of atomic coordinate records for the non-polymer entity instance.
+ *
+ * Examples:
+ * null, null
+ *
+ */
+ readonly completeness?: Maybe<Scalars['Float']>;
+ /** The number of intermolecular MolProbity clashes cacluated for reported atomic coordinate records. */
+ readonly intermolecular_clashes?: Maybe<Scalars['Int']>;
+ /**
+ * This molecular instance is ranked as the best quality instance of this nonpolymer entity.
+ *
* Allowable values:
- * Asymmetric, Cyclic, Dihedral, Tetrahedral, Octahedral, Icosahedral, Helical
+ * N, Y
+ *
*/
- readonly type: Scalars['String'];
-};
-
-export type RcsbStructSymmetryLineage = {
- /** Hierarchy depth. */
- readonly depth?: Maybe<Scalars['Int']>;
- /** A unique identifier automatically assigned to the symmetry term. */
- readonly id?: Maybe<Scalars['String']>;
+ readonly is_best_instance?: Maybe<Scalars['String']>;
/**
- * A human-readable term describing protein symmetry.
- *
+ * This molecular entity is identified as the subject of the current study.
+ *
+ * Allowable values:
+ * N, Y
+ *
+ */
+ readonly is_subject_of_investigation?: Maybe<Scalars['String']>;
+ /**
+ * The provenance for the selection of the molecular entity identified as the subject of the current study.
+ *
+ * Allowable values:
+ * Author, RCSB
+ *
+ */
+ readonly is_subject_of_investigation_provenance?: Maybe<Scalars['String']>;
+ /**
+ * Number of bond angle outliers obtained from a CCDC Mogul survey of bond angles in the CSD small
+ * molecule crystal structure database. Outliers are defined as bond angles that have a Z-score
+ * less than -2 or greater than 2.
+ */
+ readonly mogul_angle_outliers?: Maybe<Scalars['Int']>;
+ /**
+ * The root-mean-square value of the Z-scores of bond angles for the residue in degrees
+ * obtained from a CCDC Mogul survey of bond angles in the CSD small molecule crystal structure database.
+ *
* Examples:
- * Asymmetric, Global Symmetry, C1, Hetero 3-mer
+ * null, null
+ *
*/
- readonly name?: Maybe<Scalars['String']>;
-};
-
-export type PdbxReferenceMoleculeAnnotation = {
+ readonly mogul_angles_RMSZ?: Maybe<Scalars['Float']>;
/**
- * The value of _pdbx_reference_molecule_annotation.family_prd_id is a reference to
- * _pdbx_reference_molecule_list.family_prd_id in category PDBX_REFERENCE_MOLECULE_FAMILY_LIST.
+ * Number of bond distance outliers obtained from a CCDC Mogul survey of bond lengths in the CSD small
+ * molecule crystal structure database. Outliers are defined as bond distances that have a Z-score
+ * less than -2 or greater than 2.
*/
- readonly family_prd_id: Scalars['String'];
- /** This data item distinguishes anotations for this entity. */
- readonly ordinal: Scalars['Int'];
+ readonly mogul_bond_outliers?: Maybe<Scalars['Int']>;
/**
- * This data item is a pointer to _pdbx_reference_molecule.prd_id in the
- * PDB_REFERENCE_MOLECULE category.
+ * The root-mean-square value of the Z-scores of bond lengths for the residue in Angstroms
+ * obtained from a CCDC Mogul survey of bond lengths in the CSD small molecule crystal structure database.
+ *
+ * Examples:
+ * null, null
+ *
*/
- readonly prd_id?: Maybe<Scalars['String']>;
+ readonly mogul_bonds_RMSZ?: Maybe<Scalars['Float']>;
/**
- * The source of the annoation for this entity.
- *
+ * The ranking of the model fit score component.
+ *
* Examples:
- * depositor provided, from UniProt Entry P200311
+ * null, null
+ *
*/
- readonly source?: Maybe<Scalars['String']>;
+ readonly ranking_model_fit?: Maybe<Scalars['Float']>;
/**
- * Text describing the annotation for this entity.
- *
+ * The ranking of the model geometry score component.
+ *
* Examples:
- * antigen binding, glucose transporter activity
+ * null, null
+ *
*/
- readonly text?: Maybe<Scalars['String']>;
+ readonly ranking_model_geometry?: Maybe<Scalars['Float']>;
/**
- * Type of annotation for this entity.
- *
+ * The value of the model fit score component.
+ *
* Examples:
- * Function, Use, Pharmacology, Mechanism_of_Action, Biological_Activity, Inhibitor_Class, Therapeutic_Category, Research_Use, Other_annotation
+ * null, null
+ *
+ */
+ readonly score_model_fit?: Maybe<Scalars['Float']>;
+ /**
+ * The value of the model geometry score component.
+ *
+ * Examples:
+ * null, null
+ *
+ */
+ readonly score_model_geometry?: Maybe<Scalars['Float']>;
+ /** Number of stereochemical/chirality errors. */
+ readonly stereo_outliers?: Maybe<Scalars['Int']>;
+ /**
+ * Score type.
+ *
+ * Allowable values:
+ * RCSB_LIGAND_QUALITY_SCORE_2021
+ *
*/
readonly type?: Maybe<Scalars['String']>;
};
-export type PdbxReferenceMoleculeRelatedStructures = {
- /** A link to related reference information in the citation category. */
- readonly citation_id?: Maybe<Scalars['String']>;
+export type RcsbNonpolymerStructConn = {
+ readonly connect_partner?: Maybe<RcsbNonpolymerStructConnConnectPartner>;
+ readonly connect_target?: Maybe<RcsbNonpolymerStructConnConnectTarget>;
/**
- * The database accession code for the related structure reference.
- *
- * Examples:
- * 143108
+ * The connection type.
+ *
+ * Allowable values:
+ * covalent bond, disulfide bridge, hydrogen bond, ionic interaction, metal coordination, mismatched base pairs
+ *
*/
- readonly db_accession?: Maybe<Scalars['String']>;
+ readonly connect_type?: Maybe<Scalars['String']>;
/**
- * The database identifier code for the related structure reference.
- *
+ * A description of special details of the connection.
+ *
* Examples:
- * QEFHUE
+ * Watson-Crick base pair
+ *
*/
- readonly db_code?: Maybe<Scalars['String']>;
+ readonly description?: Maybe<Scalars['String']>;
+ /** Distance value for this contact. */
+ readonly dist_value?: Maybe<Scalars['Float']>;
/**
- * The database name for the related structure reference.
- *
- * Examples:
- * CCDC
+ * The value of _rcsb_nonpolymer_struct_conn.id is an identifier for connection.
+ *
+ * Note that this item need not be a number; it can be any unique
+ * identifier.
*/
- readonly db_name?: Maybe<Scalars['String']>;
+ readonly id?: Maybe<Scalars['String']>;
/**
- * The value of _pdbx_reference_molecule_related_structures.family_prd_id is a reference to
- * _pdbx_reference_molecule_list.family_prd_id in category PDBX_REFERENCE_MOLECULE_FAMILY_LIST.
+ * The value of _rcsb_nonpolymer_struct_conn.id must uniquely identify a record in
+ * the rcsb_nonpolymer_struct_conn list.
*/
- readonly family_prd_id: Scalars['String'];
+ readonly ordinal_id: Scalars['Int'];
/**
- * The formula for the reference entity. Formulae are written
- * according to the rules:
- *
- * 1. Only recognised element symbols may be used.
- *
- * 2. Each element symbol is followed by a 'count' number. A count
- * of '1' may be omitted.
- *
- * 3. A space or parenthesis must separate each element symbol and
- * its count, but in general parentheses are not used.
- *
- * 4. The order of elements depends on whether or not carbon is
- * present. If carbon is present, the order should be: C, then
- * H, then the other elements in alphabetical order of their
- * symbol. If carbon is not present, the elements are listed
- * purely in alphabetic order of their symbol. This is the
- * 'Hill' system used by Chemical Abstracts.
- *
- * Examples:
- * C18 H19 N7 O8 S
+ * The chemical or structural role of the interaction
+ *
+ * Allowable values:
+ * C-Mannosylation, N-Glycosylation, O-Glycosylation, S-Glycosylation
+ *
*/
- readonly formula?: Maybe<Scalars['String']>;
+ readonly role?: Maybe<Scalars['String']>;
/**
- * The chemical name for the structure entry in the related database
- *
- * Examples:
- * actinomycn
+ * The chemical bond order associated with the specified atoms in
+ * this contact.
+ *
+ * Allowable values:
+ * doub, quad, sing, trip
+ *
*/
- readonly name?: Maybe<Scalars['String']>;
+ readonly value_order?: Maybe<Scalars['String']>;
+};
+
+export type RcsbNonpolymerStructConnConnectPartner = {
/**
- * The value of _pdbx_reference_molecule_related_structures.ordinal distinguishes
- * related structural data for each entity.
+ * A component of the identifier for the partner in the structure
+ * connection.
+ *
+ * This data item is a pointer to _atom_site.label_alt_id in the
+ * ATOM_SITE category.
+ */
+ readonly label_alt_id?: Maybe<Scalars['String']>;
+ /**
+ * A component of the identifier for the partner in the structure
+ * connection.
+ *
+ * This data item is a pointer to _atom_site.label_asym_id in the
+ * ATOM_SITE category.
+ */
+ readonly label_asym_id: Scalars['String'];
+ /**
+ * A component of the identifier for the partner in the structure
+ * connection.
+ *
+ * This data item is a pointer to _chem_comp_atom.atom_id in the
+ * CHEM_COMP_ATOM category.
+ */
+ readonly label_atom_id?: Maybe<Scalars['String']>;
+ /**
+ * A component of the identifier for the partner in the structure
+ * connection.
+ *
+ * This data item is a pointer to _atom_site.label_comp_id in the
+ * ATOM_SITE category.
+ */
+ readonly label_comp_id: Scalars['String'];
+ /**
+ * A component of the identifier for the partner in the structure
+ * connection.
+ *
+ * This data item is a pointer to _atom_site.label_seq_id in the
+ * ATOM_SITE category.
+ */
+ readonly label_seq_id?: Maybe<Scalars['Int']>;
+ /**
+ * Describes the symmetry operation that should be applied to the
+ * atom set specified by _rcsb_nonpolymer_struct_conn.connect_partner_label* to generate the
+ * partner in the structure connection.
+ *
+ * Examples:
+ * 1_555, 7_645
+ *
*/
- readonly ordinal: Scalars['Int'];
+ readonly symmetry?: Maybe<Scalars['String']>;
};
-export type RcsbEntitySourceOrganism = {
+export type RcsbNonpolymerStructConnConnectTarget = {
/**
- * The beginning polymer sequence position for the polymer section corresponding
- * to this source.
- *
- * A reference to the sequence position in the entity_poly category.
+ * A component of the identifier for the target of the structure
+ * connection.
+ *
+ * This data item is a pointer to _atom_site.auth_asym_id in the
+ * ATOM_SITE category.
*/
- readonly beg_seq_num?: Maybe<Scalars['Int']>;
- /** The common name for the source organism assigned by the PDB depositor. */
- readonly common_name?: Maybe<Scalars['String']>;
+ readonly auth_asym_id?: Maybe<Scalars['String']>;
/**
- * The ending polymer sequence position for the polymer section corresponding
- * to this source.
- *
- * A reference to the sequence position in the entity_poly category.
+ * A component of the identifier for the target of the structure
+ * connection.
+ *
+ * This data item is a pointer to _atom_site.auth_seq_id in the
+ * ATOM_SITE category.
*/
- readonly end_seq_num?: Maybe<Scalars['Int']>;
+ readonly auth_seq_id?: Maybe<Scalars['String']>;
/**
- * Common names associated with this taxonomy code aggregated by the NCBI Taxonomy Database.
- *
- * These name correspond to the taxonomy identifier assigned by the PDB depositor.
- *
- * References:
- *
- * Sayers EW, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V,
- * Church DM, DiCuccio M, Edgar R, Federhen S, Feolo M, Geer LY,
- * Helmberg W, Kapustin Y, Landsman D, Lipman DJ, Madden TL, Maglott DR,
- * Miller V, Mizrachi I, Ostell J, Pruitt KD, Schuler GD, Sequeira E,
- * Sherry ST, Shumway M, Sirotkin K, Souvorov A, Starchenko G,
- * Tatusova TA, Wagner L, Yaschenko E, Ye J (2009). Database resources
- * of the National Center for Biotechnology Information. Nucleic Acids
- * Res. 2009 Jan;37(Database issue):D5-15. Epub 2008 Oct 21.
- *
- * Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW (2009).
- * GenBank. Nucleic Acids Res. 2009 Jan;37(Database issue):D26-31.
- * Epub 2008 Oct 21.
+ * A component of the identifier for the target of the structure
+ * connection.
+ *
+ * This data item is a pointer to _atom_site.label_alt_id in the
+ * ATOM_SITE category.
*/
- readonly ncbi_common_names?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
+ readonly label_alt_id?: Maybe<Scalars['String']>;
/**
- * The parent scientific name in the NCBI taxonomy hierarchy (depth=1) of the source organism assigned by the PDB depositor.
- *
- *
- * References:
- *
- * Sayers EW, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V,
- * Church DM, DiCuccio M, Edgar R, Federhen S, Feolo M, Geer LY,
- * Helmberg W, Kapustin Y, Landsman D, Lipman DJ, Madden TL, Maglott DR,
- * Miller V, Mizrachi I, Ostell J, Pruitt KD, Schuler GD, Sequeira E,
- * Sherry ST, Shumway M, Sirotkin K, Souvorov A, Starchenko G,
- * Tatusova TA, Wagner L, Yaschenko E, Ye J (2009). Database resources
- * of the National Center for Biotechnology Information. Nucleic Acids
- * Res. 2009 Jan;37(Database issue):D5-15. Epub 2008 Oct 21.
- *
- * Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW (2009).
- * GenBank. Nucleic Acids Res. 2009 Jan;37(Database issue):D26-31.
- * Epub 2008 Oct 21.
+ * A component of the identifier for the target of the structure
+ * connection.
+ *
+ * This data item is a pointer to _atom_site.label_asym_id in the
+ * ATOM_SITE category.
*/
- readonly ncbi_parent_scientific_name?: Maybe<Scalars['String']>;
+ readonly label_asym_id: Scalars['String'];
/**
- * The scientific name associated with this taxonomy code aggregated by the NCBI Taxonomy Database.
- *
- * This name corresponds to the taxonomy identifier assigned by the PDB depositor.
- *
- *
- * References:
- *
- * Sayers EW, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V,
- * Church DM, DiCuccio M, Edgar R, Federhen S, Feolo M, Geer LY,
- * Helmberg W, Kapustin Y, Landsman D, Lipman DJ, Madden TL, Maglott DR,
- * Miller V, Mizrachi I, Ostell J, Pruitt KD, Schuler GD, Sequeira E,
- * Sherry ST, Shumway M, Sirotkin K, Souvorov A, Starchenko G,
- * Tatusova TA, Wagner L, Yaschenko E, Ye J (2009). Database resources
- * of the National Center for Biotechnology Information. Nucleic Acids
- * Res. 2009 Jan;37(Database issue):D5-15. Epub 2008 Oct 21.
- *
- * Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW (2009).
- * GenBank. Nucleic Acids Res. 2009 Jan;37(Database issue):D26-31.
- * Epub 2008 Oct 21.
+ * A component of the identifier for the target of the structure
+ * connection.
+ *
+ * This data item is a pointer to _atom_site.label_atom_id in the
+ * ATOM_SITE category.
*/
- readonly ncbi_scientific_name?: Maybe<Scalars['String']>;
+ readonly label_atom_id?: Maybe<Scalars['String']>;
/**
- * NCBI Taxonomy identifier for the gene source organism assigned by the PDB depositor.
- *
- * Reference:
- *
- * Wheeler DL, Chappey C, Lash AE, Leipe DD, Madden TL, Schuler GD,
- * Tatusova TA, Rapp BA (2000). Database resources of the National
- * Center for Biotechnology Information. Nucleic Acids Res 2000 Jan
- * 1;28(1):10-4
- *
- * Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Rapp BA,
- * Wheeler DL (2000). GenBank. Nucleic Acids Res 2000 Jan 1;28(1):15-18.
+ * A component of the identifier for the target of the structure
+ * connection.
+ *
+ * This data item is a pointer to _atom_site.label_comp_id in the
+ * ATOM_SITE category.
*/
- readonly ncbi_taxonomy_id?: Maybe<Scalars['Int']>;
- /** An identifier for the entity segment. */
- readonly pdbx_src_id: Scalars['String'];
+ readonly label_comp_id: Scalars['String'];
/**
- * A code indicating the provenance of the source organism details for the entity
- *
- * Allowable values:
- * PDB Primary Data
+ * A component of the identifier for the target of the structure
+ * connection.
+ *
+ * This data item is a pointer to _atom_site.connect_target_label_seq_id in the
+ * ATOM_SITE category.
*/
- readonly provenance_source?: Maybe<Scalars['String']>;
- readonly rcsb_gene_name?: Maybe<ReadonlyArray<Maybe<RcsbEntitySourceOrganismRcsbGeneName>>>;
- /** The scientific name of the source organism assigned by the PDB depositor. */
- readonly scientific_name?: Maybe<Scalars['String']>;
+ readonly label_seq_id?: Maybe<Scalars['Int']>;
/**
- * The source type for the entity
- *
- * Allowable values:
- * genetically engineered, natural, synthetic
+ * Describes the symmetry operation that should be applied to the
+ * atom set specified by _rcsb_nonpolymer_struct_conn.label* to generate the
+ * target of the structure connection.
+ *
+ * Examples:
+ * 1_555, 7_645
+ *
*/
- readonly source_type?: Maybe<Scalars['String']>;
- readonly taxonomy_lineage?: Maybe<ReadonlyArray<Maybe<RcsbEntitySourceOrganismTaxonomyLineage>>>;
+ readonly symmetry?: Maybe<Scalars['String']>;
};
-export type RcsbUniprotContainerIdentifiers = {
- readonly reference_sequence_identifiers?: Maybe<ReadonlyArray<Maybe<RcsbUniprotContainerIdentifiersReferenceSequenceIdentifiers>>>;
- /** Primary accession number of a given UniProtKB entry. */
- readonly uniprot_id?: Maybe<Scalars['String']>;
+export type RcsbPfamContainerIdentifiers = {
+ /** Accession number of Pfam entry. */
+ readonly pfam_id?: Maybe<Scalars['String']>;
};
-export type DrugbankInfo = {
- /** The DrugBank drug affected organisms. */
- readonly affected_organisms?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
- /** The Anatomical Therapeutic Chemical Classification System (ATC) codes. */
- readonly atc_codes?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
- /** DrugBank drug brand names. */
- readonly brand_names?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
+export type RcsbPolymerEntity = {
+ /** A description of special aspects of the entity. */
+ readonly details?: Maybe<Scalars['String']>;
/**
- * The DrugBank assigned Chemical Abstracts Service identifier.
- *
+ * Formula mass (KDa) of the entity.
+ *
* Examples:
- * 56-65-5
+ * null, null
+ *
*/
- readonly cas_number?: Maybe<Scalars['String']>;
- /** The DrugBank drug description. */
- readonly description?: Maybe<Scalars['String']>;
- /** The DrugBank drug categories. */
- readonly drug_categories?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
- /** The DrugBank drug drug groups. */
- readonly drug_groups?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
- /** The DrugBank accession code */
- readonly drugbank_id: Scalars['String'];
+ readonly formula_weight?: Maybe<Scalars['Float']>;
/**
- * The DrugBank drug indication.
- *
+ * A description of the polymer entity.
+ *
* Examples:
- * For nutritional supplementation, also for treating dietary shortage or imbalance
+ * Green fluorescent protein, 23S ribosomal RNA, NAD-dependent protein deacylase sirtuin-5, mitochondrial
+ *
*/
- readonly indication?: Maybe<Scalars['String']>;
+ readonly pdbx_description?: Maybe<Scalars['String']>;
/**
- * The DrugBank drug mechanism of actions.
- *
+ * Enzyme Commission (EC) number(s)
+ *
* Examples:
- * ATP is able to store and transport chemical energy within cells.
+ * 2.7.7.7
+ *
*/
- readonly mechanism_of_action?: Maybe<Scalars['String']>;
- /** The DrugBank drug name. */
- readonly name?: Maybe<Scalars['String']>;
+ readonly pdbx_ec?: Maybe<Scalars['String']>;
/**
- * The DrugBank drug pharmacology.
- *
+ * Polymer entity fragment description(s).
+ *
* Examples:
- * Adenosine triphosphate (ATP) is the nucleotide known in biochemistry as the "molecular currency" of intracellular energy transfer; that is, ATP is able to store and transport chemical energy within cells. ATP also plays an important role in the synthesis of nucleic acids. The total quantity of ATP in the human body is about 0.1 mole. The energy used by human cells requires the hydrolysis of 200 to 300 moles of ATP daily. This means that each ATP molecule is recycled 2000 to 3000 times during a single day. ATP cannot be stored, hence its consumption must closely follow its synthesis.
+ * KLENOW FRAGMENT, REPLICASE OPERATOR HAIRPIN, C-TERMINAL DOMAIN
+ *
*/
- readonly pharmacology?: Maybe<Scalars['String']>;
- /** DrugBank drug name synonyms. */
- readonly synonyms?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
-};
-
-export type RcsbNonpolymerEntityFeatureSummary = {
- /** Non-polymer(ligand) chemical component identifier for the entity. */
- readonly comp_id?: Maybe<Scalars['String']>;
- /** The feature count. */
- readonly count?: Maybe<Scalars['Int']>;
- /** The maximum feature length. */
- readonly maximum_length?: Maybe<Scalars['Int']>;
- /** The maximum feature value. */
- readonly maximum_value?: Maybe<Scalars['Float']>;
- /** The minimum feature length. */
- readonly minimum_length?: Maybe<Scalars['Int']>;
- /** The minimum feature value. */
- readonly minimum_value?: Maybe<Scalars['Float']>;
+ readonly pdbx_fragment?: Maybe<Scalars['String']>;
/**
- * Type or category of the feature.
- *
- * Allowable values:
- * SUBJECT_OF_INVESTIGATION
+ * Details about any polymer entity mutation(s).
+ *
+ * Examples:
+ * Y31H, DEL(298-323)
+ *
*/
- readonly type?: Maybe<Scalars['String']>;
-};
-
-export type RcsbExternalReferences = {
- /** ID (accession) from external resource linked to this entry. */
- readonly id: Scalars['String'];
- /** Link to this entry in external resource. */
- readonly link: Scalars['String'];
+ readonly pdbx_mutation?: Maybe<Scalars['String']>;
+ /** The number of molecules of the entity in the entry. */
+ readonly pdbx_number_of_molecules?: Maybe<Scalars['Int']>;
+ readonly rcsb_ec_lineage?: Maybe<ReadonlyArray<Maybe<RcsbPolymerEntityRcsbEcLineage>>>;
+ readonly rcsb_enzyme_class_combined?: Maybe<ReadonlyArray<Maybe<RcsbPolymerEntityRcsbEnzymeClassCombined>>>;
+ readonly rcsb_macromolecular_names_combined?: Maybe<ReadonlyArray<Maybe<RcsbPolymerEntityRcsbMacromolecularNamesCombined>>>;
/**
- * Internal identifier for external resource.
- *
+ * A code indicating the entity has multiple biological sources.
+ *
* Allowable values:
- * OLDERADO, BMRB, NDB, SB GRID, STORE SYNCHROTRON, PROTEIN DIFFRACTION, EM DATA RESOURCE
+ * N, Y
+ *
*/
- readonly type: Scalars['String'];
-};
-
-export type PdbxReferenceMolecule = {
+ readonly rcsb_multiple_source_flag?: Maybe<Scalars['String']>;
/**
- * For entities represented as single molecules, the identifier
- * corresponding to the chemical definition for the molecule.
- *
- * Examples:
- * 0Z3, CD9
+ * The number of biological sources for the polymer entity. Multiple source contributions
+ * may come from the same organism (taxonomy).
*/
- readonly chem_comp_id?: Maybe<Scalars['String']>;
+ readonly rcsb_source_part_count?: Maybe<Scalars['Int']>;
+ /** The number of distinct source taxonomies for the polymer entity. Commonly used to identify chimeric polymers. */
+ readonly rcsb_source_taxonomy_count?: Maybe<Scalars['Int']>;
/**
- * Broadly defines the function of the entity.
- *
+ * The method by which the sample for the polymer entity was produced.
+ * Entities isolated directly from natural sources (tissues, soil
+ * samples etc.) are expected to have further information in the
+ * ENTITY_SRC_NAT category. Entities isolated from genetically
+ * manipulated sources are expected to have further information in
+ * the ENTITY_SRC_GEN category.
+ *
* Allowable values:
- * Antagonist, Anthelmintic, Antibiotic, Antibiotic, Anthelmintic, Antibiotic, Antimicrobial, Antibiotic, Antineoplastic, Anticancer, Anticoagulant, Anticoagulant, Antithrombotic, Antifungal, Antigen, Antiinflammatory, Antimicrobial, Antimicrobial, Antiparasitic, Antibiotic, Antimicrobial, Antiretroviral, Antimicrobial, Antitumor, Antineoplastic, Antiparasitic, Antiretroviral, Antithrombotic, Antitumor, Antiviral, CASPASE inhibitor, Chaperone binding, Drug delivery, Enzyme inhibitor, Glycan component, Growth factor, Immunosuppressant, Inducer, Inhibitor, Lantibiotic, Metabolism, Metal transport, Nutrient, Oxidation-reduction, Protein binding, Receptor, Substrate analog, Synthetic opioid, Thrombin inhibitor, Thrombin inhibitor, Trypsin inhibitor, Toxin, Transition state mimetic, Transport activator, Trypsin inhibitor, Unknown, Water retention
+ * man, nat, syn
+ *
*/
- readonly class?: Maybe<Scalars['String']>;
- /** Evidence for the assignment of _pdbx_reference_molecule.class */
- readonly class_evidence_code?: Maybe<Scalars['String']>;
- /** Special details about this molecule. */
- readonly compound_details?: Maybe<Scalars['String']>;
- /** Description of this molecule. */
- readonly description?: Maybe<Scalars['String']>;
- /**
- * The formula for the reference entity. Formulae are written
- * according to the rules:
- *
- * 1. Only recognised element symbols may be used.
- *
- * 2. Each element symbol is followed by a 'count' number. A count
- * of '1' may be omitted.
- *
- * 3. A space or parenthesis must separate each element symbol and
- * its count, but in general parentheses are not used.
- *
- * 4. The order of elements depends on whether or not carbon is
- * present. If carbon is present, the order should be: C, then
- * H, then the other elements in alphabetical order of their
- * symbol. If carbon is not present, the elements are listed
- * purely in alphabetic order of their symbol. This is the
- * 'Hill' system used by Chemical Abstracts.
- *
+ readonly src_method?: Maybe<Scalars['String']>;
+};
+
+export type RcsbPolymerEntityAlign = {
+ readonly aligned_regions?: Maybe<ReadonlyArray<Maybe<RcsbPolymerEntityAlignAlignedRegions>>>;
+ /**
+ * Code identifying the individual, organization or program that
+ * assigned the reference sequence.
+ *
* Examples:
- * C18 H19 N7 O8 S
+ * PDB, SIFTS, RCSB
+ *
*/
- readonly formula?: Maybe<Scalars['String']>;
- /** Formula mass in daltons of the entity. */
- readonly formula_weight?: Maybe<Scalars['Float']>;
+ readonly provenance_source?: Maybe<Scalars['String']>;
/**
- * A name of the entity.
- *
+ * Reference sequence accession code.
+ *
* Examples:
- * thiostrepton
+ * Q9HD40
+ *
*/
- readonly name?: Maybe<Scalars['String']>;
+ readonly reference_database_accession?: Maybe<Scalars['String']>;
/**
- * The value of _pdbx_reference_molecule.prd_id is the unique identifier
- * for the reference molecule in this family.
- *
- * By convention this ID uniquely identifies the reference molecule in
- * in the PDB reference dictionary.
- *
- * The ID has the template form PRD_dddddd (e.g. PRD_000001)
+ * Reference sequence isoform identifier.
+ *
+ * Examples:
+ * P01116-2
+ *
*/
- readonly prd_id: Scalars['String'];
+ readonly reference_database_isoform?: Maybe<Scalars['String']>;
/**
- * Defines the current PDB release status for this molecule definition.
- *
+ * Reference sequence database name.
+ *
* Allowable values:
- * HOLD, OBS, REL, WAIT
+ * EMBL, GenBank, NDB, NORINE, PDB, PIR, PRF, RefSeq, UniProt
+ *
*/
- readonly release_status?: Maybe<Scalars['String']>;
- /** Assigns the identifier of the reference molecule that has replaced this molecule. */
- readonly replaced_by?: Maybe<Scalars['String']>;
+ readonly reference_database_name?: Maybe<Scalars['String']>;
+};
+
+export type RcsbPolymerEntityAlignAlignedRegions = {
+ /** An identifier for the monomer in the entity sequence at which this segment of the alignment begins. */
+ readonly entity_beg_seq_id?: Maybe<Scalars['Int']>;
+ /** An length of the this segment of the alignment. */
+ readonly length?: Maybe<Scalars['Int']>;
+ /** An identifier for the monomer in the reference sequence at which this segment of the alignment begins. */
+ readonly ref_beg_seq_id?: Maybe<Scalars['Int']>;
+};
+
+export type RcsbPolymerEntityAnnotation = {
+ /** An identifier for the annotation. */
+ readonly annotation_id?: Maybe<Scalars['String']>;
+ readonly annotation_lineage?: Maybe<ReadonlyArray<Maybe<RcsbPolymerEntityAnnotationAnnotationLineage>>>;
/**
- * Assigns the identifier for the reference molecule which have been replaced
- * by this reference molecule.
- * Multiple molecule identifier codes should be separated by commas.
+ * Identifies the version of the annotation assignment.
+ *
+ * Examples:
+ * V4_0_2
+ *
*/
- readonly replaces?: Maybe<Scalars['String']>;
+ readonly assignment_version?: Maybe<Scalars['String']>;
+ /** A description for the annotation. */
+ readonly description?: Maybe<Scalars['String']>;
+ /** A name for the annotation. */
+ readonly name?: Maybe<Scalars['String']>;
/**
- * Defines how this entity is represented in PDB data files.
- *
- * Allowable values:
- * branched, polymer, single molecule
+ * Code identifying the individual, organization or program that
+ * assigned the annotation.
+ *
+ * Examples:
+ * PDB, UniProt
+ *
*/
- readonly represent_as?: Maybe<Scalars['String']>;
- /** The PDB accession code for the entry containing a representative example of this molecule. */
- readonly representative_PDB_id_code?: Maybe<Scalars['String']>;
+ readonly provenance_source?: Maybe<Scalars['String']>;
/**
- * Defines the structural classification of the entity.
- *
+ * A type or category of the annotation.
+ *
* Allowable values:
- * Amino acid, Aminoglycoside, Ansamycin, Anthracycline, Anthraquinone, Chalkophore, Chalkophore, Polypeptide, Chromophore, Cyclic depsipeptide, Cyclic lipopeptide, Cyclic peptide, Glycopeptide, Heterocyclic, Imino sugar, Keto acid, Lipoglycopeptide, Lipopeptide, Macrolide, Non-polymer, Nucleoside, Oligopeptide, Oligosaccharide, Peptaibol, Peptide-like, Polycyclic, Polypeptide, Polysaccharide, Quinolone, Siderophore, Thiolactone, Thiopeptide, Unknown
+ * GO, GlyCosmos, GlyGen, InterPro, MemProtMD, OPM, PDBTM, Pfam, mpstruc
+ *
*/
readonly type?: Maybe<Scalars['String']>;
- /** Evidence for the assignment of _pdbx_reference_molecule.type */
- readonly type_evidence_code?: Maybe<Scalars['String']>;
};
-export type PdbxReferenceMoleculeFamily = {
- /**
- * The value of _pdbx_reference_entity.family_prd_id must uniquely identify a record in the
- * PDBX_REFERENCE_MOLECULE_FAMILY list.
- *
- * By convention this ID uniquely identifies the reference family in
- * in the PDB reference dictionary.
- *
- * The ID has the template form FAM_dddddd (e.g. FAM_000001)
- */
- readonly family_prd_id: Scalars['String'];
+export type RcsbPolymerEntityAnnotationAnnotationLineage = {
+ /** Members of the annotation lineage as parent lineage depth (1-N) */
+ readonly depth?: Maybe<Scalars['Int']>;
+ /** Members of the annotation lineage as parent class identifiers. */
+ readonly id?: Maybe<Scalars['String']>;
+ /** Members of the annotation lineage as parent class names. */
+ readonly name?: Maybe<Scalars['String']>;
+};
+
+export type RcsbPolymerEntityContainerIdentifiers = {
+ /** Instance identifiers corresponding to copies of the entity in this container. */
+ readonly asym_ids?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
+ /** Author instance identifiers corresponding to copies of the entity in this container. */
+ readonly auth_asym_ids?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
+ /** Unique list of monomer chemical component identifiers in the polymer entity in this container. */
+ readonly chem_comp_monomers?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
+ /** Unique list of non-standard monomer chemical component identifiers in the polymer entity in this container. */
+ readonly chem_comp_nstd_monomers?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
/**
- * The entity family name.
- *
+ * The chemical reference definition identifier for the entity in this container.
+ *
* Examples:
- * actinomycin, adriamycin
+ * PRD_000010
+ *
*/
- readonly name?: Maybe<Scalars['String']>;
+ readonly chem_ref_def_id?: Maybe<Scalars['String']>;
/**
- * Assigns the current PDB release status for this family.
- *
- * Allowable values:
- * HOLD, OBS, REL, WAIT
+ * Entity identifier for the container.
+ *
+ * Examples:
+ * 1, 2
+ *
*/
- readonly release_status?: Maybe<Scalars['String']>;
- /** Assigns the identifier of the family that has replaced this component. */
- readonly replaced_by?: Maybe<Scalars['String']>;
+ readonly entity_id: Scalars['String'];
/**
- * Assigns the identifier for the family which have been replaced by this family.
- * Multiple family identifier codes should be separated by commas.
+ * Entry identifier for the container.
+ *
+ * Examples:
+ * 4HHB, 1KIP
+ *
*/
- readonly replaces?: Maybe<Scalars['String']>;
-};
-
-export type PdbxEntitySrcSyn = {
+ readonly entry_id: Scalars['String'];
/**
- * A description of special aspects of the source for the
- * synthetic entity.
- *
+ * The BIRD identifier for the entity in this container.
+ *
* Examples:
- * This sequence occurs naturally in humans.
+ * PRD_000010
+ *
*/
- readonly details?: Maybe<Scalars['String']>;
+ readonly prd_id?: Maybe<Scalars['String']>;
/**
- * NCBI Taxonomy identifier of the organism from which the sequence of
- * the synthetic entity was derived.
- *
- * Reference:
- *
- * Wheeler DL, Chappey C, Lash AE, Leipe DD, Madden TL, Schuler GD,
- * Tatusova TA, Rapp BA (2000). Database resources of the National
- * Center for Biotechnology Information. Nucleic Acids Res 2000 Jan
- * 1;28(1):10-4
- *
- * Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Rapp BA,
- * Wheeler DL (2000). GenBank. Nucleic Acids Res 2000 Jan 1;28(1):15-18.
+ * A unique identifier for each object in this entity container formed by
+ * an underscore separated concatenation of entry and entity identifiers.
+ *
+ * Examples:
+ * 6EL3_1
+ *
*/
- readonly ncbi_taxonomy_id?: Maybe<Scalars['String']>;
+ readonly rcsb_id?: Maybe<Scalars['String']>;
+ readonly reference_sequence_identifiers?: Maybe<ReadonlyArray<Maybe<RcsbPolymerEntityContainerIdentifiersReferenceSequenceIdentifiers>>>;
+ readonly uniprot_ids?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
+};
+
+export type RcsbPolymerEntityContainerIdentifiersReferenceSequenceIdentifiers = {
/**
- * The common name of the organism from which the sequence of
- * the synthetic entity was derived.
- *
+ * Reference database accession code
+ *
* Examples:
- * house mouse
+ * P01116, 55771382
+ *
*/
- readonly organism_common_name?: Maybe<Scalars['String']>;
+ readonly database_accession?: Maybe<Scalars['String']>;
/**
- * The scientific name of the organism from which the sequence of
- * the synthetic entity was derived.
- *
+ * Reference database identifier for the sequence isoform
+ *
* Examples:
- * synthetic construct, Mus musculus
+ * P01116-2
+ *
*/
- readonly organism_scientific?: Maybe<Scalars['String']>;
+ readonly database_isoform?: Maybe<Scalars['String']>;
/**
- * This data item identifies cases in which an alternative source
- * modeled.
- *
+ * Reference database name
+ *
* Allowable values:
- * model, sample
- */
- readonly pdbx_alt_source_flag?: Maybe<Scalars['String']>;
- /**
- * The beginning polymer sequence position for the polymer section corresponding
- * to this source.
- *
- * A reference to the sequence position in the entity_poly category.
+ * EMBL, GenBank, NDB, NORINE, PDB, PIR, PRF, RefSeq, UniProt
+ *
*/
- readonly pdbx_beg_seq_num?: Maybe<Scalars['Int']>;
+ readonly database_name?: Maybe<Scalars['String']>;
/**
- * The ending polymer sequence position for the polymer section corresponding
- * to this source.
- *
- * A reference to the sequence position in the entity_poly category.
+ * Source of the reference database assignment
+ *
+ * Allowable values:
+ * PDB, RCSB, SIFTS
+ *
*/
- readonly pdbx_end_seq_num?: Maybe<Scalars['Int']>;
- /** This data item is an ordinal identifier for pdbx_entity_src_syn data records. */
- readonly pdbx_src_id: Scalars['Int'];
+ readonly provenance_source?: Maybe<Scalars['String']>;
};
export type RcsbPolymerEntityFeature = {
- /** Identifies the version of the feature assignment. */
+ readonly additional_properties?: Maybe<ReadonlyArray<Maybe<RcsbPolymerEntityFeatureAdditionalProperties>>>;
+ /**
+ * Identifies the version of the feature assignment.
+ *
+ * Examples:
+ * V4_0_2
+ *
+ */
readonly assignment_version?: Maybe<Scalars['String']>;
/** A description for the feature. */
readonly description?: Maybe<Scalars['String']>;
@@ -8814,2524 +9953,3189 @@ export type RcsbPolymerEntityFeature = {
/**
* Code identifying the individual, organization or program that
* assigned the feature.
+ *
+ * Examples:
+ * PDB
+ *
*/
readonly provenance_source?: Maybe<Scalars['String']>;
/**
* Code residue coordinate system for the assigned feature.
- *
+ *
* Allowable values:
* NCBI, PDB entity, UniProt
+ *
*/
readonly reference_scheme?: Maybe<Scalars['String']>;
/**
* A type or category of the feature.
- *
+ *
* Allowable values:
- * artifact, modified_monomer, mutation
+ * CARD_MODEL, IMGT_ANTIBODY_DESCRIPTION, IMGT_ANTIBODY_DOMAIN_NAME, IMGT_ANTIBODY_GENE_ALLELE_NAME, IMGT_ANTIBODY_ORGANISM_NAME, IMGT_ANTIBODY_PROTEIN_NAME, IMGT_ANTIBODY_RECEPTOR_DESCRIPTION, IMGT_ANTIBODY_RECEPTOR_TYPE, Pfam, SABDAB_ANTIBODY_ANTIGEN_NAME, SABDAB_ANTIBODY_NAME, SABDAB_ANTIBODY_TARGET, artifact, modified_monomer, mutation, hydropathy, disorder, disorder_binding
+ *
*/
readonly type?: Maybe<Scalars['String']>;
-};
-
-export type Cell = {
- /**
- * The number of the polymeric chains in a unit cell. In the case
- * of heteropolymers, Z is the number of occurrences of the most
- * populous chain.
- *
- * This data item is provided for compatibility with the original
- * Protein Data Bank format, and only for that purpose.
- */
- readonly Z_PDB?: Maybe<Scalars['Int']>;
- /** Unit-cell angle alpha of the reported structure in degrees. */
- readonly angle_alpha?: Maybe<Scalars['Float']>;
- /** Unit-cell angle beta of the reported structure in degrees. */
- readonly angle_beta?: Maybe<Scalars['Float']>;
- /** Unit-cell angle gamma of the reported structure in degrees. */
- readonly angle_gamma?: Maybe<Scalars['Float']>;
- /**
- * The number of the formula units in the unit cell as specified
- * by _chemical_formula.structural, _chemical_formula.moiety or
- * _chemical_formula.sum.
- */
- readonly formula_units_Z?: Maybe<Scalars['Int']>;
- /**
- * Unit-cell length a corresponding to the structure reported in
- * angstroms.
- */
- readonly length_a?: Maybe<Scalars['Float']>;
- /**
- * Unit-cell length b corresponding to the structure reported in
- * angstroms.
- */
- readonly length_b?: Maybe<Scalars['Float']>;
- /**
- * Unit-cell length c corresponding to the structure reported in
- * angstroms.
- */
- readonly length_c?: Maybe<Scalars['Float']>;
- /**
- * To further identify unique axis if necessary. E.g., P 21 with
- * an unique C axis will have 'C' in this field.
- */
- readonly pdbx_unique_axis?: Maybe<Scalars['String']>;
- /**
- * Cell volume V in angstroms cubed.
- *
- * V = a b c (1 - cos^2^~alpha~ - cos^2^~beta~ - cos^2^~gamma~
- * + 2 cos~alpha~ cos~beta~ cos~gamma~)^1/2^
- *
- * a = _cell.length_a
- * b = _cell.length_b
- * c = _cell.length_c
- * alpha = _cell.angle_alpha
- * beta = _cell.angle_beta
- * gamma = _cell.angle_gamma
- */
- readonly volume?: Maybe<Scalars['Float']>;
-};
-
-export type EmDiffractionShell = {
- /** Pointer to EM CRYSTALLOGRAPHY STATS */
- readonly em_diffraction_stats_id?: Maybe<Scalars['String']>;
- /**
- * Completeness of the structure factor data within this resolution shell, in percent
- *
- * Examples:
- * 93.2
- */
- readonly fourier_space_coverage?: Maybe<Scalars['Float']>;
- /**
- * High resolution limit for this shell (Angstroms)
- *
- * Examples:
- * 3.0
- */
- readonly high_resolution?: Maybe<Scalars['Float']>;
- /** Unique identifier for the category em_diffraction_shell */
- readonly id: Scalars['String'];
- /**
- * Low resolution limit for this shell (Angstroms)
- *
- * Examples:
- * 5.5
- */
- readonly low_resolution?: Maybe<Scalars['Float']>;
- /**
- * Multiplicity (average number of measurements) for the structure factors in this resolution shell
- *
- * Examples:
- * 2.5
- */
- readonly multiplicity?: Maybe<Scalars['Float']>;
- /**
- * Number of measured structure factors in this resolution shell
- *
- * Examples:
- * 244
- */
- readonly num_structure_factors?: Maybe<Scalars['Int']>;
+};
+
+export type RcsbPolymerEntityFeatureAdditionalProperties = {
/**
- * Phase residual for this resolution shell, in degrees
- *
- * Examples:
- * 13.5
+ * The additional property name.
+ *
+ * Allowable values:
+ * CARD_MODEL_DESCRIPTION, CARD_MODEL_ORGANISM, PARENT_COMP_ID
+ *
*/
- readonly phase_residual?: Maybe<Scalars['Float']>;
+ readonly name?: Maybe<Scalars['String']>;
+ /** The value(s) of the additional property. */
+ readonly values?: Maybe<ReadonlyArray<Maybe<Scalars['ObjectScalar']>>>;
};
-export type PdbxReferenceMoleculeList = {
+export type RcsbPolymerEntityFeatureFeaturePositions = {
/**
- * The value of _pdbx_reference_molecule_list.family_prd_id is a reference to
- * _pdbx_reference_molecule_family.family_prd_id' in category PDBX_REFERENCE_MOLECULE_FAMILY.
+ * An identifier for the leading monomer corresponding to the feature assignment.
+ *
+ * Examples:
+ * TRP, VAL
+ *
*/
- readonly family_prd_id: Scalars['String'];
+ readonly beg_comp_id?: Maybe<Scalars['String']>;
+ /** An identifier for the monomer at which this segment of the feature begins. */
+ readonly beg_seq_id: Scalars['Int'];
+ /** An identifier for the monomer at which this segment of the feature ends. */
+ readonly end_seq_id?: Maybe<Scalars['Int']>;
/**
- * The value of _pdbx_reference_molecule_list.prd_id is the unique identifier
- * for the reference molecule in this family.
- *
- * By convention this ID uniquely identifies the reference molecule in
- * in the PDB reference dictionary.
- *
- * The ID has the template form PRD_dddddd (e.g. PRD_000001)
+ * The value for the feature over this monomer segment.
+ *
+ * Examples:
+ * null, null
+ *
*/
- readonly prd_id: Scalars['String'];
+ readonly value?: Maybe<Scalars['Float']>;
+ /** The value(s) for the feature over this monomer segment. */
+ readonly values?: Maybe<ReadonlyArray<Maybe<Scalars['Float']>>>;
};
-export type ExptlCrystal = {
+export type RcsbPolymerEntityFeatureSummary = {
+ /** The feature count. */
+ readonly count?: Maybe<Scalars['Int']>;
/**
- * The colour of the crystal.
- *
+ * The fractional feature coverage relative to the full entity sequence.
+ * For instance, the fraction of features such as mutations, artifacts or modified monomers
+ * relative to the length of the entity sequence.
+ *
* Examples:
- * dark green
+ * null, null
+ *
*/
- readonly colour?: Maybe<Scalars['String']>;
+ readonly coverage?: Maybe<Scalars['Float']>;
+ /** The maximum feature length. */
+ readonly maximum_length?: Maybe<Scalars['Int']>;
/**
- * The density of the crystal, expressed as the ratio of the
- * volume of the asymmetric unit to the molecular mass of a
- * monomer of the structure, in units of angstroms^3^ per dalton.
- *
- * Ref: Matthews, B. W. (1968). J. Mol. Biol. 33, 491-497.
+ * The maximum feature value.
+ *
+ * Examples:
+ * null, null
+ *
*/
- readonly density_Matthews?: Maybe<Scalars['Float']>;
+ readonly maximum_value?: Maybe<Scalars['Float']>;
+ /** The minimum feature length. */
+ readonly minimum_length?: Maybe<Scalars['Int']>;
/**
- * Density values measured using standard chemical and physical
- * methods. The units are megagrams per cubic metre (grams per
- * cubic centimetre).
+ * The minimum feature value.
+ *
+ * Examples:
+ * null, null
+ *
*/
- readonly density_meas?: Maybe<Scalars['Float']>;
+ readonly minimum_value?: Maybe<Scalars['Float']>;
/**
- * Density value P calculated from the crystal cell and contents,
- * expressed as per cent solvent.
- *
- * P = 1 - (1.23 N MMass) / V
- *
- * N = the number of molecules in the unit cell
- * MMass = the molecular mass of each molecule (gm/mole)
- * V = the volume of the unit cell (A^3^)
- * 1.23 = a conversion factor evaluated as:
- *
- * (0.74 cm^3^/g) (10^24^ A^3^/cm^3^)
- * --------------------------------------
- * (6.02*10^23^) molecules/mole
- *
- * where 0.74 is an assumed value for the partial specific
- * volume of the molecule
+ * Type or category of the feature.
+ *
+ * Allowable values:
+ * CARD_MODEL, IMGT_ANTIBODY_DESCRIPTION, IMGT_ANTIBODY_DOMAIN_NAME, IMGT_ANTIBODY_GENE_ALLELE_NAME, IMGT_ANTIBODY_ORGANISM_NAME, IMGT_ANTIBODY_PROTEIN_NAME, IMGT_ANTIBODY_RECEPTOR_DESCRIPTION, IMGT_ANTIBODY_RECEPTOR_TYPE, Pfam, SABDAB_ANTIBODY_ANTIGEN_NAME, SABDAB_ANTIBODY_NAME, SABDAB_ANTIBODY_TARGET, artifact, modified_monomer, mutation
+ *
*/
- readonly density_percent_sol?: Maybe<Scalars['Float']>;
+ readonly type?: Maybe<Scalars['String']>;
+};
+
+export type RcsbPolymerEntityInstanceContainerIdentifiers = {
+ /** Instance identifier for this container. */
+ readonly asym_id: Scalars['String'];
+ /** Author instance identifier for this container. */
+ readonly auth_asym_id?: Maybe<Scalars['String']>;
/**
- * A description of the quality and habit of the crystal.
- * The crystal dimensions should not normally be reported here;
- * use instead the specific items in the EXPTL_CRYSTAL category
- * relating to size for the gross dimensions of the crystal and
- * data items in the EXPTL_CRYSTAL_FACE category to describe the
- * relationship between individual faces.
+ * Residue index mappings between author provided and entity polymer sequence positions.
+ *
+ * Author residue indices (auth_seq_num) include insertion codes when present.
+ * The array indices correspond to the indices (1-based) of the deposited sample
+ * sequence (entity_poly_seq). Unmodelled residues are represented with a "?" value.
*/
- readonly description?: Maybe<Scalars['String']>;
+ readonly auth_to_entity_poly_seq_mapping?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
+ /** Entity identifier for the container. */
+ readonly entity_id?: Maybe<Scalars['String']>;
+ /** Entry identifier for the container. */
+ readonly entry_id: Scalars['String'];
/**
- * The value of _exptl_crystal.id must uniquely identify a record in
- * the EXPTL_CRYSTAL list.
- *
- * Note that this item need not be a number; it can be any unique
- * identifier.
+ * A unique identifier for each object in this entity instance container formed by
+ * an 'dot' (.) separated concatenation of entry and entity instance identifiers.
+ *
+ * Examples:
+ * 1KIP.A
+ *
*/
- readonly id: Scalars['String'];
+ readonly rcsb_id?: Maybe<Scalars['String']>;
+};
+
+export type RcsbPolymerEntityKeywords = {
+ /** Keywords describing this polymer entity. */
+ readonly text?: Maybe<Scalars['String']>;
+};
+
+export type RcsbPolymerEntityNameCom = {
/**
- * The of the distribution of mis-orientation angles specified in degrees
- * of all the unit cells in the crystal. Lower mosaicity indicates better
- * ordered crystals.
+ * A common name for the polymer entity.
+ *
+ * Examples:
+ * HIV protease monomer, hemoglobin alpha chain
+ *
*/
- readonly pdbx_mosaicity?: Maybe<Scalars['Float']>;
- /** The uncertainty in the mosaicity estimate for the crystal. */
- readonly pdbx_mosaicity_esd?: Maybe<Scalars['Float']>;
+ readonly name: Scalars['String'];
+};
+
+export type RcsbPolymerEntityNameSys = {
+ /** The systematic name for the polymer entity. */
+ readonly name: Scalars['String'];
/**
- * Details of crystal growth and preparation of the crystal (e.g.
- * mounting) prior to the intensity measurements.
- *
+ * The system used to generate the systematic name of the polymer entity.
+ *
* Examples:
- * mounted in an argon-filled quartz capillary
+ * Chemical Abstracts conventions
+ *
*/
- readonly preparation?: Maybe<Scalars['String']>;
+ readonly system?: Maybe<Scalars['String']>;
};
-export type EmStaining = {
+export type RcsbPolymerEntityRcsbEcLineage = {
+ /** Members of the enzyme classification lineage as parent classification hierarchy depth (1-N). */
+ readonly depth?: Maybe<Scalars['Int']>;
/**
- * Staining procedure used in the specimen preparation.
- *
+ * Members of the enzyme classification lineage as parent classification codes.
+ *
* Examples:
- * Negatively stained EM specimens were prepared using a carbon-sandwich technique
- * and uranyl-formate stain.
+ * 2, 2.7.1.153
+ *
*/
- readonly details?: Maybe<Scalars['String']>;
- /** This data item is the primary key of the category. */
- readonly id: Scalars['String'];
+ readonly id?: Maybe<Scalars['String']>;
/**
- * The staining material.
- *
+ * Members of the enzyme classification lineage as parent classification names.
+ *
* Examples:
- * Uranyl Acetate
+ * Transferases, phosphatidylinositol-4,5-bisphosphate 3-kinase
+ *
*/
- readonly material?: Maybe<Scalars['String']>;
- /** Foreign key relationship to the EMD SPECIMEN category */
- readonly specimen_id?: Maybe<Scalars['String']>;
+ readonly name?: Maybe<Scalars['String']>;
+};
+
+export type RcsbPolymerEntityRcsbEnzymeClassCombined = {
+ /** The enzyme classification hierarchy depth (1-N). */
+ readonly depth?: Maybe<Scalars['Int']>;
+ /** Combined list of enzyme class assignments. */
+ readonly ec?: Maybe<Scalars['String']>;
/**
- * type of staining
- *
+ * Combined list of enzyme class associated provenance sources.
+ *
* Allowable values:
- * NEGATIVE, NONE, POSITIVE
+ * PDB Primary Data, UniProt
+ *
*/
- readonly type?: Maybe<Scalars['String']>;
+ readonly provenance_source?: Maybe<Scalars['String']>;
};
-export type PdbxNmrSampleDetails = {
+export type RcsbPolymerEntityRcsbMacromolecularNamesCombined = {
/**
- * A complete description of each NMR sample. Include the concentration
- * and concentration units for each component (include buffers, etc.). For each
- * component describe the isotopic composition, including the % labeling level,
- * if known.
- *
- * For example:
- * 1. Uniform (random) labeling with 15N: U-15N
- * 2. Uniform (random) labeling with 13C, 15N at known labeling
- * levels: U-95% 13C;U-98% 15N
- * 3. Residue selective labeling: U-95% 15N-Thymine
- * 4. Site specific labeling: 95% 13C-Ala18,
- * 5. Natural abundance labeling in an otherwise uniformly labeled
- * biomolecule is designated by NA: U-13C; NA-K,H
- *
+ * Combined list of macromolecular names.
+ *
* Examples:
- * 2mM Ribonuclease U-15N,13C; 50mM phosphate buffer NA; 90% H2O, 10% D2O
+ * Lysozyme C, Plasmid recombination enzyme, Pyruvate carboxylase
+ *
*/
- readonly contents?: Maybe<Scalars['String']>;
+ readonly name?: Maybe<Scalars['String']>;
/**
- * Brief description of the sample providing additional information not captured by other items in the category.
- *
- * Examples:
- * The added glycerol was used to raise the viscosity of the solution to 1.05 poisson.
+ * Combined list of macromolecular names associated provenance code.
+ *
+ * ECO (https://github.com/evidenceontology/evidenceontology)
*/
- readonly details?: Maybe<Scalars['String']>;
+ readonly provenance_code?: Maybe<Scalars['String']>;
/**
- * A value that uniquely identifies this sample from the other samples listed
- * in the entry.
- *
- * Examples:
- * 15N_sample
+ * Combined list of macromolecular names associated name source.
+ *
+ * Allowable values:
+ * PDB Preferred Name, PDB Synonym
+ *
*/
- readonly label?: Maybe<Scalars['String']>;
+ readonly provenance_source?: Maybe<Scalars['String']>;
+};
+
+export type RcsbPolymerInstanceAnnotation = {
+ /** An identifier for the annotation. */
+ readonly annotation_id?: Maybe<Scalars['String']>;
+ readonly annotation_lineage?: Maybe<ReadonlyArray<Maybe<RcsbPolymerInstanceAnnotationAnnotationLineage>>>;
/**
- * The name (number) of the sample.
- *
+ * Identifies the version of the annotation assignment.
+ *
* Examples:
- * 1, 2, 3
+ * V4_0_2
+ *
*/
- readonly solution_id: Scalars['String'];
+ readonly assignment_version?: Maybe<Scalars['String']>;
+ /** A description for the annotation. */
+ readonly description?: Maybe<Scalars['String']>;
+ /** A name for the annotation. */
+ readonly name?: Maybe<Scalars['String']>;
+ /** Ordinal identifier for this category */
+ readonly ordinal: Scalars['Int'];
/**
- * The solvent system used for this sample.
- *
+ * Code identifying the individual, organization or program that
+ * assigned the annotation.
+ *
* Examples:
- * 90% H2O, 10% D2O
+ * PDB
+ *
*/
- readonly solvent_system?: Maybe<Scalars['String']>;
+ readonly provenance_source?: Maybe<Scalars['String']>;
/**
- * A descriptive term for the sample that defines the general physical properties
- * of the sample.
- *
+ * A type or category of the annotation.
+ *
* Allowable values:
- * bicelle, emulsion, fiber, fibrous protein, filamentous virus, gel solid, gel solution, liposome, lyophilized powder, membrane, micelle, oriented membrane film, polycrystalline powder, reverse micelle, single crystal, solid, solution
+ * CATH, ECOD, SCOP, SCOP2
+ *
*/
readonly type?: Maybe<Scalars['String']>;
};
-export type RcsbPolymerEntityKeywords = {
- /** Keywords describing this polymer entity. */
- readonly text?: Maybe<Scalars['String']>;
-};
-
-export type DrugbankContainerIdentifiers = {
- /** The DrugBank accession code */
- readonly drugbank_id: Scalars['String'];
+export type RcsbPolymerInstanceAnnotationAnnotationLineage = {
+ /** Members of the annotation lineage as parent lineage depth (1-N) */
+ readonly depth?: Maybe<Scalars['Int']>;
+ /** Members of the annotation lineage as parent class identifiers. */
+ readonly id?: Maybe<Scalars['String']>;
+ /** Members of the annotation lineage as parent class names. */
+ readonly name?: Maybe<Scalars['String']>;
};
-export type PdbxDatabaseRelated = {
- /**
- * The identifying content type of the related entry.
- *
- * Allowable values:
- * associated EM volume, associated NMR restraints, associated SAS data, associated structure factors, complete structure, derivative structure, ensemble, minimized average structure, native structure, other, other EM volume, protein target sequence and/or protocol data, re-refinement, representative structure, split, unspecified
- */
- readonly content_type: Scalars['String'];
+export type RcsbPolymerInstanceFeature = {
+ readonly additional_properties?: Maybe<ReadonlyArray<Maybe<RcsbPolymerInstanceFeatureAdditionalProperties>>>;
/**
- * The identifying code in the related database.
- *
+ * Identifies the version of the feature assignment.
+ *
* Examples:
- * 1ABC, BDL001
+ * V4_0_2
+ *
*/
- readonly db_id: Scalars['String'];
+ readonly assignment_version?: Maybe<Scalars['String']>;
+ /** A description for the feature. */
+ readonly description?: Maybe<Scalars['String']>;
+ /** An identifier for the feature. */
+ readonly feature_id?: Maybe<Scalars['String']>;
+ readonly feature_positions?: Maybe<ReadonlyArray<Maybe<RcsbPolymerInstanceFeatureFeaturePositions>>>;
+ /** A name for the feature. */
+ readonly name?: Maybe<Scalars['String']>;
+ /** Ordinal identifier for this category */
+ readonly ordinal: Scalars['Int'];
/**
- * The name of the database containing the related entry.
- *
+ * Code identifying the individual, organization or program that
+ * assigned the feature.
+ *
* Examples:
- * PDB - Protein Databank
- * NDB - Nucleic Acid Database
- * BMRB - BioMagResBank
- * EMDB - Electron Microscopy Database
- * BMCD - Biological Macromolecule Crystallization Database
- * TargetTrack - Target Registration and Protocol Database
- * SASBDB - Small Angle Scattering Biological Data Bank
+ * CATH, SCOP
+ *
+ */
+ readonly provenance_source?: Maybe<Scalars['String']>;
+ /**
+ * Code residue coordinate system for the assigned feature.
+ *
+ * Allowable values:
+ * NCBI, PDB entity, PDB entry, UniProt
+ *
*/
- readonly db_name: Scalars['String'];
+ readonly reference_scheme?: Maybe<Scalars['String']>;
/**
- * A description of the related entry.
- *
- * Examples:
- * 1ABC contains the same protein complexed with Netropsin.
+ * A type or category of the feature.
+ *
+ * Allowable values:
+ * ANGLE_OUTLIER, BINDING_SITE, BOND_OUTLIER, C-MANNOSYLATION_SITE, CATH, CIS-PEPTIDE, ECOD, HELIX_P, MEMBRANE_SEGMENT, MOGUL_ANGLE_OUTLIER, MOGUL_BOND_OUTLIER, N-GLYCOSYLATION_SITE, O-GLYCOSYLATION_SITE, RAMACHANDRAN_OUTLIER, ROTAMER_OUTLIER, RSCC_OUTLIER, RSRZ_OUTLIER, S-GLYCOSYLATION_SITE, SABDAB_ANTIBODY_HEAVY_CHAIN_SUBCLASS, SABDAB_ANTIBODY_LIGHT_CHAIN_SUBCLASS, SABDAB_ANTIBODY_LIGHT_CHAIN_TYPE, SCOP, SCOP2B_SUPERFAMILY, SCOP2_FAMILY, SCOP2_SUPERFAMILY, SHEET, STEREO_OUTLIER, UNASSIGNED_SEC_STRUCT, UNOBSERVED_ATOM_XYZ, UNOBSERVED_RESIDUE_XYZ, ZERO_OCCUPANCY_ATOM_XYZ, ZERO_OCCUPANCY_RESIDUE_XYZ
+ *
*/
- readonly details?: Maybe<Scalars['String']>;
+ readonly type?: Maybe<Scalars['String']>;
};
-export type RcsbUniprotProteinGene = {
- readonly name?: Maybe<ReadonlyArray<Maybe<GeneName>>>;
+export type RcsbPolymerInstanceFeatureAdditionalProperties = {
+ /**
+ * The additional property name.
+ *
+ * Allowable values:
+ * CATH_DOMAIN_ID, CATH_NAME, ECOD_DOMAIN_ID, ECOD_FAMILY_NAME, OMEGA_ANGLE, PARTNER_ASYM_ID, PARTNER_BOND_DISTANCE, PARTNER_COMP_ID, SCOP2_DOMAIN_ID, SCOP2_FAMILY_ID, SCOP2_FAMILY_NAME, SCOP2_SUPERFAMILY_ID, SCOP2_SUPERFAMILY_NAME, SCOP_DOMAIN_ID, SCOP_NAME, SCOP_SUN_ID, SHEET_SENSE
+ *
+ */
+ readonly name?: Maybe<Scalars['String']>;
+ /** The value(s) of the additional property. */
+ readonly values?: Maybe<ReadonlyArray<Maybe<Scalars['ObjectScalar']>>>;
};
-export type PdbxStructAssemblyAuthEvidence = {
- /** This item references an assembly in pdbx_struct_assembly */
- readonly assembly_id: Scalars['String'];
- /** Provides any additional information regarding the evidence of this assembly */
- readonly details?: Maybe<Scalars['String']>;
+export type RcsbPolymerInstanceFeatureFeaturePositions = {
/**
- * Provides the experimental method to determine the state of this assembly
- *
- * Allowable values:
- * NMR relaxation study, SAXS, assay for oligomerization, cross-linking, equilibrium centrifugation, fluorescence resonance energy transfer, gel filtration, homology, immunoprecipitation, isothermal titration calorimetry, light scattering, mass spectrometry, microscopy, native gel electrophoresis, none, scanning transmission electron microscopy, surface plasmon resonance
+ * An identifier for the monomer(s) corresponding to the feature assignment.
+ *
+ * Examples:
+ * TRP, VAL
+ *
*/
- readonly experimental_support?: Maybe<Scalars['String']>;
- /** Identifies a unique record in pdbx_struct_assembly_auth_evidence. */
- readonly id: Scalars['String'];
+ readonly beg_comp_id?: Maybe<Scalars['String']>;
+ /** An identifier for the monomer at which this segment of the feature begins. */
+ readonly beg_seq_id: Scalars['Int'];
+ /** An identifier for the monomer at which this segment of the feature ends. */
+ readonly end_seq_id?: Maybe<Scalars['Int']>;
+ /**
+ * The value of the feature over the monomer segment.
+ *
+ * Examples:
+ * null, null
+ *
+ */
+ readonly value?: Maybe<Scalars['Float']>;
+ /** The value(s) of the feature over the monomer segment. */
+ readonly values?: Maybe<ReadonlyArray<Maybe<Scalars['Float']>>>;
};
-export type RcsbBranchedInstanceFeatureSummary = {
- /** The feature count. */
+export type RcsbPolymerInstanceFeatureSummary = {
+ /** The feature count per polymer chain. */
readonly count?: Maybe<Scalars['Int']>;
- /** The fractional feature coverage relative to the full branched entity. */
+ /**
+ * The fractional feature coverage relative to the full entity sequence.
+ * For instance, the fraction of features such as CATH or SCOP domains, secondary structure elements,
+ * unobserved residues, or geometrical outliers relative to the length of the entity sequence.
+ *
+ * Examples:
+ * null, null
+ *
+ */
readonly coverage?: Maybe<Scalars['Float']>;
/** The maximum feature length. */
readonly maximum_length?: Maybe<Scalars['Int']>;
- /** The maximum feature value. */
+ /**
+ * The maximum feature value.
+ *
+ * Examples:
+ * null, null
+ *
+ */
readonly maximum_value?: Maybe<Scalars['Float']>;
/** The minimum feature length. */
readonly minimum_length?: Maybe<Scalars['Int']>;
- /** The minimum feature value. */
+ /**
+ * The minimum feature value.
+ *
+ * Examples:
+ * null, null
+ *
+ */
readonly minimum_value?: Maybe<Scalars['Float']>;
/**
* Type or category of the feature.
- *
+ *
* Allowable values:
- * BINDING_SITE, CATH, MOGUL_ANGLE_OUTLIER, MOGUL_BOND_OUTLIER, RSRCC_OUTLIER, RSRZ_OUTLIER, SCOP, UNOBSERVED_ATOM_XYZ, UNOBSERVED_RESIDUE_XYZ, ZERO_OCCUPANCY_ATOM_XYZ, ZERO_OCCUPANCY_RESIDUE_XYZ
+ * ANGLE_OUTLIER, BINDING_SITE, BOND_OUTLIER, C-MANNOSYLATION_SITE, CATH, CIS-PEPTIDE, ECOD, HELIX_P, MEMBRANE_SEGMENT, MOGUL_ANGLE_OUTLIER, MOGUL_BOND_OUTLIER, N-GLYCOSYLATION_SITE, O-GLYCOSYLATION_SITE, RAMACHANDRAN_OUTLIER, ROTAMER_OUTLIER, RSCC_OUTLIER, RSRZ_OUTLIER, S-GLYCOSYLATION_SITE, SABDAB_ANTIBODY_HEAVY_CHAIN_SUBCLASS, SABDAB_ANTIBODY_LIGHT_CHAIN_SUBCLASS, SABDAB_ANTIBODY_LIGHT_CHAIN_TYPE, SAbDab Antibody Heavy Chain Subclass, SAbDab Antibody Light Chain Subclass, SAbDab Antibody Light Chain Type, SCOP, SCOP2 Family, SCOP2 Superfamily, SCOP2B Superfamily, SCOP2B_SUPERFAMILY, SCOP2_FAMILY, SCOP2_SUPERFAMILY, SHEET, STEREO_OUTLIER, UNASSIGNED_SEC_STRUCT, UNOBSERVED_ATOM_XYZ, UNOBSERVED_RESIDUE_XYZ, ZERO_OCCUPANCY_ATOM_XYZ, ZERO_OCCUPANCY_RESIDUE_XYZ
+ *
*/
readonly type?: Maybe<Scalars['String']>;
};
-export type RcsbNonpolymerInstanceAnnotation = {
- /** An identifier for the annotation. */
- readonly annotation_id?: Maybe<Scalars['String']>;
- readonly annotation_lineage?: Maybe<ReadonlyArray<Maybe<RcsbNonpolymerInstanceAnnotationAnnotationLineage>>>;
- /** Identifies the version of the annotation assignment. */
- readonly assignment_version?: Maybe<Scalars['String']>;
- /** Chemical component identifier. */
- readonly comp_id?: Maybe<Scalars['String']>;
- /** A description for the annotation. */
+export type RcsbPolymerStructConn = {
+ readonly connect_partner?: Maybe<RcsbPolymerStructConnConnectPartner>;
+ readonly connect_target?: Maybe<RcsbPolymerStructConnConnectTarget>;
+ /**
+ * The connection type.
+ *
+ * Allowable values:
+ * covalent bond, covalent modification of a nucleotide base, covalent modification of a nucleotide phosphate, covalent modification of a nucleotide sugar, covalent residue modification, disulfide bridge, hydrogen bond, ionic interaction, metal coordination, mismatched base pairs
+ *
+ */
+ readonly connect_type?: Maybe<Scalars['String']>;
+ /**
+ * A description of special details of the connection.
+ *
+ * Examples:
+ * Watson-Crick base pair
+ *
+ */
readonly description?: Maybe<Scalars['String']>;
- /** A name for the annotation. */
- readonly name?: Maybe<Scalars['String']>;
- /** Ordinal identifier for this category */
- readonly ordinal: Scalars['Int'];
+ /** Distance value for this contact. */
+ readonly dist_value?: Maybe<Scalars['Float']>;
/**
- * Code identifying the individual, organization or program that
- * assigned the annotation.
+ * The value of _rcsb_polymer_struct_conn.id is an identifier for connection.
+ *
+ * Note that this item need not be a number; it can be any unique
+ * identifier.
*/
- readonly provenance_source?: Maybe<Scalars['String']>;
+ readonly id?: Maybe<Scalars['String']>;
/**
- * A type or category of the annotation.
- *
+ * The value of _rcsb_polymer_struct_conn.id must uniquely identify a record in
+ * the rcsb_polymer_struct_conn list.
+ */
+ readonly ordinal_id: Scalars['Int'];
+ /**
+ * The chemical or structural role of the interaction
+ *
* Allowable values:
- * HAS_COVALENT_LINKAGE, HAS_METAL_COORDINATION_LINKAGE
+ * C-Mannosylation, N-Glycosylation, O-Glycosylation, S-Glycosylation
+ *
*/
- readonly type?: Maybe<Scalars['String']>;
+ readonly role?: Maybe<Scalars['String']>;
+ /**
+ * The chemical bond order associated with the specified atoms in
+ * this contact.
+ *
+ * Allowable values:
+ * doub, quad, sing, trip
+ *
+ */
+ readonly value_order?: Maybe<Scalars['String']>;
};
-export type RcsbNonpolymerEntityNameCom = {
- /** A common name for the nonpolymer entity. */
- readonly name: Scalars['String'];
+export type RcsbPolymerStructConnConnectPartner = {
+ /**
+ * A component of the identifier for the partner in the structure
+ * connection.
+ *
+ * This data item is a pointer to _atom_site.label_alt_id in the
+ * ATOM_SITE category.
+ */
+ readonly label_alt_id?: Maybe<Scalars['String']>;
+ /**
+ * A component of the identifier for the partner in the structure
+ * connection.
+ *
+ * This data item is a pointer to _atom_site.label_asym_id in the
+ * ATOM_SITE category.
+ */
+ readonly label_asym_id: Scalars['String'];
+ /**
+ * A component of the identifier for the partner in the structure
+ * connection.
+ *
+ * This data item is a pointer to _chem_comp_atom.atom_id in the
+ * CHEM_COMP_ATOM category.
+ */
+ readonly label_atom_id?: Maybe<Scalars['String']>;
+ /**
+ * A component of the identifier for the partner in the structure
+ * connection.
+ *
+ * This data item is a pointer to _atom_site.label_comp_id in the
+ * ATOM_SITE category.
+ */
+ readonly label_comp_id: Scalars['String'];
+ /**
+ * A component of the identifier for the partner in the structure
+ * connection.
+ *
+ * This data item is a pointer to _atom_site.label_seq_id in the
+ * ATOM_SITE category.
+ */
+ readonly label_seq_id?: Maybe<Scalars['Int']>;
+ /**
+ * Describes the symmetry operation that should be applied to the
+ * atom set specified by _rcsb_polymer_struct_conn.connect_partner_label* to generate the
+ * partner in the structure connection.
+ *
+ * Examples:
+ * 1_555, 7_645
+ *
+ */
+ readonly symmetry?: Maybe<Scalars['String']>;
};
-export type Software = {
+export type RcsbPolymerStructConnConnectTarget = {
/**
- * The classification of the program according to its
- * major function.
- *
- * Examples:
- * data collection, data reduction, phasing, model building, refinement, validation, other
+ * A component of the identifier for the target of the structure
+ * connection.
+ *
+ * This data item is a pointer to _atom_site.auth_asym_id in the
+ * ATOM_SITE category.
*/
- readonly classification?: Maybe<Scalars['String']>;
+ readonly auth_asym_id?: Maybe<Scalars['String']>;
/**
- * The recognized contact author of the software. This could be
- * the original author, someone who has modified the code or
- * someone who maintains the code. It should be the person
- * most commonly associated with the code.
- *
- * Examples:
- * T. Alwyn Jones, Axel Brunger
+ * A component of the identifier for the target of the structure
+ * connection.
+ *
+ * This data item is a pointer to _atom_site.auth_seq_id in the
+ * ATOM_SITE category.
*/
- readonly contact_author?: Maybe<Scalars['String']>;
+ readonly auth_seq_id?: Maybe<Scalars['String']>;
/**
- * The e-mail address of the person specified in
- * _software.contact_author.
- *
- * Examples:
- * bourne@sdsc.edu
+ * A component of the identifier for the target of the structure
+ * connection.
+ *
+ * This data item is a pointer to _atom_site.label_alt_id in the
+ * ATOM_SITE category.
*/
- readonly contact_author_email?: Maybe<Scalars['String']>;
+ readonly label_alt_id?: Maybe<Scalars['String']>;
/**
- * The date the software was released.
- *
- * Examples:
- * 1991-10-01, 1990-04-30
+ * A component of the identifier for the target of the structure
+ * connection.
+ *
+ * This data item is a pointer to _atom_site.label_asym_id in the
+ * ATOM_SITE category.
*/
- readonly date?: Maybe<Scalars['String']>;
+ readonly label_asym_id: Scalars['String'];
/**
- * Description of the software.
- *
- * Examples:
- * Uses method of restrained least squares
+ * A component of the identifier for the target of the structure
+ * connection.
+ *
+ * This data item is a pointer to _atom_site.label_atom_id in the
+ * ATOM_SITE category.
*/
- readonly description?: Maybe<Scalars['String']>;
+ readonly label_atom_id?: Maybe<Scalars['String']>;
/**
- * The major computing language in which the software is
- * coded.
- *
- * Allowable values:
- * Ada, Awk, Basic, C, C++, C/C++, Fortran, Fortran 77, Fortran 90, Fortran_77, Java, Java & Fortran, Other, Pascal, Perl, Python, Python/C++, Tcl, assembler, csh, ksh, sh
+ * A component of the identifier for the target of the structure
+ * connection.
+ *
+ * This data item is a pointer to _atom_site.label_comp_id in the
+ * ATOM_SITE category.
*/
- readonly language?: Maybe<Scalars['String']>;
+ readonly label_comp_id: Scalars['String'];
/**
- * The URL for an Internet address at which
- * details of the software can be found.
- *
- * Examples:
- * http://rosebud.sdsc.edu/projects/pb/IUCr/software.html, ftp://ftp.sdsc.edu/pub/sdsc/biology/
+ * A component of the identifier for the target of the structure
+ * connection.
+ *
+ * This data item is a pointer to _atom_site.connect_target_label_seq_id in the
+ * ATOM_SITE category.
*/
- readonly location?: Maybe<Scalars['String']>;
+ readonly label_seq_id?: Maybe<Scalars['Int']>;
/**
- * The name of the software.
- *
+ * Describes the symmetry operation that should be applied to the
+ * atom set specified by _rcsb_polymer_struct_conn.label* to generate the
+ * target of the structure connection.
+ *
* Examples:
- * Merlot, O, Xengen, X-plor
+ * 1_555, 7_645
+ *
*/
- readonly name?: Maybe<Scalars['String']>;
+ readonly symmetry?: Maybe<Scalars['String']>;
+};
+
+export type RcsbPrimaryCitation = {
/**
- * The name of the operating system under which the software
- * runs.
- *
- * Examples:
- * Ultrix, OpenVMS, DOS, Windows 95, Windows NT, Irix, HPUX, DEC Unix
+ * The International Standard Book Number (ISBN) code assigned to
+ * the book cited; relevant for books or book chapters.
*/
- readonly os?: Maybe<Scalars['String']>;
+ readonly book_id_ISBN?: Maybe<Scalars['String']>;
/**
- * An ordinal index for this category
- *
+ * The name of the publisher of the citation; relevant
+ * for books or book chapters.
+ *
* Examples:
- * 1, 2
+ * John Wiley and Sons
+ *
*/
- readonly pdbx_ordinal: Scalars['Int'];
+ readonly book_publisher?: Maybe<Scalars['String']>;
/**
- * The classification of the software according to the most
- * common types.
- *
- * Allowable values:
- * filter, jiffy, library, other, package, program
+ * The location of the publisher of the citation; relevant
+ * for books or book chapters.
+ *
+ * Examples:
+ * London
+ *
*/
- readonly type?: Maybe<Scalars['String']>;
+ readonly book_publisher_city?: Maybe<Scalars['String']>;
/**
- * The version of the software.
- *
- * Examples:
- * v1.0, beta, 3.1-2, unknown
+ * The title of the book in which the citation appeared; relevant
+ * for books or book chapters.
*/
- readonly version?: Maybe<Scalars['String']>;
-};
-
-export type RcsbNonpolymerStructConn = {
- readonly connect_partner?: Maybe<RcsbNonpolymerStructConnConnectPartner>;
- readonly connect_target?: Maybe<RcsbNonpolymerStructConnConnectTarget>;
+ readonly book_title?: Maybe<Scalars['String']>;
/**
- * The connection type.
- *
+ * _rcsb_primary_citation.coordinate_linkage states whether this citation
+ * is concerned with precisely the set of coordinates given in the
+ * data block. If, for instance, the publication described the same
+ * structure, but the coordinates had undergone further refinement
+ * prior to the creation of the data block, the value of this data
+ * item would be 'no'.
+ *
* Allowable values:
- * covalent bond, disulfide bridge, hydrogen bond, ionic interaction, metal coordination, mismatched base pairs
+ * n, no, y, yes
+ *
*/
- readonly connect_type?: Maybe<Scalars['String']>;
- /** A description of special details of the connection. */
- readonly description?: Maybe<Scalars['String']>;
- /** Distance value for this contact. */
- readonly dist_value?: Maybe<Scalars['Float']>;
+ readonly coordinate_linkage?: Maybe<Scalars['String']>;
/**
- * The value of _rcsb_nonpolymer_struct_conn.id is an identifier for connection.
- *
+ * The country/region of publication; relevant for books
+ * and book chapters.
+ */
+ readonly country?: Maybe<Scalars['String']>;
+ /**
+ * The value of _rcsb_primary_citation.id must uniquely identify a record in the
+ * CITATION list.
+ *
+ * The _rcsb_primary_citation.id 'primary' should be used to indicate the
+ * citation that the author(s) consider to be the most pertinent to
+ * the contents of the data block.
+ *
* Note that this item need not be a number; it can be any unique
* identifier.
+ *
+ * Examples:
+ * primary
+ *
*/
- readonly id?: Maybe<Scalars['String']>;
+ readonly id: Scalars['String'];
/**
- * The value of _rcsb_nonpolymer_struct_conn.id must uniquely identify a record in
- * the rcsb_nonpolymer_struct_conn list.
+ * Abbreviated name of the cited journal as given in the
+ * Chemical Abstracts Service Source Index.
+ *
+ * Examples:
+ * J.Mol.Biol., J. Mol. Biol.
+ *
*/
- readonly ordinal_id: Scalars['Int'];
+ readonly journal_abbrev?: Maybe<Scalars['String']>;
/**
- * The chemical or structural role of the interaction
- *
- * Allowable values:
- * C-Mannosylation, N-Glycosylation, O-Glycosylation, S-Glycosylation
+ * The American Society for Testing and Materials (ASTM) code
+ * assigned to the journal cited (also referred to as the CODEN
+ * designator of the Chemical Abstracts Service); relevant for
+ * journal articles.
*/
- readonly role?: Maybe<Scalars['String']>;
+ readonly journal_id_ASTM?: Maybe<Scalars['String']>;
/**
- * The chemical bond order associated with the specified atoms in
- * this contact.
- *
- * Allowable values:
- * doub, quad, sing, trip
+ * The Cambridge Structural Database (CSD) code assigned to the
+ * journal cited; relevant for journal articles. This is also the
+ * system used at the Protein Data Bank (PDB).
+ *
+ * Examples:
+ * 0070
+ *
*/
- readonly value_order?: Maybe<Scalars['String']>;
-};
-
-export type PdbxPrdAudit = {
+ readonly journal_id_CSD?: Maybe<Scalars['String']>;
/**
- * The action associated with this audit record.
- *
- * Allowable values:
- * Create molecule, Initial release, Modify audit, Modify class, Modify linkage, Modify molecule name, Modify representation, Modify sequence, Modify taxonomy organism, Modify type, Obsolete molecule, Other modification
+ * The International Standard Serial Number (ISSN) code assigned to
+ * the journal cited; relevant for journal articles.
*/
- readonly action_type: Scalars['String'];
+ readonly journal_id_ISSN?: Maybe<Scalars['String']>;
/**
- * The initials of the annotator creating of modifying the molecule.
- *
+ * Issue number of the journal cited; relevant for journal
+ * articles.
+ *
* Examples:
- * JO, SJ, KB
+ * 2
+ *
*/
- readonly annotator?: Maybe<Scalars['String']>;
- /** The date associated with this audit record. */
- readonly date: Scalars['Date'];
+ readonly journal_issue?: Maybe<Scalars['String']>;
/**
- * Additional details decribing this change.
- *
+ * Volume number of the journal cited; relevant for journal
+ * articles.
+ *
* Examples:
- * Revise molecule sequence.
+ * 174
+ *
*/
- readonly details?: Maybe<Scalars['String']>;
+ readonly journal_volume?: Maybe<Scalars['String']>;
/**
- * This data item is a pointer to _pdbx_reference_molecule.prd_id in the
- * pdbx_reference_molecule category.
+ * Language in which the cited article is written.
+ *
+ * Examples:
+ * German
+ *
*/
- readonly prd_id: Scalars['String'];
+ readonly language?: Maybe<Scalars['String']>;
/**
- * An identifier for the wwPDB site creating or modifying the molecule.
- *
- * Allowable values:
- * BMRB, PDBC, PDBJ, PDBe, RCSB
+ * The first page of the citation; relevant for journal
+ * articles, books and book chapters.
*/
- readonly processing_site?: Maybe<Scalars['String']>;
-};
-
-export type CoreUniprot = {
- /** Primary accession number of a given UniProtKB entry. */
- readonly rcsb_id?: Maybe<Scalars['String']>;
- readonly rcsb_uniprot_accession?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
- /** UniProt pairwise sequence alignments. */
- readonly rcsb_uniprot_alignments?: Maybe<RcsbUniprotAlignments>;
- readonly rcsb_uniprot_annotation?: Maybe<ReadonlyArray<Maybe<RcsbUniprotAnnotation>>>;
- readonly rcsb_uniprot_container_identifiers: RcsbUniprotContainerIdentifiers;
- readonly rcsb_uniprot_entry_name?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
- readonly rcsb_uniprot_external_reference?: Maybe<ReadonlyArray<Maybe<RcsbUniprotExternalReference>>>;
- readonly rcsb_uniprot_feature?: Maybe<ReadonlyArray<Maybe<RcsbUniprotFeature>>>;
- readonly rcsb_uniprot_keyword?: Maybe<ReadonlyArray<Maybe<RcsbUniprotKeyword>>>;
- readonly rcsb_uniprot_protein?: Maybe<RcsbUniprotProtein>;
-};
-
-export type RcsbNonpolymerEntityAnnotationAnnotationLineage = {
- /** Members of the annotation lineage as parent lineage depth (1-N) */
- readonly depth?: Maybe<Scalars['Int']>;
- /** Members of the annotation lineage as parent class identifiers. */
- readonly id?: Maybe<Scalars['String']>;
- /** Members of the annotation lineage as parent class names. */
- readonly name?: Maybe<Scalars['String']>;
-};
-
-export type PdbxNmrRepresentative = {
+ readonly page_first?: Maybe<Scalars['String']>;
/**
- * If a member of the ensemble has been selected as a representative
- * structure, identify it by its model number.
- *
- * Examples:
- * 15
+ * The last page of the citation; relevant for journal
+ * articles, books and book chapters.
*/
- readonly conformer_id?: Maybe<Scalars['String']>;
+ readonly page_last?: Maybe<Scalars['String']>;
/**
- * By highlighting the appropriate choice(s), describe the criteria used to
- * select this structure as a representative structure, or if an average
- * structure has been calculated describe how this was done.
- *
+ * Document Object Identifier used by doi.org to uniquely
+ * specify bibliographic entry.
+ *
* Examples:
- * The structure closest to the average.
- * The structure with the lowest energy was selected.
- * The structure with the fewest number of violations was selected.
- * A minimized average structure was calculated.
+ * 10.2345/S1384107697000225
+ *
*/
- readonly selection_criteria?: Maybe<Scalars['String']>;
-};
-
-export type PdbxSerialCrystallographyDataReduction = {
+ readonly pdbx_database_id_DOI?: Maybe<Scalars['String']>;
/**
- * For experiments in which samples are provided in a
- * continuous stream, the total number of frames collected
- * in which the crystal was hit.
- *
- * Examples:
- * 1200, 5750
+ * Ascession number used by PubMed to categorize a specific
+ * bibliographic entry.
*/
- readonly crystal_hits?: Maybe<Scalars['Int']>;
+ readonly pdbx_database_id_PubMed?: Maybe<Scalars['Int']>;
+ /** The Open Researcher and Contributor ID (ORCID) identifiers for the citation authors. */
+ readonly rcsb_ORCID_identifiers?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
/**
- * The data item is a pointer to _diffrn.id in the DIFFRN
- * category.
- *
- * Examples:
- * 1
+ * Names of the authors of the citation; relevant for journal
+ * articles, books and book chapters. Names are separated by vertical bars.
+ *
+ * The family name(s), followed by a comma and including any
+ * dynastic components, precedes the first name(s) or initial(s).
*/
- readonly diffrn_id: Scalars['String'];
+ readonly rcsb_authors?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
/**
- * For experiments in which samples are provided in a
- * continuous stream, the total number of frames collected
- * in which a droplet was hit.
- *
+ * Normalized journal abbreviation.
+ *
* Examples:
- * 1200, 5750
+ * Nat Struct Mol Biol
+ *
*/
- readonly droplet_hits?: Maybe<Scalars['Int']>;
+ readonly rcsb_journal_abbrev?: Maybe<Scalars['String']>;
/**
- * For experiments in which samples are provided in a
- * continuous stream, the total number of data frames collected
- * in which the sample was hit.
- *
+ * The title of the citation; relevant for journal articles, books
+ * and book chapters.
+ *
* Examples:
- * 1200, 5750
+ * Structure of diferric duck ovotransferrin
+ * at 2.35 Angstroms resolution.
+ *
*/
- readonly frame_hits?: Maybe<Scalars['Int']>;
+ readonly title?: Maybe<Scalars['String']>;
/**
- * For experiments in which samples are provided in a
- * continuous stream, the total number of data frames collected
- * that contained a "hit" but failed to index.
- *
- * Examples:
- * 1200, 5750
+ * The year of the citation; relevant for journal articles, books
+ * and book chapters.
*/
- readonly frames_failed_index?: Maybe<Scalars['Int']>;
+ readonly year?: Maybe<Scalars['Int']>;
+};
+
+export type RcsbPubmedContainerIdentifiers = {
/**
- * For experiments in which samples are provided in a
- * continuous stream, the total number of data frames collected
- * that were indexed.
- *
+ * UID assigned to each PubMed record.
+ *
* Examples:
- * 1200, 5750
+ * null
+ *
*/
- readonly frames_indexed?: Maybe<Scalars['Int']>;
+ readonly pubmed_id?: Maybe<Scalars['Int']>;
+};
+
+export type RcsbPubmedMeshDescriptorsLineage = {
+ /** Hierarchy depth. */
+ readonly depth?: Maybe<Scalars['Int']>;
/**
- * The total number of data frames collected for this
- * data set.
- *
+ * Identifier for MeSH classification term.
+ *
* Examples:
- * 20, 100
+ * E01.370.225.500.388, H01.181
+ *
*/
- readonly frames_total?: Maybe<Scalars['Int']>;
+ readonly id?: Maybe<Scalars['String']>;
/**
- * For experiments in which samples are provided in a
- * continuous stream, the total number of lattices indexed.
- *
+ * MeSH classification term.
+ *
* Examples:
- * 1200, 5750
- */
- readonly lattices_indexed?: Maybe<Scalars['Int']>;
- /** For FEL experiments, the number of pulse events in the dataset. */
- readonly xfel_pulse_events?: Maybe<Scalars['Int']>;
- /**
- * For FEL experiments, in which data collection was performed
- * in batches, indicates which subset of the data collected
- * were used in producing this dataset.
+ * Chemistry, Mammals, Therapeutic Uses
+ *
*/
- readonly xfel_run_numbers?: Maybe<Scalars['String']>;
+ readonly name?: Maybe<Scalars['String']>;
};
-export type RcsbClusterFlexibility = {
- /** Average RMSD refer to average pairwise RMSD (Root Mean Square Deviation of C-alpha atoms) between structures in the cluster (95% sequence identity) where a given entity belongs. */
- readonly avg_rmsd?: Maybe<Scalars['Float']>;
- /** Structural flexibility in the cluster (95% sequence identity) where a given entity belongs. */
- readonly label?: Maybe<Scalars['String']>;
- /** Link to the associated PDBFlex database entry. */
- readonly link?: Maybe<Scalars['String']>;
- /** Maximal RMSD refer to maximal pairwise RMSD (Root Mean Square Deviation of C-alpha atoms) between structures in the cluster (95% sequence identity) where a given entity belongs. */
- readonly max_rmsd?: Maybe<Scalars['Float']>;
+export type RcsbRelatedTargetReferences = {
+ readonly aligned_target?: Maybe<ReadonlyArray<Maybe<RcsbRelatedTargetReferencesAlignedTarget>>>;
/**
+ * The related target data resource name.
+ *
* Allowable values:
- * PDBFlex
+ * ChEMBL, DrugBank, Pharos
+ *
*/
- readonly provenance_code?: Maybe<Scalars['String']>;
+ readonly related_resource_name?: Maybe<Scalars['String']>;
+ /**
+ * The version of the target data resource.
+ *
+ * Examples:
+ * 6.11.0
+ *
+ */
+ readonly related_resource_version?: Maybe<Scalars['String']>;
+ /** An identifier for the target sequence in the related data resource. */
+ readonly related_target_id?: Maybe<Scalars['String']>;
+ /**
+ * NCBI Taxonomy identifier for the target organism.
+ *
+ * Reference:
+ *
+ * Wheeler DL, Chappey C, Lash AE, Leipe DD, Madden TL, Schuler GD,
+ * Tatusova TA, Rapp BA (2000). Database resources of the National
+ * Center for Biotechnology Information. Nucleic Acids Res 2000 Jan
+ * 1;28(1):10-4
+ *
+ * Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Rapp BA,
+ * Wheeler DL (2000). GenBank. Nucleic Acids Res 2000 Jan 1;28(1):15-18.
+ */
+ readonly target_taxonomy_id?: Maybe<Scalars['Int']>;
};
-export type RcsbEntryInfoDiffrnResolutionHigh = {
+export type RcsbRelatedTargetReferencesAlignedTarget = {
+ /** The position of the monomer in the entity sequence at which the alignment begins. */
+ readonly entity_beg_seq_id?: Maybe<Scalars['Int']>;
+ /** The length of the alignment. */
+ readonly length?: Maybe<Scalars['Int']>;
+ /** The position of the monomer in the target sequence at which the alignment begins. */
+ readonly target_beg_seq_id?: Maybe<Scalars['Int']>;
+};
+
+export type RcsbRepositoryHoldingsCurrent = {
/**
- * The provenence source for the high resolution limit of data collection.
- *
+ * The list of content types associated with this entry.
+ *
* Allowable values:
- * Depositor assigned, From refinement resolution cutoff, From the high resolution shell
+ * 2fo-fc Map, Combined NMR data (NEF), Combined NMR data (NMR-STAR), FASTA sequence, Map Coefficients, NMR chemical shifts, NMR restraints V1, NMR restraints V2, assembly PDB, assembly mmCIF, entry PDB, entry PDB bundle, entry PDBML, entry mmCIF, fo-fc Map, structure factors, validation data mmCIF, validation report, validation slider image
+ *
*/
- readonly provenance_source?: Maybe<Scalars['String']>;
- /** The high resolution limit of data collection. */
- readonly value?: Maybe<Scalars['Float']>;
+ readonly repository_content_types?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
};
-export type RcsbNonpolymerEntityContainerIdentifiers = {
- /** Instance identifiers corresponding to copies of the entity in this container. */
- readonly asym_ids?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
- /** Author instance identifiers corresponding to copies of the entity in this container. */
- readonly auth_asym_ids?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
- /** Entity identifier for the container. */
- readonly entity_id: Scalars['String'];
- /** Entry identifier for the container. */
+export type RcsbRepositoryHoldingsCurrentEntryContainerIdentifiers = {
+ /** The assembly id codes. */
+ readonly assembly_ids?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
+ /**
+ * The PDB entry accession code.
+ *
+ * Examples:
+ * 1KIP
+ *
+ */
readonly entry_id: Scalars['String'];
- /** Non-polymer(ligand) chemical component identifier for the entity in this container. */
- readonly nonpolymer_comp_id?: Maybe<Scalars['String']>;
- /** The BIRD identifier for the entity in this container. */
- readonly prd_id?: Maybe<Scalars['String']>;
/**
- * A unique identifier for each object in this entity container formed by
- * an underscore separated concatenation of entry and entity identifiers.
+ * The RCSB entry identifier.
+ *
+ * Examples:
+ * 1KIP
+ *
*/
readonly rcsb_id?: Maybe<Scalars['String']>;
/**
- * Source of the reference database assignment
- *
+ * Identifier for the current data exchange status record.
+ *
+ * Examples:
+ * 2018_23
+ *
+ */
+ readonly update_id?: Maybe<Scalars['String']>;
+};
+
+export type RcsbSchemaContainerIdentifiers = {
+ /** Collection name associated with the data in the container. */
+ readonly collection_name: Scalars['String'];
+ /** Version string for the schema and collection. */
+ readonly collection_schema_version?: Maybe<Scalars['String']>;
+ /** Schema name associated with the data in the container. */
+ readonly schema_name: Scalars['String'];
+};
+
+export type RcsbStructSymmetry = {
+ /** Clusters describe grouping of 'identical' subunits. */
+ readonly clusters: ReadonlyArray<Maybe<RcsbStructSymmetryClusters>>;
+ /**
+ * The granularity at which the symmetry calculation is performed. In 'Global Symmetry' all polymeric subunits in assembly are used. In 'Local Symmetry' only a subset of polymeric subunits is considered. In 'Pseudo Symmetry' the threshold for subunits similarity is relaxed.
+ *
* Allowable values:
- * PDB, RCSB
+ * Global Symmetry, Pseudo Symmetry, Local Symmetry
+ *
*/
- readonly reference_chemical_identifiers_provenance_source?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
- /** Reference resource accession code */
- readonly reference_chemical_identifiers_resource_accession?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
+ readonly kind: Scalars['String'];
/**
- * Reference resource name
- *
+ * Oligomeric state refers to a composition of polymeric subunits in quaternary structure. Quaternary structure may be composed either exclusively of several copies of identical subunits, in which case they are termed homo-oligomers, or alternatively by at least one copy of different subunits (hetero-oligomers). Quaternary structure composed of a single subunit is denoted as 'Monomer'.
+ *
+ * Examples:
+ * Monomer, Homo 2-mer, Hetero 3-mer
+ *
+ */
+ readonly oligomeric_state: Scalars['String'];
+ /** The orientation of the principal rotation (symmetry) axis. */
+ readonly rotation_axes?: Maybe<ReadonlyArray<Maybe<RcsbStructSymmetryRotationAxes>>>;
+ /** Each type of different subunits is assigned a latter. The number of equivalent subunits is added as a coefficient after each letter (except 1 which is not added explicitly). */
+ readonly stoichiometry: ReadonlyArray<Maybe<Scalars['String']>>;
+ /**
+ * Symmetry symbol refers to point group or helical symmetry of identical polymeric subunits in Schönflies notation. Contains point group symbol (e.g., C2, C5, D2, T, O, I) or H for helical symmetry.
+ *
+ * Examples:
+ * C1, D3, H
+ *
+ */
+ readonly symbol: Scalars['String'];
+ /**
+ * Symmetry type refers to point group or helical symmetry of identical polymeric subunits. Contains point group types (e.g. Cyclic, Dihedral) or Helical for helical symmetry.
+ *
* Allowable values:
- * ChEBI, ChEMBL, DrugBank, PubChem
+ * Asymmetric, Cyclic, Dihedral, Tetrahedral, Octahedral, Icosahedral, Helical
+ *
*/
- readonly reference_chemical_identifiers_resource_name?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
+ readonly type: Scalars['String'];
};
-export type RcsbPolymerEntityNameSys = {
- /** The systematic name for the polymer entity. */
- readonly name: Scalars['String'];
+export type RcsbStructSymmetryClusters = {
+ /** Average RMSD between members of a given cluster. */
+ readonly avg_rmsd?: Maybe<Scalars['Float']>;
+ /** Subunits that belong to the cluster, identified by asym_id and optionally by assembly operator id(s). */
+ readonly members: ReadonlyArray<Maybe<ClustersMembers>>;
+};
+
+export type RcsbStructSymmetryLineage = {
+ /** Hierarchy depth. */
+ readonly depth?: Maybe<Scalars['Int']>;
/**
- * The system used to generate the systematic name of the polymer entity.
- *
+ * Automatically assigned ID to uniquely identify the symmetry term in the Protein Symmetry Browser.
+ *
* Examples:
- * Chemical Abstracts conventions
+ * Global Symmetry.Cyclic.C2.Homo 2-mer
+ *
*/
- readonly system?: Maybe<Scalars['String']>;
+ readonly id?: Maybe<Scalars['String']>;
+ /**
+ * A human-readable term describing protein symmetry.
+ *
+ * Examples:
+ * Asymmetric, Global Symmetry, C1, Hetero 3-mer
+ *
+ */
+ readonly name?: Maybe<Scalars['String']>;
};
-export type RcsbNonpolymerEntityKeywords = {
- /** Keywords describing this non-polymer entity. */
- readonly text?: Maybe<Scalars['String']>;
+export type RcsbStructSymmetryRotationAxes = {
+ /** coordinate */
+ readonly end: ReadonlyArray<Maybe<Scalars['Float']>>;
+ /** The number of times (order of rotation) that a subunit can be repeated by a rotation operation, being transformed into a new state indistinguishable from its starting state. */
+ readonly order?: Maybe<Scalars['Int']>;
+ /** coordinate */
+ readonly start: ReadonlyArray<Maybe<Scalars['Float']>>;
};
-export type PdbxAuditRevisionDetails = {
+export type RcsbTargetCofactors = {
/**
- * The type of file that the pdbx_audit_revision_history record refers to.
- *
+ * The value measured or determined by the assay.
+ *
+ * Examples:
+ * null
+ *
+ */
+ readonly binding_assay_value?: Maybe<Scalars['Float']>;
+ /**
+ * The type of measurement or value determined by the assay.
+ *
* Allowable values:
- * Chemical component, NMR restraints, NMR shifts, Structure factors, Structure model
+ * pAC50, pEC50, pIC50, pKd, pKi
+ *
*/
- readonly data_content_type: Scalars['String'];
- /** Additional details describing the revision. */
- readonly description?: Maybe<Scalars['String']>;
- /** Further details describing the revision. */
- readonly details?: Maybe<Scalars['String']>;
+ readonly binding_assay_value_type?: Maybe<Scalars['String']>;
/**
- * A unique identifier for the pdbx_audit_revision_details record.
- *
+ * Standard IUPAC International Chemical Identifier (InChI) descriptor key
+ * for the cofactor.
+ *
+ * InChI, the IUPAC International Chemical Identifier,
+ * by Stephen R Heller, Alan McNaught, Igor Pletnev, Stephen Stein and Dmitrii Tchekhovskoi,
+ * Journal of Cheminformatics, 2015, 7:23
+ *
* Examples:
- * 1
+ * BNOCDEBUFVJMQI-REOHCLBHSA-N
+ *
*/
- readonly ordinal: Scalars['Int'];
+ readonly cofactor_InChIKey?: Maybe<Scalars['String']>;
/**
- * The provider of the revision.
- *
- * Allowable values:
- * author, repository
+ * Simplified molecular-input line-entry system (SMILES) descriptor for the cofactor.
+ *
+ * Weininger D (February 1988). "SMILES, a chemical language and information system. 1.
+ * Introduction to methodology and encoding rules". Journal of Chemical Information and Modeling. 28 (1): 31-6.
+ *
+ * Weininger D, Weininger A, Weininger JL (May 1989).
+ * "SMILES. 2. Algorithm for generation of unique SMILES notation",
+ * Journal of Chemical Information and Modeling. 29 (2): 97-101.
+ *
+ * Examples:
+ * OC(=O)[CH](CF)O[P](O)(O)=O
+ *
*/
- readonly provider?: Maybe<Scalars['String']>;
+ readonly cofactor_SMILES?: Maybe<Scalars['String']>;
/**
- * A pointer to _pdbx_audit_revision_history.ordinal
- *
+ * The chemical component definition identifier for the cofactor.
+ *
* Examples:
- * 1
+ * 0Z3, CD9
+ *
*/
- readonly revision_ordinal: Scalars['Int'];
+ readonly cofactor_chem_comp_id?: Maybe<Scalars['String']>;
/**
- * A type classification of the revision
- *
- * Allowable values:
- * Coordinate replacement, Initial release, Obsolete, Remediation
+ * The cofactor description.
+ *
+ * Examples:
+ * A synthetic naphthoquinone without the isoprenoid side chain and biological activity,
+ * but can be converted to active vitamin K2, menaquinone, after alkylation in vivo.
+ *
*/
- readonly type?: Maybe<Scalars['String']>;
-};
-
-export type DrugbankTarget = {
- /** The type of target interaction. */
- readonly interaction_type?: Maybe<Scalars['String']>;
- /** The target name. */
- readonly name?: Maybe<Scalars['String']>;
+ readonly cofactor_description?: Maybe<Scalars['String']>;
/**
- * The value of _drugbank_target.ordinal distinguishes
- * related examples for each chemical component.
+ * The cofactor name.
+ *
+ * Examples:
+ * Menadione
+ *
*/
- readonly ordinal: Scalars['Int'];
- /** The organism common name. */
- readonly organism_common_name?: Maybe<Scalars['String']>;
+ readonly cofactor_name?: Maybe<Scalars['String']>;
/**
- * The reference identifier code for the target interaction reference.
- *
+ * The BIRD definition identifier for the cofactor.
+ *
* Examples:
- * Q9HD40
+ * PRD_000010
+ *
*/
- readonly reference_database_accession_code?: Maybe<Scalars['String']>;
+ readonly cofactor_prd_id?: Maybe<Scalars['String']>;
/**
- * The reference database name for the target interaction.
- *
- * Allowable values:
- * UniProt
+ * Identifier for the cofactor assigned by the resource.
+ *
+ * Examples:
+ * CHEMBL1987, DB00170
+ *
*/
- readonly reference_database_name?: Maybe<Scalars['String']>;
+ readonly cofactor_resource_id?: Maybe<Scalars['String']>;
/**
- * Target sequence expressed as string of one-letter amino acid codes.
- *
+ * Mechanism of action describes the biochemical interaction through which the
+ * cofactor produces a pharmacological effect.
+ *
* Examples:
- * MAKQRSG...
+ * Menadione (vitamin K3) is involved as a cofactor in the posttranslational gamma-carboxylation of glutamic acid residues of certain proteins i
+ * n the body. These proteins include the vitamin K-dependent coagulation factors II (prothrombin), VII (proconvertin), IX (Christmas factor), X (Stuart factor), protein
+ * C, protein S, protein Zv and a growth-arrest-specific factor (Gas6).
+ *
*/
- readonly seq_one_letter_code?: Maybe<Scalars['String']>;
- /** The actions of the target interaction. */
- readonly target_actions?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
-};
-
-export type Struct = {
+ readonly mechanism_of_action?: Maybe<Scalars['String']>;
/**
- * The item indicates whether the entry is a CASP target, a CASD-NMR target,
- * or similar target participating in methods development experiments.
- *
+ * A flag to indicate the cofactor is a structural neighbor of this
+ * entity.
+ *
* Allowable values:
* N, Y
+ *
*/
- readonly pdbx_CASP_flag?: Maybe<Scalars['String']>;
+ readonly neighbor_flag?: Maybe<Scalars['String']>;
+ /** Patent numbers reporting the pharmacology or activity data. */
+ readonly patent_nos?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
+ /** PubMed identifiers for literature supporting the pharmacology or activity data. */
+ readonly pubmed_ids?: Maybe<ReadonlyArray<Maybe<Scalars['Int']>>>;
/**
- * An automatically generated descriptor for an NDB structure or
- * the unstructured content of the PDB COMPND record.
- *
- * Examples:
- * 5'-D(*CP*GP*CP*(HYD)AP*AP*AP*TP*TP*TP*GP*CP*G)-3'
+ * Resource providing target and cofactor data.
+ *
+ * Allowable values:
+ * ChEMBL, DrugBank, Pharos
+ *
*/
- readonly pdbx_descriptor?: Maybe<Scalars['String']>;
+ readonly resource_name?: Maybe<Scalars['String']>;
/**
- * Text description of the methodology which produced this
- * model structure.
- *
+ * Version of the information distributed by the data resource.
+ *
* Examples:
- * This model was produced from a 10 nanosecond Amber/MD simulation
- * starting from PDB structure ID 1ABC.
+ * V4_0_2
+ *
*/
- readonly pdbx_model_details?: Maybe<Scalars['String']>;
+ readonly resource_version?: Maybe<Scalars['String']>;
/**
- * A description of the type of structure model.
- *
+ * Identifier for the target assigned by the resource.
+ *
* Examples:
- * MINIMIZED AVERAGE
+ * P00734, CHEMBL2242
+ *
*/
- readonly pdbx_model_type_details?: Maybe<Scalars['String']>;
+ readonly target_resource_id?: Maybe<Scalars['String']>;
+};
+
+export type RcsbTargetNeighbors = {
+ /** Alternate conformer identifier for the non-polymer entity instance. */
+ readonly alt_id?: Maybe<Scalars['String']>;
/**
- * A title for the data block. The author should attempt to convey
- * the essence of the structure archived in the CIF in the title,
- * and to distinguish this structural result from others.
- *
+ * The atom identifier for the non-polymer entity instance.
+ *
* Examples:
- * T4 lysozyme mutant - S32A, 5'-D(*(I)CP*CP*GP*G)-3, T4 lysozyme mutant - S32A, hen egg white lysozyme at -30 degrees C, quail egg white lysozyme at 2 atmospheres
+ * O1, N1, C1
+ *
*/
- readonly title?: Maybe<Scalars['String']>;
-};
-
-export type RcsbBranchedInstanceFeatureFeatureValue = {
- /** The chemical component identifier for the instance of the feature value. */
+ readonly atom_id?: Maybe<Scalars['String']>;
+ /** Component identifier for the non-polymer entity instance. */
readonly comp_id?: Maybe<Scalars['String']>;
- /** Specific details about the feature. */
- readonly details?: Maybe<Scalars['String']>;
- /** The reference value of the feature. */
- readonly reference?: Maybe<Scalars['Float']>;
- /** The reported value of the feature. */
- readonly reported?: Maybe<Scalars['Float']>;
- /** The estimated uncertainty of the reported feature value. */
- readonly uncertainty_estimate?: Maybe<Scalars['Float']>;
+ /** Distance value for this target interaction. */
+ readonly distance?: Maybe<Scalars['Float']>;
/**
- * The type of estimated uncertainty for the reported feature value.
- *
- * Allowable values:
- * Z-Score
+ * The entity instance identifier for the target of interaction.
+ *
+ * Examples:
+ * A, B
+ *
*/
- readonly uncertainty_estimate_type?: Maybe<Scalars['String']>;
-};
-
-export type RcsbNonpolymerStructConnConnectPartner = {
+ readonly target_asym_id?: Maybe<Scalars['String']>;
/**
- * A component of the identifier for the partner in the structure
- * connection.
- *
- * This data item is a pointer to _atom_site.label_alt_id in the
- * ATOM_SITE category.
+ * The atom identifier for the target of interaction.
+ *
+ * Examples:
+ * OG, OE1, CD1
+ *
*/
- readonly label_alt_id?: Maybe<Scalars['String']>;
+ readonly target_atom_id?: Maybe<Scalars['String']>;
+ /** The author residue index for the target of interaction. */
+ readonly target_auth_seq_id?: Maybe<Scalars['Int']>;
/**
- * A component of the identifier for the partner in the structure
- * connection.
- *
- * This data item is a pointer to _atom_site.label_asym_id in the
- * ATOM_SITE category.
+ * The chemical component identifier for the target of interaction.
+ *
+ * Examples:
+ * ASN, TRP, SER
+ *
*/
- readonly label_asym_id: Scalars['String'];
+ readonly target_comp_id?: Maybe<Scalars['String']>;
/**
- * A component of the identifier for the partner in the structure
- * connection.
- *
- * This data item is a pointer to _chem_comp_atom.atom_id in the
- * CHEM_COMP_ATOM category.
+ * The entity identifier for the target of interaction.
+ *
+ * Examples:
+ * 1, 2
+ *
*/
- readonly label_atom_id?: Maybe<Scalars['String']>;
+ readonly target_entity_id?: Maybe<Scalars['String']>;
/**
- * A component of the identifier for the partner in the structure
- * connection.
- *
- * This data item is a pointer to _atom_site.label_comp_id in the
- * ATOM_SITE category.
+ * A flag to indicate the nature of the target interaction is covalent or metal-coordination.
+ *
+ * Allowable values:
+ * N, Y
+ *
*/
- readonly label_comp_id: Scalars['String'];
+ readonly target_is_bound?: Maybe<Scalars['String']>;
+ /** Model identifier for the target of interaction. */
+ readonly target_model_id?: Maybe<Scalars['Int']>;
+ /** The sequence position for the target of interaction. */
+ readonly target_seq_id?: Maybe<Scalars['Int']>;
+};
+
+export type RcsbUniprotAlignments = {
+ /** List of alignments with core_entity canonical sequences */
+ readonly core_entity_alignments?: Maybe<ReadonlyArray<Maybe<RcsbUniprotAlignmentsCoreEntityAlignments>>>;
+};
+
+export type RcsbUniprotAlignmentsCoreEntityAlignments = {
+ /** Aligned region */
+ readonly aligned_regions?: Maybe<ReadonlyArray<Maybe<CoreEntityAlignmentsAlignedRegions>>>;
+ /** core_entity identifiers */
+ readonly core_entity_identifiers?: Maybe<CoreEntityAlignmentsCoreEntityIdentifiers>;
+ /** Alignment scores */
+ readonly scores?: Maybe<CoreEntityAlignmentsScores>;
+};
+
+export type RcsbUniprotAnnotation = {
+ /** An identifier for the annotation. */
+ readonly annotation_id?: Maybe<Scalars['String']>;
+ readonly annotation_lineage?: Maybe<ReadonlyArray<Maybe<RcsbUniprotAnnotationAnnotationLineage>>>;
+ /** Identifies the version of the annotation assignment. */
+ readonly assignment_version?: Maybe<Scalars['String']>;
+ /** A description for the annotation. */
+ readonly description?: Maybe<Scalars['String']>;
+ /** A name for the annotation. */
+ readonly name?: Maybe<Scalars['String']>;
/**
- * A component of the identifier for the partner in the structure
- * connection.
- *
- * This data item is a pointer to _atom_site.label_seq_id in the
- * ATOM_SITE category.
+ * Code identifying the individual, organization or program that
+ * assigned the annotation.
*/
- readonly label_seq_id?: Maybe<Scalars['Int']>;
+ readonly provenance_source?: Maybe<Scalars['String']>;
/**
- * Describes the symmetry operation that should be applied to the
- * atom set specified by _rcsb_nonpolymer_struct_conn.connect_partner_label* to generate the
- * partner in the structure connection.
- *
- * Examples:
- * 1_555, 7_645
+ * A type or category of the annotation.
+ *
+ * Allowable values:
+ * disease, phenotype
+ *
*/
- readonly symmetry?: Maybe<Scalars['String']>;
+ readonly type?: Maybe<Scalars['String']>;
};
-export type PdbxSerialCrystallographySampleDeliveryFixedTarget = {
- /** The number of crystals per dropplet or pore in fixed target */
- readonly crystals_per_unit?: Maybe<Scalars['Int']>;
- /** For a fixed target sample, a description of sample preparation */
+export type RcsbUniprotAnnotationAnnotationLineage = {
+ /** Members of the annotation lineage as parent lineage depth (1-N) */
+ readonly depth?: Maybe<Scalars['Int']>;
+ /** Members of the annotation lineage as parent class identifiers. */
+ readonly id?: Maybe<Scalars['String']>;
+ /** Members of the annotation lineage as parent class names. */
+ readonly name?: Maybe<Scalars['String']>;
+};
+
+export type RcsbUniprotContainerIdentifiers = {
+ readonly reference_sequence_identifiers?: Maybe<ReadonlyArray<Maybe<RcsbUniprotContainerIdentifiersReferenceSequenceIdentifiers>>>;
+ /** Primary accession number of a given UniProtKB entry. */
+ readonly uniprot_id?: Maybe<Scalars['String']>;
+};
+
+export type RcsbUniprotContainerIdentifiersReferenceSequenceIdentifiers = {
+ /** Reference database accession code */
+ readonly database_accession?: Maybe<Scalars['String']>;
+ /** Reference database identifier for the sequence isoform */
+ readonly database_isoform?: Maybe<Scalars['String']>;
+ /** Reference database name */
+ readonly database_name?: Maybe<Scalars['String']>;
+ /** Source of the reference database assignment */
+ readonly provenance_source?: Maybe<Scalars['String']>;
+};
+
+export type RcsbUniprotExternalReference = {
+ readonly provenance_source?: Maybe<Scalars['String']>;
+ readonly reference_id?: Maybe<Scalars['String']>;
+ /** Allowable values: IMPC, GTEX, PHAROS. */
+ readonly reference_name?: Maybe<Scalars['String']>;
+};
+
+export type RcsbUniprotFeature = {
+ /** Identifies the version of the feature assignment. */
+ readonly assignment_version?: Maybe<Scalars['String']>;
+ /** A description for the feature. */
readonly description?: Maybe<Scalars['String']>;
- /** Any details pertinent to the fixed sample target */
- readonly details?: Maybe<Scalars['String']>;
+ /** An identifier for the feature. */
+ readonly feature_id?: Maybe<Scalars['String']>;
+ readonly feature_positions?: Maybe<ReadonlyArray<Maybe<RcsbUniprotFeatureFeaturePositions>>>;
+ /** A name for the feature. */
+ readonly name?: Maybe<Scalars['String']>;
/**
- * The data item is a pointer to _diffrn.id in the DIFFRN
- * category.
- *
- * Examples:
- * 1
+ * Code identifying the individual, organization or program that
+ * assigned the feature.
*/
- readonly diffrn_id: Scalars['String'];
+ readonly provenance_source?: Maybe<Scalars['String']>;
+ /** Code residue coordinate system for the assigned feature. */
+ readonly reference_scheme?: Maybe<Scalars['String']>;
/**
- * Device used to control movement of the fixed sample
- *
- * Examples:
- * DMC-4080
+ * A type or category of the feature.
+ *
+ * Allowable values:
+ * ACTIVE_SITE, BINDING_SITE, CALCIUM_BINDING_REGION, CHAIN, COMPOSITIONALLY_BIASED_REGION, CROSS_LINK, DNA_BINDING_REGION, DOMAIN, GLYCOSYLATION_SITE, INITIATOR_METHIONINE, LIPID_MOIETY_BINDING_REGION, METAL_ION_BINDING_SITE, MODIFIED_RESIDUE, MUTAGENESIS_SITE, NON_CONSECUTIVE_RESIDUES, NON_TERMINAL_RESIDUE, NUCLEOTIDE_PHOSPHATE_BINDING_REGION, PEPTIDE, PROPEPTIDE, REGION_OF_INTEREST, REPEAT, NON_STANDARD_AMINO_ACID, SEQUENCE_CONFLICT, SEQUENCE_VARIANT, SHORT_SEQUENCE_MOTIF, SIGNAL_PEPTIDE, SITE, SPLICE_VARIANT, TOPOLOGICAL_DOMAIN, TRANSIT_PEPTIDE, TRANSMEMBRANE_REGION, UNSURE_RESIDUE, ZINC_FINGER_REGION, INTRAMEMBRANE_REGION
+ *
*/
- readonly motion_control?: Maybe<Scalars['String']>;
+ readonly type?: Maybe<Scalars['String']>;
+};
+
+export type RcsbUniprotFeatureFeaturePositions = {
+ /** An identifier for the monomer(s) corresponding to the feature assignment. */
+ readonly beg_comp_id?: Maybe<Scalars['String']>;
+ /** An identifier for the monomer at which this segment of the feature begins. */
+ readonly beg_seq_id: Scalars['Int'];
+ /** An identifier for the monomer at which this segment of the feature ends. */
+ readonly end_seq_id?: Maybe<Scalars['Int']>;
+ /** The value for the feature over this monomer segment. */
+ readonly value?: Maybe<Scalars['Float']>;
+};
+
+export type RcsbUniprotKeyword = {
/**
- * Method to prevent dehydration of sample
- *
+ * A unique keyword identifier.
+ *
* Examples:
- * seal, humidifed gas, flash freezing
+ * KW-0275, KW-0597
+ *
*/
- readonly sample_dehydration_prevention?: Maybe<Scalars['String']>;
+ readonly id?: Maybe<Scalars['String']>;
/**
- * For a fixed target sample, mechanism to hold sample in the beam
- *
+ * Human-readable keyword term.
+ *
* Examples:
- * mesh, loop, grid
- */
- readonly sample_holding?: Maybe<Scalars['String']>;
- /** The sample solution content and concentration */
- readonly sample_solvent?: Maybe<Scalars['String']>;
- /**
- * Size of pore in grid supporting sample. Diameter or length in micrometres,
- * e.g. pore diameter
+ * Lipid metabolism, Phosphoprotein, Fatty acid biosynthesis
+ *
*/
- readonly sample_unit_size?: Maybe<Scalars['Float']>;
+ readonly value?: Maybe<Scalars['String']>;
+};
+
+export type RcsbUniprotProtein = {
+ /** Enzyme Commission (EC) number(s). */
+ readonly ec?: Maybe<ReadonlyArray<Maybe<RcsbUniprotProteinEc>>>;
+ readonly function?: Maybe<RcsbUniprotProteinFunction>;
+ /** The name(s) of the gene(s) that code for the protein sequence(s) described in the entry. */
+ readonly gene?: Maybe<ReadonlyArray<Maybe<RcsbUniprotProteinGene>>>;
+ readonly name?: Maybe<RcsbUniprotProteinName>;
+ /** Protein sequence data for canonical protein sequence. */
+ readonly sequence?: Maybe<Scalars['String']>;
+ /** Taxonomy information on the organism that is the source of the protein sequence. */
+ readonly source_organism?: Maybe<RcsbUniprotProteinSourceOrganism>;
+};
+
+export type RcsbUniprotProteinEc = {
+ readonly number?: Maybe<Scalars['String']>;
+ /** Historical record of the data attribute. */
+ readonly provenance_code?: Maybe<Scalars['String']>;
+};
+
+export type RcsbUniprotProteinFunction = {
+ /** General function(s) of a protein. */
+ readonly details?: Maybe<Scalars['String']>;
+ /** Historical record of the data attribute. */
+ readonly provenance_code?: Maybe<Scalars['String']>;
+};
+
+export type RcsbUniprotProteinGene = {
+ readonly name?: Maybe<ReadonlyArray<Maybe<GeneName>>>;
+};
+
+export type RcsbUniprotProteinName = {
+ /** Historical record of the data attribute. */
+ readonly provenance_code: Scalars['String'];
/**
- * Type of base holding the support
- *
+ * Name that allows to unambiguously identify a protein.
+ *
* Examples:
- * goniometer
+ * Hemoglobin alpha
+ *
*/
- readonly support_base?: Maybe<Scalars['String']>;
- /** Velocity of sample horizontally relative to a perpendicular beam in millimetres/second */
- readonly velocity_horizontal?: Maybe<Scalars['Float']>;
- /** Velocity of sample vertically relative to a perpendicular beam in millimetres/second */
- readonly velocity_vertical?: Maybe<Scalars['Float']>;
+ readonly value: Scalars['String'];
};
-export type PdbxReferenceEntityPolyLink = {
- /**
- * The atom identifier/name in the first of the two components making
- * the linkage.
- */
- readonly atom_id_1?: Maybe<Scalars['String']>;
- /**
- * The atom identifier/name in the second of the two components making
- * the linkage.
- */
- readonly atom_id_2?: Maybe<Scalars['String']>;
+export type RcsbUniprotProteinSourceOrganism = {
+ /** Historical record of the data attribute. */
+ readonly provenance_code: Scalars['String'];
+ /** The scientific name of the organism in which a protein occurs. */
+ readonly scientific_name: Scalars['String'];
+ /** NCBI Taxonomy identifier for the organism in which a protein occurs. */
+ readonly taxonomy_id?: Maybe<Scalars['Int']>;
+};
+
+export type Refine = {
/**
- * The component identifier in the first of the two components making the
- * linkage.
- *
- * This data item is a pointer to _pdbx_reference_entity_poly_seq.mon_id
- * in the PDBX_REFERENCE_ENTITY_POLY_SEQ category.
+ * The maximum isotropic displacement parameter (B value)
+ * found in the coordinate set.
*/
- readonly comp_id_1?: Maybe<Scalars['String']>;
+ readonly B_iso_max?: Maybe<Scalars['Float']>;
/**
- * The component identifier in the second of the two components making the
- * linkage.
- *
- * This data item is a pointer to _pdbx_reference_entity_poly_seq.mon_id
- * in the PDBX_REFERENCE_ENTITY_POLY_SEQ category.
+ * The mean isotropic displacement parameter (B value)
+ * for the coordinate set.
*/
- readonly comp_id_2?: Maybe<Scalars['String']>;
- /** The entity component identifier entity containing the linkage. */
- readonly component_id: Scalars['Int'];
+ readonly B_iso_mean?: Maybe<Scalars['Float']>;
/**
- * For a polymer entity, the sequence number in the first of
- * the two components making the linkage.
- *
- * This data item is a pointer to _pdbx_reference_entity_poly_seq.num
- * in the PDBX_REFERENCE_ENTITY_POLY_SEQ category.
+ * The minimum isotropic displacement parameter (B value)
+ * found in the coordinate set.
*/
- readonly entity_seq_num_1?: Maybe<Scalars['Int']>;
+ readonly B_iso_min?: Maybe<Scalars['Float']>;
/**
- * For a polymer entity, the sequence number in the second of
- * the two components making the linkage.
- *
- * This data item is a pointer to _pdbx_reference_entity_poly_seq.num
- * in the PDBX_REFERENCE_ENTITY_POLY_SEQ category.
+ * The [1][1] element of the matrix that defines the overall
+ * anisotropic displacement model if one was refined for this
+ * structure.
*/
- readonly entity_seq_num_2?: Maybe<Scalars['Int']>;
+ readonly aniso_B_1_1?: Maybe<Scalars['Float']>;
/**
- * The value of _pdbx_reference_entity_poly_link.link_id uniquely identifies
- * a linkage within a polymer entity.
+ * The [1][2] element of the matrix that defines the overall
+ * anisotropic displacement model if one was refined for this
+ * structure.
*/
- readonly link_id: Scalars['Int'];
+ readonly aniso_B_1_2?: Maybe<Scalars['Float']>;
/**
- * The value of _pdbx_reference_entity_poly_link.prd_id is a reference
- * _pdbx_reference_entity_list.prd_id in the PDBX_REFERENCE_ENTITY_POLY category.
+ * The [1][3] element of the matrix that defines the overall
+ * anisotropic displacement model if one was refined for this
+ * structure.
*/
- readonly prd_id: Scalars['String'];
+ readonly aniso_B_1_3?: Maybe<Scalars['Float']>;
/**
- * The reference entity id of the polymer entity containing the linkage.
- *
- * This data item is a pointer to _pdbx_reference_entity_poly.ref_entity_id
- * in the PDBX_REFERENCE_ENTITY_POLY category.
+ * The [2][2] element of the matrix that defines the overall
+ * anisotropic displacement model if one was refined for this
+ * structure.
*/
- readonly ref_entity_id: Scalars['String'];
+ readonly aniso_B_2_2?: Maybe<Scalars['Float']>;
/**
- * The bond order target for the non-standard linkage.
- *
- * Allowable values:
- * arom, delo, doub, pi, poly, quad, sing, trip
+ * The [2][3] element of the matrix that defines the overall
+ * anisotropic displacement model if one was refined for this
+ * structure.
*/
- readonly value_order?: Maybe<Scalars['String']>;
-};
-
-export type RcsbStructSymmetryRotationAxes = {
- /** coordinate */
- readonly end: ReadonlyArray<Maybe<Scalars['Float']>>;
- /** The number of times (order of rotation) that a subunit can be repeated by a rotation operation, being transformed into a new state indistinguishable from its starting state. */
- readonly order?: Maybe<Scalars['Int']>;
- /** coordinate */
- readonly start: ReadonlyArray<Maybe<Scalars['Float']>>;
-};
-
-export type Em3dFitting = {
- /**
- * Any additional details regarding fitting of atomic coordinates into
- * the 3DEM volume, including data and considerations from other
- * methods used in computation of the model.
- *
- * Examples:
- * Initial local fitting was done using Chimera and then NMFF was used for flexible fitting.
+ readonly aniso_B_2_3?: Maybe<Scalars['Float']>;
+ /**
+ * The [3][3] element of the matrix that defines the overall
+ * anisotropic displacement model if one was refined for this
+ * structure.
*/
- readonly details?: Maybe<Scalars['String']>;
+ readonly aniso_B_3_3?: Maybe<Scalars['Float']>;
/**
- * The value of _em_3d_fitting.id must uniquely identify
- * a fitting procedure of atomic coordinates
- * into 3dem reconstructed map volume.
+ * The correlation coefficient between the observed and
+ * calculated structure factors for reflections included in
+ * the refinement.
+ *
+ * The correlation coefficient is scale-independent and gives
+ * an idea of the quality of the refined model.
+ *
+ * sum~i~(Fo~i~ Fc~i~ - <Fo><Fc>)
+ * R~corr~ = ------------------------------------------------------------
+ * SQRT{sum~i~(Fo~i~)^2^-<Fo>^2^} SQRT{sum~i~(Fc~i~)^2^-<Fc>^2^}
+ *
+ * Fo = observed structure factors
+ * Fc = calculated structure factors
+ * <> denotes average value
+ *
+ * summation is over reflections included in the refinement
*/
- readonly id: Scalars['String'];
+ readonly correlation_coeff_Fo_to_Fc?: Maybe<Scalars['Float']>;
/**
- * The method used to fit atomic coordinates
- * into the 3dem reconstructed map.
+ * The correlation coefficient between the observed and
+ * calculated structure factors for reflections not included
+ * in the refinement (free reflections).
+ *
+ * The correlation coefficient is scale-independent and gives
+ * an idea of the quality of the refined model.
+ *
+ * sum~i~(Fo~i~ Fc~i~ - <Fo><Fc>)
+ * R~corr~ = ------------------------------------------------------------
+ * SQRT{sum~i~(Fo~i~)^2^-<Fo>^2^} SQRT{sum~i~(Fc~i~)^2^-<Fc>^2^}
+ *
+ * Fo = observed structure factors
+ * Fc = calculated structure factors
+ * <> denotes average value
+ *
+ * summation is over reflections not included
+ * in the refinement (free reflections)
*/
- readonly method?: Maybe<Scalars['String']>;
+ readonly correlation_coeff_Fo_to_Fc_free?: Maybe<Scalars['Float']>;
/**
- * The overall B (temperature factor) value for the 3d-em volume.
- *
+ * Description of special aspects of the refinement process.
+ *
* Examples:
- * 200
+ * HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
+ *
*/
- readonly overall_b_value?: Maybe<Scalars['Float']>;
+ readonly details?: Maybe<Scalars['String']>;
/**
- * The refinement protocol used.
- *
- * Allowable values:
- * AB INITIO MODEL, BACKBONE TRACE, FLEXIBLE FIT, OTHER, RIGID BODY FIT
+ * Residual factor R for reflections that satisfy the resolution
+ * limits established by _refine.ls_d_res_high and
+ * _refine.ls_d_res_low and the observation limit established by
+ * _reflns.observed_criterion, and that were used as the test
+ * reflections (i.e. were excluded from the refinement) when the
+ * refinement included the calculation of a 'free' R factor.
+ * Details of how reflections were assigned to the working and
+ * test sets are given in _reflns.R_free_details.
+ *
+ * sum|F~obs~ - F~calc~|
+ * R = ---------------------
+ * sum|F~obs~|
+ *
+ * F~obs~ = the observed structure-factor amplitudes
+ * F~calc~ = the calculated structure-factor amplitudes
+ *
+ * sum is taken over the specified reflections
*/
- readonly ref_protocol?: Maybe<Scalars['String']>;
+ readonly ls_R_factor_R_free?: Maybe<Scalars['Float']>;
/**
- * A flag to indicate whether fitting was carried out in real
- * or reciprocal refinement space.
- *
- * Allowable values:
- * REAL, RECIPROCAL
+ * The estimated error in _refine.ls_R_factor_R_free.
+ * The method used to estimate the error is described in the
+ * item _refine.ls_R_factor_R_free_error_details.
*/
- readonly ref_space?: Maybe<Scalars['String']>;
+ readonly ls_R_factor_R_free_error?: Maybe<Scalars['Float']>;
/**
- * The measure used to assess quality of fit of the atomic coordinates in the
- * 3DEM map volume.
- *
- * Examples:
- * Cross-correlation coefficient
+ * Special aspects of the method used to estimated the error in
+ * _refine.ls_R_factor_R_free.
*/
- readonly target_criteria?: Maybe<Scalars['String']>;
-};
-
-export type RcsbNonpolymerEntity = {
- /** A description of special aspects of the entity. */
- readonly details?: Maybe<Scalars['String']>;
- /** Formula mass (KDa) of the entity. */
- readonly formula_weight?: Maybe<Scalars['Float']>;
- /** A description of the nonpolymer entity. */
- readonly pdbx_description?: Maybe<Scalars['String']>;
+ readonly ls_R_factor_R_free_error_details?: Maybe<Scalars['String']>;
/**
- * The number of molecules of the nonpolymer entity in the entry.
- *
- * Examples:
- * 1, 2, 3
+ * Residual factor R for reflections that satisfy the resolution
+ * limits established by _refine.ls_d_res_high and
+ * _refine.ls_d_res_low and the observation limit established by
+ * _reflns.observed_criterion, and that were used as the working
+ * reflections (i.e. were included in the refinement) when the
+ * refinement included the calculation of a 'free' R factor.
+ * Details of how reflections were assigned to the working and
+ * test sets are given in _reflns.R_free_details.
+ *
+ * _refine.ls_R_factor_obs should not be confused with
+ * _refine.ls_R_factor_R_work; the former reports the results of a
+ * refinement in which all observed reflections were used, the
+ * latter a refinement in which a subset of the observed
+ * reflections were excluded from refinement for the calculation
+ * of a 'free' R factor. However, it would be meaningful to quote
+ * both values if a 'free' R factor were calculated for most of
+ * the refinement, but all of the observed reflections were used
+ * in the final rounds of refinement; such a protocol should be
+ * explained in _refine.details.
+ *
+ * sum|F~obs~ - F~calc~|
+ * R = ---------------------
+ * sum|F~obs~|
+ *
+ * F~obs~ = the observed structure-factor amplitudes
+ * F~calc~ = the calculated structure-factor amplitudes
+ *
+ * sum is taken over the specified reflections
*/
- readonly pdbx_number_of_molecules?: Maybe<Scalars['Int']>;
-};
-
-export type RcsbBranchedEntityInstanceContainerIdentifiers = {
- /** Instance identifier for this container. */
- readonly asym_id: Scalars['String'];
- /** Author instance identifier for this container. */
- readonly auth_asym_id?: Maybe<Scalars['String']>;
- /** Entity identifier for the container. */
- readonly entity_id?: Maybe<Scalars['String']>;
- /** Entry identifier for the container. */
- readonly entry_id: Scalars['String'];
+ readonly ls_R_factor_R_work?: Maybe<Scalars['Float']>;
/**
- * A unique identifier for each object in this entity instance container formed by
- * an 'dot' (.) separated concatenation of entry and entity instance identifiers.
+ * Residual factor R for all reflections that satisfy the resolution
+ * limits established by _refine.ls_d_res_high and
+ * _refine.ls_d_res_low.
+ *
+ * sum|F~obs~ - F~calc~|
+ * R = ---------------------
+ * sum|F~obs~|
+ *
+ * F~obs~ = the observed structure-factor amplitudes
+ * F~calc~ = the calculated structure-factor amplitudes
+ *
+ * sum is taken over the specified reflections
*/
- readonly rcsb_id?: Maybe<Scalars['String']>;
-};
-
-export type EntitySrcGen = {
+ readonly ls_R_factor_all?: Maybe<Scalars['Float']>;
/**
- * A unique identifier for the expression system. This
- * should be extracted from a local list of expression
- * systems.
+ * Residual factor R for reflections that satisfy the resolution
+ * limits established by _refine.ls_d_res_high and
+ * _refine.ls_d_res_low and the observation limit established by
+ * _reflns.observed_criterion.
+ *
+ * _refine.ls_R_factor_obs should not be confused with
+ * _refine.ls_R_factor_R_work; the former reports the results of a
+ * refinement in which all observed reflections were used, the
+ * latter a refinement in which a subset of the observed
+ * reflections were excluded from refinement for the calculation
+ * of a 'free' R factor. However, it would be meaningful to quote
+ * both values if a 'free' R factor were calculated for most of
+ * the refinement, but all of the observed reflections were used
+ * in the final rounds of refinement; such a protocol should be
+ * explained in _refine.details.
+ *
+ * sum|F~obs~ - F~calc~|
+ * R = ---------------------
+ * sum|F~obs~|
+ *
+ * F~obs~ = the observed structure-factor amplitudes
+ * F~calc~ = the calculated structure-factor amplitudes
+ *
+ * sum is taken over the specified reflections
*/
- readonly expression_system_id?: Maybe<Scalars['String']>;
+ readonly ls_R_factor_obs?: Maybe<Scalars['Float']>;
/**
- * The common name of the natural organism from which the gene was
- * obtained.
- *
- * Examples:
- * man, yeast, bacteria
+ * The smallest value for the interplanar spacings for the
+ * reflection data used in the refinement in angstroms. This is
+ * called the highest resolution.
*/
- readonly gene_src_common_name?: Maybe<Scalars['String']>;
+ readonly ls_d_res_high?: Maybe<Scalars['Float']>;
/**
- * A description of special aspects of the natural organism from
- * which the gene was obtained.
+ * The largest value for the interplanar spacings for
+ * the reflection data used in the refinement in angstroms.
+ * This is called the lowest resolution.
*/
- readonly gene_src_details?: Maybe<Scalars['String']>;
+ readonly ls_d_res_low?: Maybe<Scalars['Float']>;
/**
- * The genus of the natural organism from which the gene was
- * obtained.
- *
- * Examples:
- * Homo, Saccharomyces, Escherichia
+ * Type of matrix used to accumulate the least-squares derivatives.
+ *
+ * Allowable values:
+ * atomblock, diagonal, full, fullcycle, sparse, userblock
+ *
*/
- readonly gene_src_genus?: Maybe<Scalars['String']>;
+ readonly ls_matrix_type?: Maybe<Scalars['String']>;
/**
- * The species of the natural organism from which the gene was
- * obtained.
- *
- * Examples:
- * sapiens, cerevisiae, coli
+ * The number of parameters refined in the least-squares process.
+ * If possible, this number should include some contribution from
+ * the restrained parameters. The restrained parameters are
+ * distinct from the constrained parameters (where one or more
+ * parameters are linearly dependent on the refined value of
+ * another). Least-squares restraints often depend on geometry or
+ * energy considerations and this makes their direct contribution
+ * to this number, and to the goodness-of-fit calculation,
+ * difficult to assess.
*/
- readonly gene_src_species?: Maybe<Scalars['String']>;
+ readonly ls_number_parameters?: Maybe<Scalars['Int']>;
/**
- * The strain of the natural organism from which the gene was
- * obtained, if relevant.
- *
- * Examples:
- * DH5a, BMH 71-18
+ * The number of reflections that satisfy the resolution limits
+ * established by _refine.ls_d_res_high and _refine.ls_d_res_low
+ * and the observation limit established by
+ * _reflns.observed_criterion, and that were used as the test
+ * reflections (i.e. were excluded from the refinement) when the
+ * refinement included the calculation of a 'free' R factor.
+ * Details of how reflections were assigned to the working and
+ * test sets are given in _reflns.R_free_details.
*/
- readonly gene_src_strain?: Maybe<Scalars['String']>;
+ readonly ls_number_reflns_R_free?: Maybe<Scalars['Int']>;
/**
- * The tissue of the natural organism from which the gene was
- * obtained.
- *
- * Examples:
- * heart, liver, eye lens
+ * The number of reflections that satisfy the resolution limits
+ * established by _refine.ls_d_res_high and _refine.ls_d_res_low
+ * and the observation limit established by
+ * _reflns.observed_criterion, and that were used as the working
+ * reflections (i.e. were included in the refinement) when the
+ * refinement included the calculation of a 'free' R factor.
+ * Details of how reflections were assigned to the working and
+ * test sets are given in _reflns.R_free_details.
*/
- readonly gene_src_tissue?: Maybe<Scalars['String']>;
+ readonly ls_number_reflns_R_work?: Maybe<Scalars['Int']>;
/**
- * The subcellular fraction of the tissue of the natural organism
- * from which the gene was obtained.
- *
- * Examples:
- * mitochondria, nucleus, membrane
+ * The number of reflections that satisfy the resolution limits
+ * established by _refine.ls_d_res_high and _refine.ls_d_res_low.
*/
- readonly gene_src_tissue_fraction?: Maybe<Scalars['String']>;
+ readonly ls_number_reflns_all?: Maybe<Scalars['Int']>;
/**
- * The common name of the organism that served as host for the
- * production of the entity. Where full details of the protein
- * production are available it would be expected that this item
- * be derived from _entity_src_gen_express.host_org_common_name
- * or via _entity_src_gen_express.host_org_tax_id
- *
- * Examples:
- * yeast, bacteria
+ * The number of reflections that satisfy the resolution limits
+ * established by _refine.ls_d_res_high and _refine.ls_d_res_low
+ * and the observation limit established by
+ * _reflns.observed_criterion.
*/
- readonly host_org_common_name?: Maybe<Scalars['String']>;
+ readonly ls_number_reflns_obs?: Maybe<Scalars['Int']>;
/**
- * A description of special aspects of the organism that served as
- * host for the production of the entity. Where full details of
- * the protein production are available it would be expected that
- * this item would derived from _entity_src_gen_express.host_org_details
+ * The number of restrained parameters. These are parameters which
+ * are not directly dependent on another refined parameter.
+ * Restrained parameters often involve geometry or energy
+ * dependencies.
+ * See also _atom_site.constraints and _atom_site.refinement_flags.
+ * A general description of refinement constraints may appear in
+ * _refine.details.
*/
- readonly host_org_details?: Maybe<Scalars['String']>;
+ readonly ls_number_restraints?: Maybe<Scalars['Int']>;
/**
- * The genus of the organism that served as host for the production
- * of the entity.
- *
- * Examples:
- * Saccharomyces, Escherichia
+ * The number of reflections that satisfy the resolution limits
+ * established by _refine.ls_d_res_high and _refine.ls_d_res_low
+ * and the observation limit established by
+ * _reflns.observed_criterion, and that were used as the test
+ * reflections (i.e. were excluded from the refinement) when the
+ * refinement included the calculation of a 'free' R factor,
+ * expressed as a percentage of the number of geometrically
+ * observable reflections that satisfy the resolution limits.
*/
- readonly host_org_genus?: Maybe<Scalars['String']>;
+ readonly ls_percent_reflns_R_free?: Maybe<Scalars['Float']>;
/**
- * The species of the organism that served as host for the
- * production of the entity.
- *
- * Examples:
- * cerevisiae, coli
+ * The number of reflections that satisfy the resolution limits
+ * established by _refine.ls_d_res_high and _refine.ls_d_res_low
+ * and the observation limit established by
+ * _reflns.observed_criterion, expressed as a percentage of the
+ * number of geometrically observable reflections that satisfy
+ * the resolution limits.
*/
- readonly host_org_species?: Maybe<Scalars['String']>;
+ readonly ls_percent_reflns_obs?: Maybe<Scalars['Float']>;
/**
- * This data item identifies cases in which an alternative source
- * modeled.
- *
- * Allowable values:
- * model, sample
+ * The ratio of the total number of observations of the
+ * reflections that satisfy the resolution limits established by
+ * _refine.ls_d_res_high and _refine.ls_d_res_low to the number
+ * of crystallographically unique reflections that satisfy the
+ * same limits.
*/
- readonly pdbx_alt_source_flag?: Maybe<Scalars['String']>;
+ readonly ls_redundancy_reflns_all?: Maybe<Scalars['Float']>;
/**
- * The beginning polymer sequence position for the polymer section corresponding
- * to this source.
- *
- * A reference to the sequence position in the entity_poly category.
+ * The ratio of the total number of observations of the
+ * reflections that satisfy the resolution limits established by
+ * _refine.ls_d_res_high and _refine.ls_d_res_low and the
+ * observation limit established by _reflns.observed_criterion to
+ * the number of crystallographically unique reflections that
+ * satisfy the same limits.
*/
- readonly pdbx_beg_seq_num?: Maybe<Scalars['Int']>;
- /** Information on the source which is not given elsewhere. */
- readonly pdbx_description?: Maybe<Scalars['String']>;
+ readonly ls_redundancy_reflns_obs?: Maybe<Scalars['Float']>;
/**
- * The ending polymer sequence position for the polymer section corresponding
- * to this source.
- *
- * A reference to the sequence position in the entity_poly category.
+ * Weighted residual factor wR for reflections that satisfy the
+ * resolution limits established by _refine.ls_d_res_high and
+ * _refine.ls_d_res_low and the observation limit established by
+ * _reflns.observed_criterion, and that were used as the test
+ * reflections (i.e. were excluded from the refinement) when the
+ * refinement included the calculation of a 'free' R factor.
+ * Details of how reflections were assigned to the working and
+ * test sets are given in _reflns.R_free_details.
+ *
+ * ( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^
+ * wR = ( ---------------------------- )
+ * ( sum|w Y~obs~^2^| )
+ *
+ * Y~obs~ = the observed amplitude specified by
+ * _refine.ls_structure_factor_coef
+ * Y~calc~ = the calculated amplitude specified by
+ * _refine.ls_structure_factor_coef
+ * w = the least-squares weight
+ *
+ * sum is taken over the specified reflections
*/
- readonly pdbx_end_seq_num?: Maybe<Scalars['Int']>;
+ readonly ls_wR_factor_R_free?: Maybe<Scalars['Float']>;
/**
- * American Type Culture Collection tissue culture number.
- *
- * Examples:
- * 6051
+ * Weighted residual factor wR for reflections that satisfy the
+ * resolution limits established by _refine.ls_d_res_high and
+ * _refine.ls_d_res_low and the observation limit established by
+ * _reflns.observed_criterion, and that were used as the working
+ * reflections (i.e. were included in the refinement) when the
+ * refinement included the calculation of a 'free' R factor.
+ * Details of how reflections were assigned to the working and
+ * test sets are given in _reflns.R_free_details.
+ *
+ * ( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^
+ * wR = ( ---------------------------- )
+ * ( sum|w Y~obs~^2^| )
+ *
+ * Y~obs~ = the observed amplitude specified by
+ * _refine.ls_structure_factor_coef
+ * Y~calc~ = the calculated amplitude specified by
+ * _refine.ls_structure_factor_coef
+ * w = the least-squares weight
+ *
+ * sum is taken over the specified reflections
*/
- readonly pdbx_gene_src_atcc?: Maybe<Scalars['String']>;
+ readonly ls_wR_factor_R_work?: Maybe<Scalars['Float']>;
+ /** The maximum value for occupancy found in the coordinate set. */
+ readonly occupancy_max?: Maybe<Scalars['Float']>;
+ /** The minimum value for occupancy found in the coordinate set. */
+ readonly occupancy_min?: Maybe<Scalars['Float']>;
/**
- * Cell type.
- *
- * Examples:
- * ENDOTHELIAL
+ * Average figure of merit of phases of reflections not included
+ * in the refinement.
+ *
+ * This value is derived from the likelihood function.
+ *
+ * FOM = I~1~(X)/I~0~(X)
+ *
+ * I~0~, I~1~ = zero- and first-order modified Bessel functions
+ * of the first kind
+ * X = sigma~A~ |E~o~| |E~c~|/SIGMA
+ * E~o~, E~c~ = normalized observed and calculated structure
+ * factors
+ * sigma~A~ = <cos 2 pi s delta~x~> SQRT(Sigma~P~/Sigma~N~)
+ * estimated using maximum likelihood
+ * Sigma~P~ = sum~{atoms in model}~ f^2^
+ * Sigma~N~ = sum~{atoms in crystal}~ f^2^
+ * f = form factor of atoms
+ * delta~x~ = expected error
+ * SIGMA = (sigma~{E;exp}~)^2^ + epsilon [1-(sigma~A~)^2^]
+ * sigma~{E;exp}~ = uncertainties of normalized observed
+ * structure factors
+ * epsilon = multiplicity of the diffracting plane
+ *
+ * Ref: Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997).
+ * Acta Cryst. D53, 240-255.
*/
- readonly pdbx_gene_src_cell?: Maybe<Scalars['String']>;
+ readonly overall_FOM_free_R_set?: Maybe<Scalars['Float']>;
/**
- * The specific line of cells.
- *
- * Examples:
- * HELA CELLS
+ * Average figure of merit of phases of reflections included in
+ * the refinement.
+ *
+ * This value is derived from the likelihood function.
+ *
+ * FOM = I~1~(X)/I~0~(X)
+ *
+ * I~0~, I~1~ = zero- and first-order modified Bessel functions
+ * of the first kind
+ * X = sigma~A~ |E~o~| |E~c~|/SIGMA
+ * E~o~, E~c~ = normalized observed and calculated structure
+ * factors
+ * sigma~A~ = <cos 2 pi s delta~x~> SQRT(Sigma~P~/Sigma~N~)
+ * estimated using maximum likelihood
+ * Sigma~P~ = sum~{atoms in model}~ f^2^
+ * Sigma~N~ = sum~{atoms in crystal}~ f^2^
+ * f = form factor of atoms
+ * delta~x~ = expected error
+ * SIGMA = (sigma~{E;exp}~)^2^ + epsilon [1-(sigma~A~)^2^]
+ * sigma~{E;exp}~ = uncertainties of normalized observed
+ * structure factors
+ * epsilon = multiplicity of the diffracting plane
+ *
+ * Ref: Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997).
+ * Acta Cryst. D53, 240-255.
*/
- readonly pdbx_gene_src_cell_line?: Maybe<Scalars['String']>;
+ readonly overall_FOM_work_R_set?: Maybe<Scalars['Float']>;
/**
- * Identifies the location inside (or outside) the cell.
- *
- * Examples:
- * CYTOPLASM, NUCLEUS
+ * The overall standard uncertainty (estimated standard deviation)
+ * of the displacement parameters based on a maximum-likelihood
+ * residual.
+ *
+ * The overall standard uncertainty (sigma~B~)^2^ gives an idea
+ * of the uncertainty in the B values of averagely defined
+ * atoms (atoms with B values equal to the average B value).
+ *
+ * N~a~
+ * (sigma~B~)^2^ = 8 ----------------------------------------------
+ * sum~i~ {[1/Sigma - (E~o~)^2^ (1-m^2^)](SUM_AS)s^4^}
+ *
+ * N~a~ = number of atoms
+ * E~o~ = normalized structure factors
+ * m = figure of merit of phases of reflections
+ * included in the summation
+ * s = reciprocal-space vector
+ *
+ * SUM_AS = (sigma~A~)^2^/Sigma^2^
+ * Sigma = (sigma~{E;exp}~)^2^ + epsilon [1-(sigma~A~)^2^]
+ * sigma~{E;exp}~ = experimental uncertainties of normalized
+ * structure factors
+ * sigma~A~ = <cos 2 pi s delta~x~> SQRT(Sigma~P~/Sigma~N~)
+ * estimated using maximum likelihood
+ * Sigma~P~ = sum~{atoms in model}~ f^2^
+ * Sigma~N~ = sum~{atoms in crystal}~ f^2^
+ * f = atom form factor
+ * delta~x~ = expected error
+ * epsilon = multiplicity of diffracting plane
+ *
+ * summation is over all reflections included in refinement
+ *
+ * Ref: (sigma~A~ estimation) "Refinement of macromolecular
+ * structures by the maximum-likelihood method",
+ * Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997).
+ * Acta Cryst. D53, 240-255.
+ *
+ * (SU B estimation) Murshudov, G. N. & Dodson,
+ * E. J. (1997). Simplified error estimation a la
+ * Cruickshank in macromolecular crystallography.
+ * CCP4 Newsletter on Protein Crystallography, No. 33,
+ * January 1997, pp. 31-39.
+ *
+ * http://www.ccp4.ac.uk/newsletters/newsletter33/murshudov.html
*/
- readonly pdbx_gene_src_cellular_location?: Maybe<Scalars['String']>;
+ readonly overall_SU_B?: Maybe<Scalars['Float']>;
/**
- * A domain or fragment of the molecule.
- *
- * Examples:
- * CYTOPLASM, NUCLEUS
+ * The overall standard uncertainty (estimated standard deviation)
+ * of the positional parameters based on a maximum likelihood
+ * residual.
+ *
+ * The overall standard uncertainty (sigma~X~)^2^ gives an
+ * idea of the uncertainty in the position of averagely
+ * defined atoms (atoms with B values equal to average B value)
+ *
+ * 3 N~a~
+ * (sigma~X~)^2^ = ---------------------------------------------------------
+ * 8 pi^2^ sum~i~ {[1/Sigma - (E~o~)^2^ (1-m^2^)](SUM_AS)s^2^}
+ *
+ * N~a~ = number of atoms
+ * E~o~ = normalized structure factors
+ * m = figure of merit of phases of reflections
+ * included in the summation
+ * s = reciprocal-space vector
+ *
+ * SUM_AS = (sigma~A~)^2^/Sigma^2^
+ * Sigma = (sigma~{E;exp}~)^2^ + epsilon [1-(sigma~A~)^2^]
+ * sigma~{E;exp}~ = experimental uncertainties of normalized
+ * structure factors
+ * sigma~A~ = <cos 2 pi s delta~x~> SQRT(Sigma~P~/Sigma~N~)
+ * estimated using maximum likelihood
+ * Sigma~P~ = sum~{atoms in model}~ f^2^
+ * Sigma~N~ = sum~{atoms in crystal}~ f^2^
+ * f = atom form factor
+ * delta~x~ = expected error
+ * epsilon = multiplicity of diffracting plane
+ *
+ * summation is over all reflections included in refinement
+ *
+ * Ref: (sigma_A estimation) "Refinement of macromolecular
+ * structures by the maximum-likelihood method",
+ * Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997).
+ * Acta Cryst. D53, 240-255.
+ *
+ * (SU ML estimation) Murshudov, G. N. & Dodson,
+ * E. J. (1997). Simplified error estimation a la
+ * Cruickshank in macromolecular crystallography.
+ * CCP4 Newsletter on Protein Crystallography, No. 33,
+ * January 1997, pp. 31-39.
+ *
+ * http://www.ccp4.ac.uk/newsletters/newsletter33/murshudov.html
*/
- readonly pdbx_gene_src_fragment?: Maybe<Scalars['String']>;
- /** Identifies the gene. */
- readonly pdbx_gene_src_gene?: Maybe<Scalars['String']>;
+ readonly overall_SU_ML?: Maybe<Scalars['Float']>;
/**
- * NCBI Taxonomy identifier for the gene source organism.
- *
- * Reference:
- *
- * Wheeler DL, Chappey C, Lash AE, Leipe DD, Madden TL, Schuler GD,
- * Tatusova TA, Rapp BA (2000). Database resources of the National
- * Center for Biotechnology Information. Nucleic Acids Res 2000 Jan
- * 1;28(1):10-4
- *
- * Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Rapp BA,
- * Wheeler DL (2000). GenBank. Nucleic Acids Res 2000 Jan 1;28(1):15-18.
+ * The overall standard uncertainty (estimated standard deviation)
+ * of the displacement parameters based on the crystallographic
+ * R value, expressed in a formalism known as the dispersion
+ * precision indicator (DPI).
+ *
+ * The overall standard uncertainty (sigma~B~) gives an idea
+ * of the uncertainty in the B values of averagely defined
+ * atoms (atoms with B values equal to the average B value).
+ *
+ * N~a~
+ * (sigma~B~)^2^ = 0.65 ---------- (R~value~)^2^ (D~min~)^2^ C^-2/3^
+ * (N~o~-N~p~)
+ *
+ *
+ * N~a~ = number of atoms included in refinement
+ * N~o~ = number of observations
+ * N~p~ = number of parameters refined
+ * R~value~ = conventional crystallographic R value
+ * D~min~ = maximum resolution
+ * C = completeness of data
+ *
+ * Ref: Cruickshank, D. W. J. (1999). Acta Cryst. D55, 583-601.
+ *
+ * Murshudov, G. N. & Dodson,
+ * E. J. (1997). Simplified error estimation a la
+ * Cruickshank in macromolecular crystallography.
+ * CCP4 Newsletter on Protein Crystallography, No. 33,
+ * January 1997, pp. 31-39.
+ *
+ * http://www.ccp4.ac.uk/newsletters/newsletter33/murshudov.html
*/
- readonly pdbx_gene_src_ncbi_taxonomy_id?: Maybe<Scalars['String']>;
+ readonly overall_SU_R_Cruickshank_DPI?: Maybe<Scalars['Float']>;
/**
- * Organized group of tissues that carries on a specialized function.
- *
- * Examples:
- * KIDNEY, LIVER, PANCREAS
+ * The overall standard uncertainty (estimated standard deviation)
+ * of the displacement parameters based on the free R value.
+ *
+ * The overall standard uncertainty (sigma~B~) gives an idea
+ * of the uncertainty in the B values of averagely defined
+ * atoms (atoms with B values equal to the average B value).
+ *
+ * N~a~
+ * (sigma~B~)^2^ = 0.65 ---------- (R~free~)^2^ (D~min~)^2^ C^-2/3^
+ * (N~o~-N~p~)
+ *
+ *
+ * N~a~ = number of atoms included in refinement
+ * N~o~ = number of observations
+ * N~p~ = number of parameters refined
+ * R~free~ = conventional free crystallographic R value calculated
+ * using reflections not included in refinement
+ * D~min~ = maximum resolution
+ * C = completeness of data
+ *
+ * Ref: Cruickshank, D. W. J. (1999). Acta Cryst. D55, 583-601.
+ *
+ * Murshudov, G. N. & Dodson,
+ * E. J. (1997). Simplified error estimation a la
+ * Cruickshank in macromolecular crystallography.
+ * CCP4 Newsletter on Protein Crystallography, No. 33,
+ * January 1997, pp. 31-39.
+ *
+ * http://www.ccp4.ac.uk/newsletters/newsletter33/murshudov.html
*/
- readonly pdbx_gene_src_organ?: Maybe<Scalars['String']>;
+ readonly overall_SU_R_free?: Maybe<Scalars['Float']>;
/**
- * Organized structure within cell.
- *
+ * Details of the manner in which the cross validation
+ * reflections were selected.
+ *
* Examples:
- * MITOCHONDRIA
+ * Random selection
+ *
*/
- readonly pdbx_gene_src_organelle?: Maybe<Scalars['String']>;
+ readonly pdbx_R_Free_selection_details?: Maybe<Scalars['String']>;
/**
- * Scientific name of the organism.
- *
- * Examples:
- * Homo sapiens, ESCHERICHIA COLI
- * HOMO SAPIENS
- * SACCHAROMYCES CEREVISIAE
+ * A flag for TLS refinements identifying the type of atomic displacement parameters stored
+ * in _atom_site.B_iso_or_equiv.
+ *
+ * Allowable values:
+ * LIKELY RESIDUAL, UNVERIFIED
+ *
*/
- readonly pdbx_gene_src_scientific_name?: Maybe<Scalars['String']>;
+ readonly pdbx_TLS_residual_ADP_flag?: Maybe<Scalars['String']>;
/**
- * Identifies the variant.
- *
- * Examples:
- * DELTAH1DELTATRP
+ * Average Fourier Shell Correlation (avgFSC) between model and
+ * observed structure factors for reflections not included in refinement.
+ *
+ * The average FSC is a measure of the agreement between observed
+ * and calculated structure factors.
+ *
+ * sum(N~i~ FSC~free-i~)
+ * avgFSC~free~ = ---------------------
+ * sum(N~i~)
+ *
+ *
+ * N~i~ = the number of free reflections in the resolution shell i
+ * FSC~free-i~ = FSC for free reflections in the i-th resolution shell calculated as:
+ *
+ * (sum(|F~o~| |F~c~| fom cos(phi~c~-phi~o~)))
+ * FSC~free-i~ = -------------------------------------------
+ * (sum(|F~o~|^2^) (sum(|F~c~|^2^)))^1/2^
+ *
+ * |F~o~| = amplitude of observed structure factor
+ * |F~c~| = amplitude of calculated structure factor
+ * phi~o~ = phase of observed structure factor
+ * phi~c~ = phase of calculated structure factor
+ * fom = figure of merit of the experimental phases.
+ *
+ * Summation of FSC~free-i~ is carried over all free reflections in the resolution shell.
+ *
+ * Summation of avgFSC~free~ is carried over all resolution shells.
+ *
+ *
+ * Ref: Rosenthal P.B., Henderson R.
+ * "Optimal determination of particle orientation, absolute hand,
+ * and contrast loss in single-particle electron cryomicroscopy.
+ * Journal of Molecular Biology. 2003;333(4):721-745, equation (A6).
*/
- readonly pdbx_gene_src_variant?: Maybe<Scalars['String']>;
+ readonly pdbx_average_fsc_free?: Maybe<Scalars['Float']>;
/**
- * Americal Tissue Culture Collection of the expression system. Where
- * full details of the protein production are available it would
- * be expected that this item would be derived from
- * _entity_src_gen_express.host_org_culture_collection
+ * Overall average Fourier Shell Correlation (avgFSC) between model and
+ * observed structure factors for all reflections.
+ *
+ * The average FSC is a measure of the agreement between observed
+ * and calculated structure factors.
+ *
+ * sum(N~i~ FSC~i~)
+ * avgFSC = ----------------
+ * sum(N~i~)
+ *
+ *
+ * N~i~ = the number of all reflections in the resolution shell i
+ * FSC~i~ = FSC for all reflections in the i-th resolution shell calculated as:
+ *
+ * (sum(|F~o~| |F~c~| fom cos(phi~c~-phi~o~)))
+ * FSC~i~ = -------------------------------------------
+ * (sum(|F~o~|^2^) (sum(|F~c~|^2^)))^1/2^
+ *
+ * |F~o~| = amplitude of observed structure factor
+ * |F~c~| = amplitude of calculated structure factor
+ * phi~o~ = phase of observed structure factor
+ * phi~c~ = phase of calculated structure factor
+ * fom = figure of merit of the experimental phases.
+ *
+ * Summation of FSC~i~ is carried over all reflections in the resolution shell.
+ *
+ * Summation of avgFSC is carried over all resolution shells.
+ *
+ *
+ * Ref: Rosenthal P.B., Henderson R.
+ * "Optimal determination of particle orientation, absolute hand,
+ * and contrast loss in single-particle electron cryomicroscopy.
+ * Journal of Molecular Biology. 2003;333(4):721-745, equation (A6).
*/
- readonly pdbx_host_org_atcc?: Maybe<Scalars['String']>;
+ readonly pdbx_average_fsc_overall?: Maybe<Scalars['Float']>;
/**
- * Cell type from which the gene is derived. Where
- * entity.target_id is provided this should be derived from
- * details of the target.
- *
- * Examples:
- * ENDOTHELIAL
+ * Average Fourier Shell Correlation (avgFSC) between model and
+ * observed structure factors for reflections included in refinement.
+ *
+ * The average FSC is a measure of the agreement between observed
+ * and calculated structure factors.
+ *
+ * sum(N~i~ FSC~work-i~)
+ * avgFSC~work~ = ---------------------
+ * sum(N~i~)
+ *
+ *
+ * N~i~ = the number of working reflections in the resolution shell i
+ * FSC~work-i~ = FSC for working reflections in the i-th resolution shell calculated as:
+ *
+ * (sum(|F~o~| |F~c~| fom cos(phi~c~-phi~o~)))
+ * FSC~work-i~ = -------------------------------------------
+ * (sum(|F~o~|^2^) (sum(|F~c~|^2^)))^1/2^
+ *
+ * |F~o~| = amplitude of observed structure factor
+ * |F~c~| = amplitude of calculated structure factor
+ * phi~o~ = phase of observed structure factor
+ * phi~c~ = phase of calculated structure factor
+ * fom = figure of merit of the experimental phases.
+ *
+ * Summation of FSC~work-i~ is carried over all working reflections in the resolution shell.
+ *
+ * Summation of avgFSC~work~ is carried over all resolution shells.
+ *
+ *
+ * Ref: Rosenthal P.B., Henderson R.
+ * "Optimal determination of particle orientation, absolute hand,
+ * and contrast loss in single-particle electron cryomicroscopy.
+ * Journal of Molecular Biology. 2003;333(4):721-745, equation (A6).
*/
- readonly pdbx_host_org_cell?: Maybe<Scalars['String']>;
+ readonly pdbx_average_fsc_work?: Maybe<Scalars['Float']>;
+ /** Value of F at "high end" of data cutoff. */
+ readonly pdbx_data_cutoff_high_absF?: Maybe<Scalars['Float']>;
/**
- * A specific line of cells used as the expression system. Where
- * full details of the protein production are available it would
- * be expected that this item would be derived from
- * entity_src_gen_express.host_org_cell_line
- *
+ * Value of RMS |F| used as high data cutoff.
+ *
* Examples:
- * HELA
+ * null
+ *
*/
- readonly pdbx_host_org_cell_line?: Maybe<Scalars['String']>;
+ readonly pdbx_data_cutoff_high_rms_absF?: Maybe<Scalars['Float']>;
/**
- * Identifies the location inside (or outside) the cell which
- * expressed the molecule.
- *
+ * Value of F at "low end" of data cutoff.
+ *
* Examples:
- * CYTOPLASM, NUCLEUS
+ * null
+ *
*/
- readonly pdbx_host_org_cellular_location?: Maybe<Scalars['String']>;
+ readonly pdbx_data_cutoff_low_absF?: Maybe<Scalars['Float']>;
/**
- * Culture collection of the expression system. Where
- * full details of the protein production are available it would
- * be expected that this item would be derived somehwere, but
- * exactly where is not clear.
+ * An identifier for the diffraction data set used in this refinement.
+ *
+ * Multiple diffraction data sets specified as a comma separated list.
*/
- readonly pdbx_host_org_culture_collection?: Maybe<Scalars['String']>;
+ readonly pdbx_diffrn_id?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
/**
- * Specific gene which expressed the molecule.
- *
+ * Whether the structure was refined with indvidual
+ * isotropic, anisotropic or overall temperature factor.
+ *
* Examples:
- * HIV-1 POL, GLNS7, U1A (2-98, Y31H, Q36R)
- */
- readonly pdbx_host_org_gene?: Maybe<Scalars['String']>;
- /**
- * NCBI Taxonomy identifier for the expression system organism.
- *
- * Reference:
- *
- * Wheeler DL, Chappey C, Lash AE, Leipe DD, Madden TL, Schuler GD,
- * Tatusova TA, Rapp BA (2000). Database resources of the National
- * Center for Biotechnology Information. Nucleic Acids Res 2000 Jan
- * 1;28(1):10-4
- *
- * Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Rapp BA,
- * Wheeler DL (2000). GenBank. Nucleic Acids Res 2000 Jan 1;28(1):15-18.
+ * Isotropic, Overall
+ *
*/
- readonly pdbx_host_org_ncbi_taxonomy_id?: Maybe<Scalars['String']>;
+ readonly pdbx_isotropic_thermal_model?: Maybe<Scalars['String']>;
/**
- * Specific organ which expressed the molecule.
- *
+ * Whether the cross validataion method was used through
+ * out or only at the end.
+ *
* Examples:
- * KIDNEY
+ * FREE R-VALUE
+ *
*/
- readonly pdbx_host_org_organ?: Maybe<Scalars['String']>;
+ readonly pdbx_ls_cross_valid_method?: Maybe<Scalars['String']>;
+ /** Data cutoff (SIGMA(F)) */
+ readonly pdbx_ls_sigma_F?: Maybe<Scalars['Float']>;
+ /** Data cutoff (SIGMA(F^2)) */
+ readonly pdbx_ls_sigma_Fsqd?: Maybe<Scalars['Float']>;
+ /** Data cutoff (SIGMA(I)) */
+ readonly pdbx_ls_sigma_I?: Maybe<Scalars['Float']>;
/**
- * Specific organelle which expressed the molecule.
- *
+ * Method(s) used to determine the structure.
+ *
* Examples:
- * MITOCHONDRIA
+ * AB INITIO PHASING, DM, ISAS, ISIR, ISIRAS, MAD, MIR, MIRAS, MR, SIR, SIRAS
+ *
*/
- readonly pdbx_host_org_organelle?: Maybe<Scalars['String']>;
+ readonly pdbx_method_to_determine_struct?: Maybe<Scalars['String']>;
/**
- * The scientific name of the organism that served as host for the
- * production of the entity. Where full details of the protein
- * production are available it would be expected that this item
- * would be derived from _entity_src_gen_express.host_org_scientific_name
- * or via _entity_src_gen_express.host_org_tax_id
- *
- * Examples:
- * ESCHERICHIA COLI, SACCHAROMYCES CEREVISIAE
+ * Overall estimated standard uncertainties of positional
+ * parameters based on R value.
*/
- readonly pdbx_host_org_scientific_name?: Maybe<Scalars['String']>;
+ readonly pdbx_overall_ESU_R?: Maybe<Scalars['Float']>;
+ /** Overall estimated standard uncertainties of positional parameters based on R free value. */
+ readonly pdbx_overall_ESU_R_Free?: Maybe<Scalars['Float']>;
/**
- * The strain of the organism in which the entity was
- * expressed.
- *
- * Examples:
- * AR120
+ * The overall standard uncertainty (estimated standard deviation)
+ * of the displacement parameters based on the crystallographic
+ * R value, expressed in a formalism known as the dispersion
+ * precision indicator (DPI).
+ *
+ * Ref: Blow, D (2002) Acta Cryst. D58, 792-797
*/
- readonly pdbx_host_org_strain?: Maybe<Scalars['String']>;
+ readonly pdbx_overall_SU_R_Blow_DPI?: Maybe<Scalars['Float']>;
/**
- * The specific tissue which expressed the molecule. Where full details
- * of the protein production are available it would be expected that this
- * item would be derived from _entity_src_gen_express.host_org_tissue
- *
- * Examples:
- * heart, liver, eye lens
+ * The overall standard uncertainty (estimated standard deviation)
+ * of the displacement parameters based on the crystallographic
+ * R-free value, expressed in a formalism known as the dispersion
+ * precision indicator (DPI).
+ *
+ * Ref: Blow, D (2002) Acta Cryst. D58, 792-797
*/
- readonly pdbx_host_org_tissue?: Maybe<Scalars['String']>;
+ readonly pdbx_overall_SU_R_free_Blow_DPI?: Maybe<Scalars['Float']>;
/**
- * The fraction of the tissue which expressed the
- * molecule.
- *
- * Examples:
- * mitochondria, nucleus, membrane
+ * The overall standard uncertainty (estimated standard deviation)
+ * of the displacement parameters based on the crystallographic
+ * R-free value, expressed in a formalism known as the dispersion
+ * precision indicator (DPI).
+ *
+ * Ref: Cruickshank, D. W. J. (1999). Acta Cryst. D55, 583-601.
*/
- readonly pdbx_host_org_tissue_fraction?: Maybe<Scalars['String']>;
+ readonly pdbx_overall_SU_R_free_Cruickshank_DPI?: Maybe<Scalars['Float']>;
/**
- * Variant of the organism used as the expression system. Where
- * full details of the protein production are available it would
- * be expected that this item be derived from
- * entity_src_gen_express.host_org_variant or via
- * _entity_src_gen_express.host_org_tax_id
- *
+ * The overall phase error for all reflections after refinement using
+ * the current refinement target.
+ *
* Examples:
- * TRP-LAC, LAMBDA DE3
+ * null
+ *
*/
- readonly pdbx_host_org_variant?: Maybe<Scalars['String']>;
+ readonly pdbx_overall_phase_error?: Maybe<Scalars['Float']>;
/**
- * Identifies the vector used. Where full details of the protein
- * production are available it would be expected that this item
- * would be derived from _entity_src_gen_clone.vector_name.
- *
- * Examples:
- * PBIT36, PET15B, PUC18
+ * This data item uniquely identifies a refinement within an entry.
+ * _refine.pdbx_refine_id can be used to distinguish the results of
+ * joint refinements.
*/
- readonly pdbx_host_org_vector?: Maybe<Scalars['String']>;
+ readonly pdbx_refine_id: Scalars['String'];
+ /** For bulk solvent mask calculation, the amount that the ionic radii of atoms, which can be ions, are increased used. */
+ readonly pdbx_solvent_ion_probe_radii?: Maybe<Scalars['Float']>;
+ /** For bulk solvent mask calculation, amount mask is shrunk after taking away atoms with new radii and a constant value assigned to this new region. */
+ readonly pdbx_solvent_shrinkage_radii?: Maybe<Scalars['Float']>;
+ /** For bulk solvent mask calculation, the value by which the vdw radii of non-ion atoms (like carbon) are increased and used. */
+ readonly pdbx_solvent_vdw_probe_radii?: Maybe<Scalars['Float']>;
/**
- * Identifies the type of vector used (plasmid, virus, or cosmid).
- * Where full details of the protein production are available it
- * would be expected that this item would be derived from
- * _entity_src_gen_express.vector_type.
- *
+ * Starting model for refinement. Starting model for
+ * molecular replacement should refer to a previous
+ * structure or experiment.
+ *
* Examples:
- * COSMID, PLASMID
+ * 1XYZ, 2XYZ, BDL001
+ *
*/
- readonly pdbx_host_org_vector_type?: Maybe<Scalars['String']>;
+ readonly pdbx_starting_model?: Maybe<Scalars['String']>;
/**
- * This data item povides additional information about the sequence type.
- *
- * Allowable values:
- * Biological sequence, C-terminal tag, Linker, N-terminal tag
+ * Special case of stereochemistry target values used
+ * in SHELXL refinement.
*/
- readonly pdbx_seq_type?: Maybe<Scalars['String']>;
- /** This data item is an ordinal identifier for entity_src_gen data records. */
- readonly pdbx_src_id: Scalars['Int'];
+ readonly pdbx_stereochem_target_val_spec_case?: Maybe<Scalars['String']>;
+ /** Stereochemistry target values used in refinement. */
+ readonly pdbx_stereochemistry_target_values?: Maybe<Scalars['String']>;
+ /** Special aspects of the solvent model used during refinement. */
+ readonly solvent_model_details?: Maybe<Scalars['String']>;
/**
- * A description of special aspects of the plasmid that produced the
- * entity in the host organism. Where full details of the protein
- * production are available it would be expected that this item
- * would be derived from _pdbx_construct.details of the construct
- * pointed to from _entity_src_gen_express.plasmid_id.
+ * The value of the BSOL solvent-model parameter describing
+ * the average isotropic displacement parameter of disordered
+ * solvent atoms.
+ *
+ * This is one of the two parameters (the other is
+ * _refine.solvent_model_param_ksol) in Tronrud's method of
+ * modelling the contribution of bulk solvent to the
+ * scattering. The standard scale factor is modified according
+ * to the expression
+ *
+ * k0 exp(-B0 * s^2^)[1-KSOL * exp(-BSOL * s^2^)]
+ *
+ * where k0 and B0 are the scale factors for the protein.
+ *
+ * Ref: Tronrud, D. E. (1997). Methods Enzymol. 277, 243-268.
*/
- readonly plasmid_details?: Maybe<Scalars['String']>;
+ readonly solvent_model_param_bsol?: Maybe<Scalars['Float']>;
/**
- * The name of the plasmid that produced the entity in the host
- * organism. Where full details of the protein production are available
- * it would be expected that this item would be derived from
- * _pdbx_construct.name of the construct pointed to from
- * _entity_src_gen_express.plasmid_id.
- *
- * Examples:
- * pET3C, pT123sab
+ * The value of the KSOL solvent-model parameter describing
+ * the ratio of the electron density in the bulk solvent to the
+ * electron density in the molecular solute.
+ *
+ * This is one of the two parameters (the other is
+ * _refine.solvent_model_param_bsol) in Tronrud's method of
+ * modelling the contribution of bulk solvent to the
+ * scattering. The standard scale factor is modified according
+ * to the expression
+ *
+ * k0 exp(-B0 * s^2^)[1-KSOL * exp(-BSOL * s^2^)]
+ *
+ * where k0 and B0 are the scale factors for the protein.
+ *
+ * Ref: Tronrud, D. E. (1997). Methods Enzymol. 277, 243-268.
*/
- readonly plasmid_name?: Maybe<Scalars['String']>;
+ readonly solvent_model_param_ksol?: Maybe<Scalars['Float']>;
};
-export type Symmetry = {
+export type RefineAnalyze = {
/**
- * Space-group number from International Tables for Crystallography
- * Vol. A (2002).
+ * The estimated coordinate error obtained from the plot of
+ * the R value versus sin(theta)/lambda for the reflections
+ * treated as a test set during refinement.
+ *
+ * Ref: Luzzati, V. (1952). Traitement statistique des erreurs
+ * dans la determination des structures cristallines. Acta
+ * Cryst. 5, 802-810.
*/
- readonly Int_Tables_number?: Maybe<Scalars['Int']>;
+ readonly Luzzati_coordinate_error_free?: Maybe<Scalars['Float']>;
/**
- * The cell settings for this space-group symmetry.
- *
- * Allowable values:
- * cubic, hexagonal, monoclinic, orthorhombic, rhombohedral, tetragonal, triclinic, trigonal
+ * The estimated coordinate error obtained from the plot of
+ * the R value versus sin(theta)/lambda for reflections classified
+ * as observed.
+ *
+ * Ref: Luzzati, V. (1952). Traitement statistique des erreurs
+ * dans la determination des structures cristallines. Acta
+ * Cryst. 5, 802-810.
*/
- readonly cell_setting?: Maybe<Scalars['String']>;
+ readonly Luzzati_coordinate_error_obs?: Maybe<Scalars['Float']>;
/**
- * Used for PDB space group:
- *
- * Example: 'C 1 2 1' (instead of C 2)
- * 'P 1 2 1' (instead of P 2)
- * 'P 1 21 1' (instead of P 21)
- * 'P 1 1 21' (instead of P 21 -unique C axis)
- * 'H 3' (instead of R 3 -hexagonal)
- * 'H 3 2' (instead of R 3 2 -hexagonal)
- *
- * Examples:
- * Example: 'C 1 2 1' (instead of C 2)
- * 'P 1 2 1' (instead of P 2)
- * 'P 1 21 1' (instead of P 21)
- * 'P 1 1 21' (instead of P 21 -unique C axis)
- * 'H 3' (instead of R 3 -hexagonal)
- * 'H 3 2' (instead of R 3 2 -hexagonal)
+ * The value of the low-resolution cutoff used in constructing the
+ * Luzzati plot for reflections treated as a test set during
+ * refinement.
+ *
+ * Ref: Luzzati, V. (1952). Traitement statistique des erreurs
+ * dans la determination des structures cristallines. Acta
+ * Cryst. 5, 802-810.
*/
- readonly pdbx_full_space_group_name_H_M?: Maybe<Scalars['String']>;
+ readonly Luzzati_d_res_low_free?: Maybe<Scalars['Float']>;
/**
- * Hermann-Mauguin space-group symbol. Note that the
- * Hermann-Mauguin symbol does not necessarily contain complete
- * information about the symmetry and the space-group origin. If
- * used, always supply the FULL symbol from International Tables
- * for Crystallography Vol. A (2002) and indicate the origin and
- * the setting if it is not implicit. If there is any doubt that
- * the equivalent positions can be uniquely deduced from this
- * symbol, specify the _symmetry_equiv.pos_as_xyz or
- * _symmetry.space_group_name_Hall data items as well. Leave
- * spaces between symbols referring to
- * different axes.
- *
- * Examples:
- * A 1, A 1 2 1, A 2, B 1 1 2, B 2, B 2 21 2, C 2, C 1 2 1, C 21, C 1 21 1, C 2(A 112), C 2 2 2, C 2 2 21, C 4 21 2, F 2 2 2, F 2 3, F 4 2 2, F 4 3 2, F 41 3 2, I 1 2 1, I 1 21 1, I 2, I 2 2 2, I 2 3, I 21, I 21 3, I 21 21 21, I 4, I 4 2 2, I 4 3 2, I 41, I 41/a, I 41 2 2, I 41 3 2, P 1, P 1-, P 2, P 1 2 1, P 1 1 2, P 2 2 2, P 2 3, P 2 2 21, P 2 21 21, P 21, P 1 21 1, P 1 21/c 1, P 1 1 21, P 21(C), P 21 2 21, P 21 3, P 21 21 2, P 21 21 2 A, P 21 21 21, P 3, P 3 1 2, P 3 2 1, P 31, P 31 1 2, P 31 2 1, P 32, P 32 1 2, P 32 2 1, P 4, P 4 2 2, P 4 3 2, P 4 21 2, P 41, P 41 2 2, P 41 3 2, P 41 21 2, P 42, P 42 2 2, P 42 3 2, P 42 21 2, P 43, P 43 2 2, P 43 3 2, P 43 21 2, P 6, P 6 2 2, P 61, P 61 2 2, P 62, P 62 2 2, P 63, P 63 2 2, P 64, P 64 2 2, P 65, P 65 2 2, H 3, R 3, H 3 2, R 3 2
+ * The value of the low-resolution cutoff used in
+ * constructing the Luzzati plot for reflections classified as
+ * observed.
+ *
+ * Ref: Luzzati, V. (1952). Traitement statistique des erreurs
+ * dans la determination des structures cristallines. Acta
+ * Cryst. 5, 802-810.
*/
- readonly space_group_name_H_M?: Maybe<Scalars['String']>;
+ readonly Luzzati_d_res_low_obs?: Maybe<Scalars['Float']>;
/**
- * Space-group symbol as described by Hall (1981). This symbol
- * gives the space-group setting explicitly. Leave spaces between
- * the separate components of the symbol.
- *
- * Ref: Hall, S. R. (1981). Acta Cryst. A37, 517-525; erratum
- * (1981) A37, 921.
- *
- * Examples:
- * -P 2ac 2n, -R 3 2", P 61 2 2 (0 0 -1)
+ * The value of sigma~a~ used in constructing the Luzzati plot for
+ * the reflections treated as a test set during refinement.
+ * Details of the estimation of sigma~a~ can be specified
+ * in _refine_analyze.Luzzati_sigma_a_free_details.
+ *
+ * Ref: Luzzati, V. (1952). Traitement statistique des erreurs
+ * dans la determination des structures cristallines. Acta
+ * Cryst. 5, 802-810.
*/
- readonly space_group_name_Hall?: Maybe<Scalars['String']>;
-};
-
-export type PdbxFamilyPrdAudit = {
+ readonly Luzzati_sigma_a_free?: Maybe<Scalars['Float']>;
/**
- * The action associated with this audit record.
- *
- * Allowable values:
- * Add PRD, Create family, Initial release, Modify annotation, Modify citation, Modify family classification, Modify family name, Modify feature, Modify molecule details, Modify related structures, Modify sequence, Modify synonyms, Obsolete family, Obsolete familyt, Other modification, Remove PRD
+ * The value of sigma~a~ used in constructing the Luzzati plot for
+ * reflections classified as observed. Details of the
+ * estimation of sigma~a~ can be specified in
+ * _refine_analyze.Luzzati_sigma_a_obs_details.
+ *
+ * Ref: Luzzati, V. (1952). Traitement statistique des erreurs
+ * dans la determination des structures cristallines. Acta
+ * Cryst. 5, 802-810.
*/
- readonly action_type: Scalars['String'];
+ readonly Luzzati_sigma_a_obs?: Maybe<Scalars['Float']>;
/**
- * The initials of the annotator creating of modifying the family.
- *
- * Examples:
- * JO, SJ, KB
+ * The number of discretely disordered residues in the refined
+ * model.
*/
- readonly annotator?: Maybe<Scalars['String']>;
- /** The date associated with this audit record. */
- readonly date: Scalars['Date'];
+ readonly number_disordered_residues?: Maybe<Scalars['Float']>;
/**
- * Additional details decribing this change.
- *
- * Examples:
- * Revise molecule sequence.
+ * The sum of the occupancies of the hydrogen atoms in the refined
+ * model.
*/
- readonly details?: Maybe<Scalars['String']>;
+ readonly occupancy_sum_hydrogen?: Maybe<Scalars['Float']>;
/**
- * This data item is a pointer to _pdbx_reference_molecule_family.family_prd_id in the
- * pdbx_reference_molecule category.
+ * The sum of the occupancies of the non-hydrogen atoms in the
+ * refined model.
*/
- readonly family_prd_id: Scalars['String'];
+ readonly occupancy_sum_non_hydrogen?: Maybe<Scalars['Float']>;
+ /** record the high resolution for calculating Luzzati statistics. */
+ readonly pdbx_Luzzati_d_res_high_obs?: Maybe<Scalars['Float']>;
/**
- * An identifier for the wwPDB site creating or modifying the family.
- *
- * Examples:
- * RCSB, PDBE, PDBJ, BMRB, PDBC
+ * This data item uniquely identifies a refinement within an entry.
+ * _refine_analyze.pdbx_refine_id can be used to distinguish the results
+ * of joint refinements.
*/
- readonly processing_site?: Maybe<Scalars['String']>;
+ readonly pdbx_refine_id: Scalars['String'];
};
-export type EmSoftware = {
+export type RefineHist = {
/**
- * The purpose of the software.
- *
- * Allowable values:
- * CLASSIFICATION, CRYSTALLOGRAPHY MERGING, CTF CORRECTION, DIFFRACTION INDEXING, FINAL EULER ASSIGNMENT, IMAGE ACQUISITION, INITIAL EULER ASSIGNMENT, LATTICE DISTORTION CORRECTION, LAYERLINE INDEXING, MASKING, MODEL FITTING, MODEL REFINEMENT, MOLECULAR REPLACEMENT, OTHER, PARTICLE SELECTION, RECONSTRUCTION, SERIES ALIGNMENT, SYMMETRY DETERMINATION, VOLUME SELECTION
+ * The value of _refine_hist.cycle_id must uniquely identify a
+ * record in the REFINE_HIST list.
+ *
+ * Note that this item need not be a number; it can be any unique
+ * identifier.
*/
- readonly category?: Maybe<Scalars['String']>;
+ readonly cycle_id: Scalars['String'];
/**
- * Details about the software used.
- *
- * Examples:
- * EMAN2 e2boxer.py was used to automatically select particle images.
+ * The lowest value for the interplanar spacings for the
+ * reflection data for this cycle of refinement. This is called
+ * the highest resolution.
*/
- readonly details?: Maybe<Scalars['String']>;
- /** pointer to _em_3d_fitting.id in the EM_3D_FITTING category. */
- readonly fitting_id?: Maybe<Scalars['String']>;
- /** Unique identifier for each software description. */
- readonly id: Scalars['String'];
- /** pointer to _em_image_processing.id in the EM_IMAGE_PROCESSING category. */
- readonly image_processing_id?: Maybe<Scalars['String']>;
- /** pointer to _em_imaging.id in the EM_IMAGING category. */
- readonly imaging_id?: Maybe<Scalars['String']>;
+ readonly d_res_high?: Maybe<Scalars['Float']>;
/**
- * The name of the software package used, e.g., RELION. Depositors are strongly
- * encouraged to provide a value in this field.
- *
- * Examples:
- * EMAN, Imagic, Spider, Bsoft, UCSF-Chimera
+ * The highest value for the interplanar spacings for the
+ * reflection data for this cycle of refinement. This is
+ * called the lowest resolution.
*/
- readonly name?: Maybe<Scalars['String']>;
+ readonly d_res_low?: Maybe<Scalars['Float']>;
/**
- * The version of the software.
- *
- * Examples:
- * 9.03, 2.1
+ * The number of solvent atoms that were included in the model at
+ * this cycle of the refinement.
+ */
+ readonly number_atoms_solvent?: Maybe<Scalars['Int']>;
+ /**
+ * The total number of atoms that were included in the model at
+ * this cycle of the refinement.
*/
- readonly version?: Maybe<Scalars['String']>;
-};
-
-export type PdbxEntityBranch = {
- /** Number of constituent chemical components in the branched entity. */
- readonly rcsb_branched_component_count?: Maybe<Scalars['Int']>;
+ readonly number_atoms_total?: Maybe<Scalars['Int']>;
+ /** Mean isotropic B-value for ligand molecules included in refinement. */
+ readonly pdbx_B_iso_mean_ligand?: Maybe<Scalars['Float']>;
+ /** Mean isotropic B-value for solvent molecules included in refinement. */
+ readonly pdbx_B_iso_mean_solvent?: Maybe<Scalars['Float']>;
+ /** Number of ligand atoms included in refinement */
+ readonly pdbx_number_atoms_ligand?: Maybe<Scalars['Int']>;
+ /** Number of nucleic atoms included in refinement */
+ readonly pdbx_number_atoms_nucleic_acid?: Maybe<Scalars['Int']>;
+ /** Number of protein atoms included in refinement */
+ readonly pdbx_number_atoms_protein?: Maybe<Scalars['Int']>;
+ /** Total number of polymer residues included in refinement. */
+ readonly pdbx_number_residues_total?: Maybe<Scalars['Int']>;
/**
- * The type of this branched oligosaccharide.
- *
- * Allowable values:
- * oligosaccharide
+ * This data item uniquely identifies a refinement within an entry.
+ * _refine_hist.pdbx_refine_id can be used to distinguish the results
+ * of joint refinements.
*/
- readonly type?: Maybe<Scalars['String']>;
+ readonly pdbx_refine_id: Scalars['String'];
};
-export type RcsbAccessionInfo = {
- /** The entry deposition date. */
- readonly deposit_date?: Maybe<Scalars['Date']>;
+export type RefineLsRestr = {
/**
- * A code indicating the current availibility of experimental data in the repository.
- *
- * Allowable values:
- * N, Y
+ * For the given parameter type, the root-mean-square deviation
+ * between the ideal values used as restraints in the least-squares
+ * refinement and the values obtained by refinement. For instance,
+ * bond distances may deviate by 0.018 \%A (r.m.s.) from ideal
+ * values in the current model.
*/
- readonly has_released_experimental_data?: Maybe<Scalars['String']>;
- /** The entry initial release date. */
- readonly initial_release_date?: Maybe<Scalars['Date']>;
- /** The latest entry major revision number. */
- readonly major_revision?: Maybe<Scalars['Int']>;
- /** The latest entry minor revision number. */
- readonly minor_revision?: Maybe<Scalars['Int']>;
- /** The latest entry revision date. */
- readonly revision_date?: Maybe<Scalars['Date']>;
+ readonly dev_ideal?: Maybe<Scalars['Float']>;
/**
- * The release status for the entry.
- *
- * Allowable values:
- * AUCO, AUTH, HOLD, HPUB', POLC, PROC, REFI, REL, REPL, WAIT, WDRN
+ * For the given parameter type, the target root-mean-square
+ * deviation between the ideal values used as restraints in the
+ * least-squares refinement and the values obtained by refinement.
*/
- readonly status_code?: Maybe<Scalars['String']>;
-};
-
-export type DiffrnRadiation = {
+ readonly dev_ideal_target?: Maybe<Scalars['Float']>;
/**
- * The collimation or focusing applied to the radiation.
- *
- * Examples:
- * 0.3 mm double-pinhole, 0.5 mm, focusing mirrors
+ * The number of parameters of this type subjected to restraint in
+ * least-squares refinement.
*/
- readonly collimation?: Maybe<Scalars['String']>;
+ readonly number?: Maybe<Scalars['Int']>;
/**
- * This data item is a pointer to _diffrn.id in the DIFFRN
- * category.
+ * This data item uniquely identifies a refinement within an entry.
+ * _refine_ls_restr.pdbx_refine_id can be used to distinguish the results
+ * of joint refinements.
*/
- readonly diffrn_id: Scalars['String'];
+ readonly pdbx_refine_id: Scalars['String'];
/**
- * The method used to obtain monochromatic radiation. If a mono-
- * chromator crystal is used, the material and the indices of the
- * Bragg reflection are specified.
- *
+ * The functional form of the restraint function used in the least-squares
+ * refinement.
+ *
* Examples:
- * Zr filter, Ge 220, none, equatorial mounted graphite
+ * SINUSOIDAL, HARMONIC, SEMIHARMONIC
+ *
*/
- readonly monochromator?: Maybe<Scalars['String']>;
+ readonly pdbx_restraint_function?: Maybe<Scalars['String']>;
/**
- * SINGLE WAVELENGTH, LAUE, or MAD.
- *
+ * The type of the parameter being restrained.
+ * Explicit sets of data values are provided for the programs
+ * PROTIN/PROLSQ (beginning with p_) and RESTRAIN (beginning with
+ * RESTRAIN_). As computer programs change, these data values
+ * are given as examples, not as an enumeration list. Computer
+ * programs that convert a data block to a refinement table will
+ * expect the exact form of the data values given here to be used.
+ *
* Examples:
- * SINGLE WAVELENGTH, MONOCHROMATIC, LAUE, MAD, OTHER
+ * p_bond_d, p_angle_d, p_planar_d, p_xhbond_d, p_xhangle_d, p_hydrog_d, p_special_d, p_planar, p_chiral, p_singtor_nbd, p_multtor_nbd, p_xyhbond_nbd, p_xhyhbond_nbd, p_special_tor, p_planar_tor, p_staggered_tor, p_orthonormal_tor, p_mcbond_it, p_mcangle_it, p_scbond_it, p_scangle_it, p_xhbond_it, p_xhangle_it, p_special_it, RESTRAIN_Distances < 2.12, RESTRAIN_Distances 2.12 < D < 2.625, RESTRAIN_Distances > 2.625, RESTRAIN_Peptide Planes, RESTRAIN_Ring and other planes, RESTRAIN_rms diffs for Uiso atoms at dist 1.2-1.4, RESTRAIN_rms diffs for Uiso atoms at dist 1.4-1.6, RESTRAIN_rms diffs for Uiso atoms at dist 1.8-2.0, RESTRAIN_rms diffs for Uiso atoms at dist 2.0-2.2, RESTRAIN_rms diffs for Uiso atoms at dist 2.2-2.4, RESTRAIN_rms diffs for Uiso atoms at dist >2.4
+ *
*/
- readonly pdbx_diffrn_protocol?: Maybe<Scalars['String']>;
+ readonly type: Scalars['String'];
/**
- * Monochromatic or Laue.
- *
- * Allowable values:
- * L, M
+ * The weighting value applied to this type of restraint in
+ * the least-squares refinement.
*/
- readonly pdbx_monochromatic_or_laue_m_l?: Maybe<Scalars['String']>;
+ readonly weight?: Maybe<Scalars['Float']>;
+};
+
+export type Reflns = {
/**
- * The radiation scattering type for this diffraction data set.
- *
- * Allowable values:
- * electron, neutron, x-ray
+ * The value of the overall isotropic displacement parameter
+ * estimated from the slope of the Wilson plot.
*/
- readonly pdbx_scattering_type?: Maybe<Scalars['String']>;
- /** Wavelength of radiation. */
- readonly pdbx_wavelength?: Maybe<Scalars['String']>;
- /** Comma separated list of wavelengths or wavelength range. */
- readonly pdbx_wavelength_list?: Maybe<Scalars['String']>;
+ readonly B_iso_Wilson_estimate?: Maybe<Scalars['Float']>;
/**
- * The nature of the radiation. This is typically a description
- * of the X-ray wavelength in Siegbahn notation.
- *
+ * A description of the method by which a subset of reflections was
+ * selected for exclusion from refinement so as to be used in the
+ * calculation of a 'free' R factor.
+ *
* Examples:
- * CuK\a, Cu K\a~1~, Cu K-L~2,3~, white-beam
+ * The data set was sorted with l varying most
+ * rapidly and h varying least rapidly. Every
+ * 10th reflection in this sorted list was
+ * excluded from refinement and included in the
+ * calculation of a 'free' R factor.
+ *
*/
- readonly type?: Maybe<Scalars['String']>;
+ readonly R_free_details?: Maybe<Scalars['String']>;
/**
- * This data item is a pointer to _diffrn_radiation_wavelength.id
- * in the DIFFRN_RADIATION_WAVELENGTH category.
+ * Residual factor Rmerge for all reflections that satisfy the
+ * resolution limits established by _reflns.d_resolution_high
+ * and _reflns.d_resolution_low.
+ *
+ * sum~i~(sum~j~|F~j~ - <F>|)
+ * Rmerge(F) = --------------------------
+ * sum~i~(sum~j~<F>)
+ *
+ * F~j~ = the amplitude of the jth observation of reflection i
+ * <F> = the mean of the amplitudes of all observations of
+ * reflection i
+ *
+ * sum~i~ is taken over all reflections
+ * sum~j~ is taken over all observations of each reflection
*/
- readonly wavelength_id?: Maybe<Scalars['String']>;
-};
-
-export type RcsbNonpolymerInstanceFeatureSummary = {
- /** Component identifier for non-polymer entity instance. */
- readonly comp_id?: Maybe<Scalars['String']>;
- /** The feature count. */
- readonly count?: Maybe<Scalars['Int']>;
- /** The maximum feature length. */
- readonly maximum_length?: Maybe<Scalars['Int']>;
- /** The maximum feature value. */
- readonly maximum_value?: Maybe<Scalars['Float']>;
- /** The minimum feature length. */
- readonly minimum_length?: Maybe<Scalars['Int']>;
- /** The minimum feature value. */
- readonly minimum_value?: Maybe<Scalars['Float']>;
+ readonly Rmerge_F_all?: Maybe<Scalars['Float']>;
/**
- * Type or category of the feature.
- *
- * Allowable values:
- * HAS_COVALENT_LINKAGE, HAS_METAL_COORDINATION_LINKAGE, MOGUL_ANGLE_OUTLIER, MOGUL_BOND_OUTLIER, RSRCC_OUTLIER, RSRZ_OUTLIER
+ * Residual factor Rmerge for reflections that satisfy the
+ * resolution limits established by _reflns.d_resolution_high
+ * and _reflns.d_resolution_low and the observation limit
+ * established by _reflns.observed_criterion.
+ *
+ * sum~i~(sum~j~|F~j~ - <F>|)
+ * Rmerge(F) = --------------------------
+ * sum~i~(sum~j~<F>)
+ *
+ * F~j~ = the amplitude of the jth observation of reflection i
+ * <F> = the mean of the amplitudes of all observations of
+ * reflection i
+ *
+ * sum~i~ is taken over all reflections
+ * sum~j~ is taken over all observations of each reflection
*/
- readonly type?: Maybe<Scalars['String']>;
-};
-
-export type RcsbClusterMembership = {
- /** Identifier for a cluster at the specified level of sequence identity within the cluster data set. */
- readonly cluster_id?: Maybe<Scalars['Int']>;
- /** Sequence identity expressed as an integer percent value. */
- readonly identity?: Maybe<Scalars['Int']>;
-};
-
-
-export type EntitySrcNat = {
+ readonly Rmerge_F_obs?: Maybe<Scalars['Float']>;
/**
- * The common name of the organism from which the entity
- * was isolated.
- *
- * Examples:
- * man, yeast, bacteria
+ * The smallest value in angstroms for the interplanar spacings
+ * for the reflection data. This is called the highest resolution.
*/
- readonly common_name?: Maybe<Scalars['String']>;
+ readonly d_resolution_high?: Maybe<Scalars['Float']>;
/**
- * A description of special aspects of the organism from which the
- * entity was isolated.
+ * The largest value in angstroms for the interplanar spacings
+ * for the reflection data. This is called the lowest resolution.
*/
- readonly details?: Maybe<Scalars['String']>;
+ readonly d_resolution_low?: Maybe<Scalars['Float']>;
/**
- * The genus of the organism from which the entity was isolated.
- *
+ * A description of special aspects of the data-reduction
+ * procedures.
+ *
* Examples:
- * Homo, Saccharomyces, Escherichia
+ * Merging and scaling based on only those
+ * reflections with I > sig(I).
+ *
*/
- readonly genus?: Maybe<Scalars['String']>;
+ readonly data_reduction_details?: Maybe<Scalars['String']>;
/**
- * This data item identifies cases in which an alternative source
- * modeled.
- *
- * Allowable values:
- * model, sample
+ * The method used for data reduction.
+ *
+ * Note that this is not the computer program used, which is
+ * described in the SOFTWARE category, but the method
+ * itself.
+ *
+ * This data item should be used to describe significant
+ * methodological options used within the data-reduction programs.
+ *
+ * Examples:
+ * Profile fitting by method of Kabsch (1987).
+ * Scaling used spherical harmonic coefficients.
+ *
*/
- readonly pdbx_alt_source_flag?: Maybe<Scalars['String']>;
+ readonly data_reduction_method?: Maybe<Scalars['String']>;
/**
- * Americal Tissue Culture Collection number.
- *
- * Examples:
- * 6051
+ * A description of reflection data not covered by other data
+ * names. This should include details of the Friedel pairs.
*/
- readonly pdbx_atcc?: Maybe<Scalars['String']>;
+ readonly details?: Maybe<Scalars['String']>;
/**
- * The beginning polymer sequence position for the polymer section corresponding
- * to this source.
- *
- * A reference to the sequence position in the entity_poly category.
+ * Maximum value of the Miller index h for the reflection data. This
+ * need not have the same value as _diffrn_reflns.limit_h_max.
*/
- readonly pdbx_beg_seq_num?: Maybe<Scalars['Int']>;
+ readonly limit_h_max?: Maybe<Scalars['Int']>;
/**
- * A particular cell type.
- *
- * Examples:
- * BHK-21
+ * Minimum value of the Miller index h for the reflection data. This
+ * need not have the same value as _diffrn_reflns.limit_h_min.
*/
- readonly pdbx_cell?: Maybe<Scalars['String']>;
+ readonly limit_h_min?: Maybe<Scalars['Int']>;
/**
- * The specific line of cells.
- *
- * Examples:
- * HELA
+ * Maximum value of the Miller index k for the reflection data. This
+ * need not have the same value as _diffrn_reflns.limit_k_max.
*/
- readonly pdbx_cell_line?: Maybe<Scalars['String']>;
- /** Identifies the location inside (or outside) the cell. */
- readonly pdbx_cellular_location?: Maybe<Scalars['String']>;
+ readonly limit_k_max?: Maybe<Scalars['Int']>;
/**
- * The ending polymer sequence position for the polymer section corresponding
- * to this source.
- *
- * A reference to the sequence position in the entity_poly category.
+ * Minimum value of the Miller index k for the reflection data. This
+ * need not have the same value as _diffrn_reflns.limit_k_min.
*/
- readonly pdbx_end_seq_num?: Maybe<Scalars['Int']>;
- /** A domain or fragment of the molecule. */
- readonly pdbx_fragment?: Maybe<Scalars['String']>;
+ readonly limit_k_min?: Maybe<Scalars['Int']>;
+ /**
+ * Maximum value of the Miller index l for the reflection data. This
+ * need not have the same value as _diffrn_reflns.limit_l_max.
+ */
+ readonly limit_l_max?: Maybe<Scalars['Int']>;
/**
- * NCBI Taxonomy identifier for the source organism.
- *
- * Reference:
- *
- * Wheeler DL, Chappey C, Lash AE, Leipe DD, Madden TL, Schuler GD,
- * Tatusova TA, Rapp BA (2000). Database resources of the National
- * Center for Biotechnology Information. Nucleic Acids Res 2000 Jan
- * 1;28(1):10-4
- *
- * Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Rapp BA,
- * Wheeler DL (2000). GenBank. Nucleic Acids Res 2000 Jan 1;28(1):15-18.
+ * Minimum value of the Miller index l for the reflection data. This
+ * need not have the same value as _diffrn_reflns.limit_l_min.
*/
- readonly pdbx_ncbi_taxonomy_id?: Maybe<Scalars['String']>;
+ readonly limit_l_min?: Maybe<Scalars['Int']>;
/**
- * Organized group of tissues that carries on a specialized function.
- *
- * Examples:
- * KIDNEY
+ * The total number of reflections in the REFLN list (not the
+ * DIFFRN_REFLN list). This number may contain Friedel-equivalent
+ * reflections according to the nature of the structure and the
+ * procedures used. The item _reflns.details describes the
+ * reflection data.
*/
- readonly pdbx_organ?: Maybe<Scalars['String']>;
+ readonly number_all?: Maybe<Scalars['Int']>;
/**
- * Organized structure within cell.
- *
- * Examples:
- * MITOCHONDRIA
+ * The number of reflections in the REFLN list (not the DIFFRN_REFLN
+ * list) classified as observed (see _reflns.observed_criterion).
+ * This number may contain Friedel-equivalent reflections according
+ * to the nature of the structure and the procedures used.
*/
- readonly pdbx_organelle?: Maybe<Scalars['String']>;
+ readonly number_obs?: Maybe<Scalars['Int']>;
/**
- * Scientific name of the organism of the natural source.
- *
+ * The criterion used to classify a reflection as 'observed'. This
+ * criterion is usually expressed in terms of a sigma(I) or
+ * sigma(F) threshold.
+ *
* Examples:
- * Bos taurus, BOS TAURUS, SUS SCROFA, ASPERGILLUS ORYZAE
+ * >2sigma(I)
+ *
*/
- readonly pdbx_organism_scientific?: Maybe<Scalars['String']>;
+ readonly observed_criterion?: Maybe<Scalars['String']>;
/**
- * Details about the plasmid.
- *
- * Examples:
- * PLC28 DERIVATIVE
+ * The criterion used to classify a reflection as 'observed'
+ * expressed as an upper limit for the value of F.
*/
- readonly pdbx_plasmid_details?: Maybe<Scalars['String']>;
+ readonly observed_criterion_F_max?: Maybe<Scalars['Float']>;
/**
- * The plasmid containing the gene.
- *
- * Examples:
- * pB322
+ * The criterion used to classify a reflection as 'observed'
+ * expressed as a lower limit for the value of F.
*/
- readonly pdbx_plasmid_name?: Maybe<Scalars['String']>;
+ readonly observed_criterion_F_min?: Maybe<Scalars['Float']>;
/**
- * Identifies the secretion from which the molecule was isolated.
- *
- * Examples:
- * saliva, urine, venom
+ * The criterion used to classify a reflection as 'observed'
+ * expressed as an upper limit for the value of I.
*/
- readonly pdbx_secretion?: Maybe<Scalars['String']>;
- /** This data item is an ordinal identifier for entity_src_nat data records. */
- readonly pdbx_src_id: Scalars['Int'];
- /** Identifies the variant. */
- readonly pdbx_variant?: Maybe<Scalars['String']>;
+ readonly observed_criterion_I_max?: Maybe<Scalars['Float']>;
/**
- * The species of the organism from which the entity was isolated.
- *
- * Examples:
- * sapiens, cerevisiae, coli
+ * The criterion used to classify a reflection as 'observed'
+ * expressed as a lower limit for the value of I.
*/
- readonly species?: Maybe<Scalars['String']>;
+ readonly observed_criterion_I_min?: Maybe<Scalars['Float']>;
/**
- * The strain of the organism from which the entity was isolated.
- *
- * Examples:
- * DH5a, BMH 71-18
+ * The criterion used to classify a reflection as 'observed'
+ * expressed as a multiple of the value of sigma(F).
*/
- readonly strain?: Maybe<Scalars['String']>;
+ readonly observed_criterion_sigma_F?: Maybe<Scalars['Float']>;
/**
- * The tissue of the organism from which the entity was isolated.
- *
- * Examples:
- * heart, liver, eye lens
+ * The criterion used to classify a reflection as 'observed'
+ * expressed as a multiple of the value of sigma(I).
*/
- readonly tissue?: Maybe<Scalars['String']>;
+ readonly observed_criterion_sigma_I?: Maybe<Scalars['Float']>;
/**
- * The subcellular fraction of the tissue of the organism from
- * which the entity was isolated.
- *
- * Examples:
- * mitochondria, nucleus, membrane
+ * The Pearson's correlation coefficient expressed as a decimal value
+ * between the average intensities from randomly selected
+ * half-datasets.
+ *
+ * Ref: Karplus & Diederichs (2012), Science 336, 1030-33
*/
- readonly tissue_fraction?: Maybe<Scalars['String']>;
-};
-
-export type EmImaging = {
+ readonly pdbx_CC_half?: Maybe<Scalars['Float']>;
/**
- * A value of accelerating voltage (in kV) used for imaging.
- *
- * Examples:
- * 300
+ * R split measures the agreement between the sets of intensities created by merging
+ * odd- and even-numbered images from the overall data.
+ *
+ * Ref: T. A. White, R. A. Kirian, A. V. Martin, A. Aquila, K. Nass, A. Barty
+ * and H. N. Chapman (2012), J. Appl. Cryst. 45, 335-341
*/
- readonly accelerating_voltage?: Maybe<Scalars['Int']>;
+ readonly pdbx_R_split?: Maybe<Scalars['Float']>;
/**
- * microscope alignment procedure
- *
- * Allowable values:
- * BASIC, COMA FREE, NONE, OTHER, ZEMLIN TABLEAU
+ * The R value for merging intensities satisfying the observed
+ * criteria in this data set.
*/
- readonly alignment_procedure?: Maybe<Scalars['String']>;
- /** astigmatism */
- readonly astigmatism?: Maybe<Scalars['String']>;
+ readonly pdbx_Rmerge_I_obs?: Maybe<Scalars['Float']>;
/**
- * The open diameter of the c2 condenser lens,
- * in microns.
+ * The precision-indicating merging R factor value Rpim,
+ * for merging all intensities in this data set.
+ *
+ * sum~i~ [1/(N~i~ - 1)]1/2^ sum~j~ | I~j~ - <I~i~> |
+ * Rpim = --------------------------------------------------
+ * sum~i~ ( sum~j~ I~j~ )
+ *
+ * I~j~ = the intensity of the jth observation of reflection i
+ * <I~i~> = the mean of the intensities of all observations
+ * of reflection i
+ * N~i~ = the redundancy (the number of times reflection i
+ * has been measured).
+ *
+ * sum~i~ is taken over all reflections
+ * sum~j~ is taken over all observations of each reflection.
+ *
+ * Ref: Diederichs, K. & Karplus, P. A. (1997). Nature Struct.
+ * Biol. 4, 269-275.
+ * Weiss, M. S. & Hilgenfeld, R. (1997). J. Appl. Cryst.
+ * 30, 203-205.
+ * Weiss, M. S. (2001). J. Appl. Cryst. 34, 130-135.
*/
- readonly c2_aperture_diameter?: Maybe<Scalars['Float']>;
+ readonly pdbx_Rpim_I_all?: Maybe<Scalars['Float']>;
/**
- * The maximum defocus value of the objective lens (in nanometers) used
- * to obtain the recorded images.
- *
- * Examples:
- * 5000
+ * The redundancy-independent merging R factor value Rrim,
+ * also denoted Rmeas, for merging all intensities in this
+ * data set.
+ *
+ * sum~i~ [N~i~/(N~i~ - 1)]1/2^ sum~j~ | I~j~ - <I~i~> |
+ * Rrim = ----------------------------------------------------
+ * sum~i~ ( sum~j~ I~j~ )
+ *
+ * I~j~ = the intensity of the jth observation of reflection i
+ * <I~i~> = the mean of the intensities of all observations of
+ * reflection i
+ * N~i~ = the redundancy (the number of times reflection i
+ * has been measured).
+ *
+ * sum~i~ is taken over all reflections
+ * sum~j~ is taken over all observations of each reflection.
+ *
+ * Ref: Diederichs, K. & Karplus, P. A. (1997). Nature Struct.
+ * Biol. 4, 269-275.
+ * Weiss, M. S. & Hilgenfeld, R. (1997). J. Appl. Cryst.
+ * 30, 203-205.
+ * Weiss, M. S. (2001). J. Appl. Cryst. 34, 130-135.
*/
- readonly calibrated_defocus_max?: Maybe<Scalars['Float']>;
+ readonly pdbx_Rrim_I_all?: Maybe<Scalars['Float']>;
/**
- * The minimum defocus value of the objective lens (in nanometers) used
- * to obtain the recorded images.
- *
+ * The R sym value as a decimal number.
+ *
* Examples:
- * 1200
+ * null
+ *
*/
- readonly calibrated_defocus_min?: Maybe<Scalars['Float']>;
+ readonly pdbx_Rsym_value?: Maybe<Scalars['Float']>;
+ /** Overall Chi-squared statistic. */
+ readonly pdbx_chi_squared?: Maybe<Scalars['Float']>;
/**
- * The magnification value obtained for a known standard just
- * prior to, during or just after the imaging experiment.
- *
- * Examples:
- * 61200
+ * An identifier for the diffraction data set for this set of summary statistics.
+ *
+ * Multiple diffraction data sets entered as a comma separated list.
*/
- readonly calibrated_magnification?: Maybe<Scalars['Int']>;
+ readonly pdbx_diffrn_id?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
/**
- * Cryogen type used to maintain the specimen stage temperature during imaging
- * in the microscope.
- *
- * Allowable values:
- * HELIUM, NITROGEN
+ * The ratio of the average intensity to the average uncertainty,
+ * <I>/<sigma(I)>.
*/
- readonly cryogen?: Maybe<Scalars['String']>;
+ readonly pdbx_netI_over_av_sigmaI?: Maybe<Scalars['Float']>;
/**
- * Date (YYYY-MM-DD) of imaging experiment or the date at which
- * a series of experiments began.
- *
- * Examples:
- * 2001-05-08
+ * The mean of the ratio of the intensities to their
+ * standard uncertainties, <I/sigma(I)>.
*/
- readonly date?: Maybe<Scalars['Date']>;
+ readonly pdbx_netI_over_sigmaI?: Maybe<Scalars['Float']>;
+ /** Total number of measured reflections. */
+ readonly pdbx_number_measured_all?: Maybe<Scalars['Int']>;
+ /** An ordinal identifier for this set of reflection statistics. */
+ readonly pdbx_ordinal: Scalars['Int'];
+ /** Overall redundancy for this data set. */
+ readonly pdbx_redundancy?: Maybe<Scalars['Float']>;
+ /** Number of reflections rejected in scaling operations. */
+ readonly pdbx_scaling_rejects?: Maybe<Scalars['Int']>;
/**
- * Any additional imaging details.
- *
- * Examples:
- * Preliminary grid screening was performed manually.
+ * The percentage of geometrically possible reflections represented
+ * by reflections that satisfy the resolution limits established
+ * by _reflns.d_resolution_high and _reflns.d_resolution_low and
+ * the observation limit established by
+ * _reflns.observed_criterion.
*/
- readonly details?: Maybe<Scalars['String']>;
+ readonly percent_possible_obs?: Maybe<Scalars['Float']>;
/**
- * The camera length (in millimeters). The camera length is the
- * product of the objective focal length and the combined magnification
- * of the intermediate and projector lenses when the microscope is
- * operated in the diffraction mode.
+ * The value of _reflns.phase_calculation_details describes a
+ * special details about calculation of phases in _refln.phase_calc.
+ *
+ * Examples:
+ * From model, NCS averaging, Solvent flipping, Solvent flattening, Multiple crystal averaging, Multiple phase modification, Other phase modification
+ *
*/
- readonly detector_distance?: Maybe<Scalars['Float']>;
- /** electron beam tilt params */
- readonly electron_beam_tilt_params?: Maybe<Scalars['String']>;
- /** The source of electrons. The electron gun. */
- readonly electron_source?: Maybe<Scalars['String']>;
+ readonly phase_calculation_details?: Maybe<Scalars['String']>;
+};
+
+export type ReflnsShell = {
/**
- * The value of _em_imaging.id must uniquely identify
- * each imaging experiment.
+ * Residual factor Rmerge for all reflections that satisfy the
+ * resolution limits established by _reflns_shell.d_res_high and
+ * _reflns_shell.d_res_low.
+ *
+ * sum~i~(sum~j~|F~j~ - <F>|)
+ * Rmerge(F) = --------------------------
+ * sum~i~(sum~j~<F>)
+ *
+ * F~j~ = the amplitude of the jth observation of reflection i
+ * <F> = the mean of the amplitudes of all observations of
+ * reflection i
+ *
+ * sum~i~ is taken over all reflections
+ * sum~j~ is taken over all observations of each reflection
*/
- readonly id: Scalars['String'];
+ readonly Rmerge_F_all?: Maybe<Scalars['Float']>;
/**
- * The mode of illumination.
- *
- * Allowable values:
- * FLOOD BEAM, OTHER, SPOT SCAN
+ * Residual factor Rmerge for reflections that satisfy the
+ * resolution limits established by _reflns_shell.d_res_high and
+ * _reflns_shell.d_res_low and the observation criterion
+ * established by _reflns.observed_criterion.
+ *
+ * sum~i~(sum~j~|F~j~ - <F>|)
+ * Rmerge(F) = --------------------------
+ * sum~i~(sum~j~<F>)
+ *
+ * F~j~ = the amplitude of the jth observation of reflection i
+ * <F> = the mean of the amplitudes of all observations of
+ * reflection i
+ *
+ * sum~i~ is taken over all reflections
+ * sum~j~ is taken over all observations of each reflection
*/
- readonly illumination_mode?: Maybe<Scalars['String']>;
+ readonly Rmerge_F_obs?: Maybe<Scalars['Float']>;
/**
- * The name of the model of microscope.
- *
- * Allowable values:
- * FEI MORGAGNI, FEI POLARA 300, FEI TALOS ARCTICA, FEI TECNAI 10, FEI TECNAI 12, FEI TECNAI 20, FEI TECNAI ARCTICA, FEI TECNAI F20, FEI TECNAI F30, FEI TECNAI SPHERA, FEI TECNAI SPIRIT, FEI TITAN, FEI TITAN KRIOS, FEI/PHILIPS CM10, FEI/PHILIPS CM12, FEI/PHILIPS CM120T, FEI/PHILIPS CM200FEG, FEI/PHILIPS CM200FEG/SOPHIE, FEI/PHILIPS CM200FEG/ST, FEI/PHILIPS CM200FEG/UT, FEI/PHILIPS CM200T, FEI/PHILIPS CM300FEG/HE, FEI/PHILIPS CM300FEG/ST, FEI/PHILIPS CM300FEG/T, FEI/PHILIPS EM400, FEI/PHILIPS EM420, HITACHI EF2000, HITACHI EF3000, HITACHI H-9500SD, HITACHI H3000 UHVEM, HITACHI H7600, HITACHI HF2000, HITACHI HF3000, JEOL 100B, JEOL 100CX, JEOL 1010, JEOL 1200, JEOL 1200EX, JEOL 1200EXII, JEOL 1230, JEOL 1400, JEOL 2000EX, JEOL 2000EXII, JEOL 2010, JEOL 2010F, JEOL 2010HC, JEOL 2010HT, JEOL 2010UHR, JEOL 2011, JEOL 2100, JEOL 2100F, JEOL 2200FS, JEOL 2200FSC, JEOL 3000SFF, JEOL 3100FEF, JEOL 3100FFC, JEOL 3200FS, JEOL 3200FSC, JEOL 4000, JEOL 4000EX, JEOL CRYO ARM 200, JEOL CRYO ARM 300, JEOL KYOTO-3000SFF, SIEMENS SULEIKA, TFS GLACIOS, TFS KRIOS, TFS TALOS, TFS TALOS F200C, TFS TALOS L120C, ZEISS LEO912, ZEISS LIBRA120PLUS
+ * The value of Rmerge(I) for all reflections in a given shell.
+ *
+ * sum~i~(sum~j~|I~j~ - <I>|)
+ * Rmerge(I) = --------------------------
+ * sum~i~(sum~j~<I>)
+ *
+ * I~j~ = the intensity of the jth observation of reflection i
+ * <I> = the mean of the intensities of all observations of
+ * reflection i
+ *
+ * sum~i~ is taken over all reflections
+ * sum~j~ is taken over all observations of each reflection
*/
- readonly microscope_model?: Maybe<Scalars['String']>;
+ readonly Rmerge_I_all?: Maybe<Scalars['Float']>;
/**
- * The mode of imaging.
- *
- * Allowable values:
- * BRIGHT FIELD, DARK FIELD, DIFFRACTION, OTHER
+ * The value of Rmerge(I) for reflections classified as 'observed'
+ * (see _reflns.observed_criterion) in a given shell.
+ *
+ * sum~i~(sum~j~|I~j~ - <I>|)
+ * Rmerge(I) = --------------------------
+ * sum~i~(sum~j~<I>)
+ *
+ * I~j~ = the intensity of the jth observation of reflection i
+ * <I> = the mean of the intensities of all observations of
+ * reflection i
+ *
+ * sum~i~ is taken over all reflections
+ * sum~j~ is taken over all observations of each reflection
*/
- readonly mode?: Maybe<Scalars['String']>;
+ readonly Rmerge_I_obs?: Maybe<Scalars['Float']>;
/**
- * The spherical aberration coefficient (Cs) in millimeters,
- * of the objective lens.
- *
- * Examples:
- * 2.0
+ * The smallest value in angstroms for the interplanar spacings
+ * for the reflections in this shell. This is called the highest
+ * resolution.
*/
- readonly nominal_cs?: Maybe<Scalars['Float']>;
+ readonly d_res_high?: Maybe<Scalars['Float']>;
/**
- * The maximum defocus value of the objective lens (in nanometers) used
- * to obtain the recorded images.
- *
- * Examples:
- * 5000
+ * The highest value in angstroms for the interplanar spacings
+ * for the reflections in this shell. This is called the lowest
+ * resolution.
*/
- readonly nominal_defocus_max?: Maybe<Scalars['Float']>;
+ readonly d_res_low?: Maybe<Scalars['Float']>;
/**
- * The minimum defocus value of the objective lens (in nanometers) used
- * to obtain the recorded images.
- *
- * Examples:
- * 1200
+ * The ratio of the mean of the intensities of all reflections
+ * in this shell to the mean of the standard uncertainties of the
+ * intensities of all reflections in this shell.
*/
- readonly nominal_defocus_min?: Maybe<Scalars['Float']>;
+ readonly meanI_over_sigI_all?: Maybe<Scalars['Float']>;
/**
- * The magnification indicated by the microscope readout.
- *
- * Examples:
- * 60000
+ * The ratio of the mean of the intensities of the reflections
+ * classified as 'observed' (see _reflns.observed_criterion) in
+ * this shell to the mean of the standard uncertainties of the
+ * intensities of the 'observed' reflections in this
+ * shell.
*/
- readonly nominal_magnification?: Maybe<Scalars['Int']>;
+ readonly meanI_over_sigI_obs?: Maybe<Scalars['Float']>;
/**
- * The specimen temperature maximum (degrees Kelvin) for the duration
- * of imaging.
+ * The ratio of the mean of the intensities of all reflections
+ * in this shell to the mean of the standard uncertainties of the
+ * intensities of all reflections in this shell.
*/
- readonly recording_temperature_maximum?: Maybe<Scalars['Float']>;
+ readonly meanI_over_uI_all?: Maybe<Scalars['Float']>;
/**
- * The specimen temperature minimum (degrees Kelvin) for the duration
- * of imaging.
+ * The total number of reflections measured for this
+ * shell.
*/
- readonly recording_temperature_minimum?: Maybe<Scalars['Float']>;
- /** residual tilt of the electron beam */
- readonly residual_tilt?: Maybe<Scalars['Float']>;
+ readonly number_measured_all?: Maybe<Scalars['Int']>;
/**
- * The name of the model of specimen holder used during imaging.
- *
- * Allowable values:
- * FEI TITAN KRIOS AUTOGRID HOLDER, FISCHIONE 2550, FISCHIONE INSTRUMENTS DUAL AXIS TOMOGRAPHY HOLDER, GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER, GATAN 910 MULTI-SPECIMEN SINGLE TILT CRYO TRANSFER HOLDER, GATAN 914 HIGH TILT LIQUID NITROGEN CRYO TRANSFER TOMOGRAPHY HOLDER, GATAN 915 DOUBLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER, GATAN CHDT 3504 DOUBLE TILT HIGH RESOLUTION NITROGEN COOLING HOLDER, GATAN CT3500 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER, GATAN CT3500TR SINGLE TILT ROTATION LIQUID NITROGEN CRYO TRANSFER HOLDER, GATAN ELSA 698 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER, GATAN HC 3500 SINGLE TILT HEATING/NITROGEN COOLING HOLDER, GATAN HCHDT 3010 DOUBLE TILT HIGH RESOLUTION HELIUM COOLING HOLDER, GATAN HCHST 3008 SINGLE TILT HIGH RESOLUTION HELIUM COOLING HOLDER, GATAN HELIUM, GATAN LIQUID NITROGEN, GATAN UHRST 3500 SINGLE TILT ULTRA HIGH RESOLUTION NITROGEN COOLING HOLDER, GATAN ULTDT ULTRA LOW TEMPERATURE DOUBLE TILT HELIUM COOLING HOLDER, GATAN ULTST ULTRA LOW TEMPERATURE SINGLE TILT HELIUM COOLING HOLDER, HOME BUILD, JEOL, JEOL 3200FSC CRYOHOLDER, JEOL CRYOSPECPORTER, OTHER, PHILIPS ROTATION HOLDER, SIDE ENTRY, EUCENTRIC
+ * The number of reflections classified as 'observed'
+ * (see _reflns.observed_criterion) for this
+ * shell.
*/
- readonly specimen_holder_model?: Maybe<Scalars['String']>;
+ readonly number_measured_obs?: Maybe<Scalars['Int']>;
/**
- * The type of specimen holder used during imaging.
- *
- * Examples:
- * cryo
+ * The number of unique reflections it is possible to measure in
+ * this shell.
*/
- readonly specimen_holder_type?: Maybe<Scalars['String']>;
- /** Foreign key to the EM_SPECIMEN category */
- readonly specimen_id?: Maybe<Scalars['String']>;
+ readonly number_possible?: Maybe<Scalars['Int']>;
/**
- * The mean specimen stage temperature (degrees Kelvin) during imaging
- * in the microscope.
- *
- * Examples:
- * 70
+ * The total number of measured reflections which are symmetry-
+ * unique after merging for this shell.
*/
- readonly temperature?: Maybe<Scalars['Float']>;
+ readonly number_unique_all?: Maybe<Scalars['Int']>;
/**
- * The maximum angle at which the specimen was tilted to obtain
- * recorded images.
- *
- * Examples:
- * 70
+ * The total number of measured reflections classified as 'observed'
+ * (see _reflns.observed_criterion) which are symmetry-unique
+ * after merging for this shell.
*/
- readonly tilt_angle_max?: Maybe<Scalars['Float']>;
+ readonly number_unique_obs?: Maybe<Scalars['Int']>;
/**
- * The minimum angle at which the specimen was tilted to obtain
- * recorded images.
- *
- * Examples:
- * -70
+ * The Pearson's correlation coefficient expressed as a decimal value
+ * between the average intensities from randomly selected
+ * half-datasets within the resolution shell.
+ *
+ * Ref: Karplus & Diederichs (2012), Science 336, 1030-33
*/
- readonly tilt_angle_min?: Maybe<Scalars['Float']>;
-};
-
-export type PdbxSerialCrystallographyMeasurement = {
+ readonly pdbx_CC_half?: Maybe<Scalars['Float']>;
/**
- * The total number of hours required to measure this data set.
- *
- * Examples:
- * 120.0
+ * R split measures the agreement between the sets of intensities created by merging
+ * odd- and even-numbered images from the data within the resolution shell.
+ *
+ * Ref: T. A. White, R. A. Kirian, A. V. Martin, A. Aquila, K. Nass,
+ * A. Barty and H. N. Chapman (2012), J. Appl. Cryst. 45, 335-341
*/
- readonly collection_time_total?: Maybe<Scalars['Float']>;
+ readonly pdbx_R_split?: Maybe<Scalars['Float']>;
/**
- * The collimation or type of focusing optics applied to the radiation.
- *
- * Examples:
- * Kirkpatrick-Baez mirrors, Beryllium compound refractive lenses, Fresnel zone plates
+ * The precision-indicating merging R factor value Rpim,
+ * for merging all intensities in a given shell.
+ *
+ * sum~i~ [1/(N~i~ - 1)]1/2^ sum~j~ | I~j~ - <I~i~> |
+ * Rpim = --------------------------------------------------
+ * sum~i~ ( sum~j~ I~j~ )
+ *
+ * I~j~ = the intensity of the jth observation of reflection i
+ * <I~i~> = the mean of the intensities of all observations of
+ * reflection i
+ * N~i~ = the redundancy (the number of times reflection i
+ * has been measured).
+ *
+ * sum~i~ is taken over all reflections
+ * sum~j~ is taken over all observations of each reflection.
+ *
+ * Ref: Diederichs, K. & Karplus, P. A. (1997). Nature Struct.
+ * Biol. 4, 269-275.
+ * Weiss, M. S. & Hilgenfeld, R. (1997). J. Appl. Cryst.
+ * 30, 203-205.
+ * Weiss, M. S. (2001). J. Appl. Cryst. 34, 130-135.
*/
- readonly collimation?: Maybe<Scalars['String']>;
+ readonly pdbx_Rpim_I_all?: Maybe<Scalars['Float']>;
/**
- * The data item is a pointer to _diffrn.id in the DIFFRN
- * category.
- *
- * Examples:
- * 1
+ * The redundancy-independent merging R factor value Rrim,
+ * also denoted Rmeas, for merging all intensities in a
+ * given shell.
+ *
+ * sum~i~ [N~i~ /( N~i~ - 1)]1/2^ sum~j~ | I~j~ - <I~i~> |
+ * Rrim = --------------------------------------------------------
+ * sum~i~ ( sum~j~ I~j~ )
+ *
+ * I~j~ = the intensity of the jth observation of reflection i
+ * <I~i~> = the mean of the intensities of all observations of
+ * reflection i
+ * N~i~ = the redundancy (the number of times reflection i
+ * has been measured).
+ *
+ * sum~i~ is taken over all reflections
+ * sum~j~ is taken over all observations of each reflection.
+ *
+ * Ref: Diederichs, K. & Karplus, P. A. (1997). Nature Struct.
+ * Biol. 4, 269-275.
+ * Weiss, M. S. & Hilgenfeld, R. (1997). J. Appl. Cryst.
+ * 30, 203-205.
+ * Weiss, M. S. (2001). J. Appl. Cryst. 34, 130-135.
*/
- readonly diffrn_id: Scalars['String'];
+ readonly pdbx_Rrim_I_all?: Maybe<Scalars['Float']>;
+ /** R sym value in percent. */
+ readonly pdbx_Rsym_value?: Maybe<Scalars['Float']>;
+ /** Chi-squared statistic for this resolution shell. */
+ readonly pdbx_chi_squared?: Maybe<Scalars['Float']>;
/**
- * The focal spot size of the beam
- * impinging on the sample (micrometres squared).
+ * An identifier for the diffraction data set corresponding to this resolution shell.
+ *
+ * Multiple diffraction data sets specified as a comma separated list.
*/
- readonly focal_spot_size?: Maybe<Scalars['Float']>;
- /** The photons per pulse measured in (tera photons (10^(12)^)/pulse units). */
- readonly photons_per_pulse?: Maybe<Scalars['Float']>;
+ readonly pdbx_diffrn_id?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
/**
- * The average duration (femtoseconds)
- * of the pulse energy measured at the sample.
+ * The mean of the ratio of the intensities to their
+ * standard uncertainties of all reflections in the
+ * resolution shell.
+ *
+ * _reflns_shell.pdbx_netI_over_sigmaI_all = <I/sigma(I)>
*/
- readonly pulse_duration?: Maybe<Scalars['Float']>;
- /** The energy/pulse of the X-ray pulse impacting the sample measured in microjoules. */
- readonly pulse_energy?: Maybe<Scalars['Float']>;
- /** The photon energy of the X-ray pulse measured in KeV. */
- readonly pulse_photon_energy?: Maybe<Scalars['Float']>;
- /** The distance from source to the sample along the optical axis (metres). */
- readonly source_distance?: Maybe<Scalars['Float']>;
- /** The dimension of the source beam measured at the source (micrometres squared). */
- readonly source_size?: Maybe<Scalars['Float']>;
- /** For FEL experiments, the pulse repetition rate measured in cycles per seconds. */
- readonly xfel_pulse_repetition_rate?: Maybe<Scalars['Float']>;
-};
-
-export type RcsbBranchedStructConnConnectPartner = {
+ readonly pdbx_netI_over_sigmaI_all?: Maybe<Scalars['Float']>;
/**
- * A component of the identifier for the partner in the structure
- * connection.
- *
- * This data item is a pointer to _atom_site.label_alt_id in the
- * ATOM_SITE category.
+ * The mean of the ratio of the intensities to their
+ * standard uncertainties of observed reflections
+ * (see _reflns.observed_criterion) in the resolution shell.
+ *
+ * _reflns_shell.pdbx_netI_over_sigmaI_obs = <I/sigma(I)>
*/
- readonly label_alt_id?: Maybe<Scalars['String']>;
+ readonly pdbx_netI_over_sigmaI_obs?: Maybe<Scalars['Float']>;
+ /** An ordinal identifier for this resolution shell. */
+ readonly pdbx_ordinal: Scalars['Int'];
+ /** Redundancy for the current shell. */
+ readonly pdbx_redundancy?: Maybe<Scalars['Float']>;
/**
- * A component of the identifier for the partner in the structure
- * connection.
- *
- * This data item is a pointer to _atom_site.label_asym_id in the
- * ATOM_SITE category.
+ * The number of rejected reflections in the resolution
+ * shell. Reflections may be rejected from scaling
+ * by setting the observation criterion,
+ * _reflns.observed_criterion.
*/
- readonly label_asym_id: Scalars['String'];
+ readonly pdbx_rejects?: Maybe<Scalars['Int']>;
/**
- * A component of the identifier for the partner in the structure
- * connection.
- *
- * This data item is a pointer to _chem_comp_atom.atom_id in the
- * CHEM_COMP_ATOM category.
+ * The percentage of geometrically possible reflections represented
+ * by all reflections measured for this shell.
*/
- readonly label_atom_id?: Maybe<Scalars['String']>;
+ readonly percent_possible_all?: Maybe<Scalars['Float']>;
/**
- * A component of the identifier for the partner in the structure
- * connection.
- *
- * This data item is a pointer to _atom_site.label_comp_id in the
- * ATOM_SITE category.
+ * The percentage of geometrically possible reflections represented
+ * by reflections classified as 'observed' (see
+ * _reflns.observed_criterion) for this shell.
*/
- readonly label_comp_id: Scalars['String'];
+ readonly percent_possible_obs?: Maybe<Scalars['Float']>;
+};
+
+export type Software = {
/**
- * A component of the identifier for the partner in the structure
- * connection.
- *
- * This data item is a pointer to _atom_site.label_seq_id in the
- * ATOM_SITE category.
+ * The classification of the program according to its
+ * major function.
+ *
+ * Examples:
+ * data collection, data reduction, phasing, model building, refinement, validation, other
+ *
*/
- readonly label_seq_id?: Maybe<Scalars['Int']>;
- /**
- * Describes the symmetry operation that should be applied to the
- * atom set specified by _rcsb_branched_struct_conn.connect_partner_label* to generate the
- * partner in the structure connection.
- *
+ readonly classification?: Maybe<Scalars['String']>;
+ /**
+ * The recognized contact author of the software. This could be
+ * the original author, someone who has modified the code or
+ * someone who maintains the code. It should be the person
+ * most commonly associated with the code.
+ *
* Examples:
- * 1_555, 7_645
+ * T. Alwyn Jones, Axel Brunger
+ *
*/
- readonly symmetry?: Maybe<Scalars['String']>;
-};
-
-export type RcsbBranchedEntityFeature = {
- /** Identifies the version of the feature assignment. */
- readonly assignment_version?: Maybe<Scalars['String']>;
- /** A description for the feature. */
- readonly description?: Maybe<Scalars['String']>;
- /** An identifier for the feature. */
- readonly feature_id?: Maybe<Scalars['String']>;
- readonly feature_positions?: Maybe<ReadonlyArray<Maybe<RcsbBranchedEntityFeatureFeaturePositions>>>;
- /** A name for the feature. */
- readonly name?: Maybe<Scalars['String']>;
+ readonly contact_author?: Maybe<Scalars['String']>;
/**
- * Code identifying the individual, organization or program that
- * assigned the feature.
+ * The e-mail address of the person specified in
+ * _software.contact_author.
+ *
+ * Examples:
+ * bourne@sdsc.edu
+ *
*/
- readonly provenance_source?: Maybe<Scalars['String']>;
+ readonly contact_author_email?: Maybe<Scalars['String']>;
/**
- * Code residue coordinate system for the assigned feature.
- *
- * Allowable values:
- * PDB entity
+ * The date the software was released.
+ *
+ * Examples:
+ * 1991-10-01, 1990-04-30
+ *
*/
- readonly reference_scheme?: Maybe<Scalars['String']>;
+ readonly date?: Maybe<Scalars['String']>;
/**
- * A type or category of the feature.
- *
- * Allowable values:
- * mutation
+ * Description of the software.
+ *
+ * Examples:
+ * Uses method of restrained least squares
+ *
*/
- readonly type?: Maybe<Scalars['String']>;
-};
-
-export type RcsbRepositoryHoldingsCurrent = {
+ readonly description?: Maybe<Scalars['String']>;
/**
- * The list of content types associated with this entry.
- *
+ * The major computing language in which the software is
+ * coded.
+ *
* Allowable values:
- * 2fo-fc Map, Combined NMR data (NEF), Combined NMR data (NMR-STAR), FASTA sequence, Map Coefficients, NMR chemical shifts, NMR restraints V1, NMR restraints V2, assembly PDB, assembly mmCIF, entry PDB, entry PDB bundle, entry PDBML, entry mmCIF, fo-fc Map, structure factors, validation report
+ * Ada, Awk, Basic, C, C++, C/C++, Fortran, Fortran 77, Fortran 90, Fortran_77, Java, Java & Fortran, Other, Pascal, Perl, Python, Python/C++, Tcl, assembler, csh, ksh, sh
+ *
*/
- readonly repository_content_types?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
-};
-
-
-export type PdbxMoleculeFeatures = {
+ readonly language?: Maybe<Scalars['String']>;
/**
- * Broadly defines the function of the molecule.
- *
- * Allowable values:
- * Antagonist, Anthelmintic, Antibiotic, Antibiotic, Anthelmintic, Antibiotic, Antimicrobial, Antibiotic, Antineoplastic, Anticancer, Anticoagulant, Anticoagulant, Antithrombotic, Antifungal, Antigen, Antiinflammatory, Antimicrobial, Antimicrobial, Antiparasitic, Antibiotic, Antimicrobial, Antiretroviral, Antimicrobial, Antitumor, Antineoplastic, Antiparasitic, Antiretroviral, Antithrombotic, Antitumor, Antiviral, CASPASE inhibitor, Chaperone binding, Drug delivery, Enzyme inhibitor, Glycan component, Growth factor, Immunosuppressant, Inducer, Inhibitor, Lantibiotic, Metabolism, Metal transport, Nutrient, Oxidation-reduction, Protein binding, Receptor, Substrate analog, Synthetic opioid, Thrombin inhibitor, Thrombin inhibitor, Trypsin inhibitor, Toxin, Transition state mimetic, Transport activator, Trypsin inhibitor, Unknown, Water retention
+ * The URL for an Internet address at which
+ * details of the software can be found.
+ *
+ * Examples:
+ * http://rosebud.sdsc.edu/projects/pb/IUCr/software.html, ftp://ftp.sdsc.edu/pub/sdsc/biology/
+ *
*/
- readonly class?: Maybe<Scalars['String']>;
- /** Additional details describing the molecule. */
- readonly details?: Maybe<Scalars['String']>;
+ readonly location?: Maybe<Scalars['String']>;
/**
- * A name of the molecule.
- *
+ * The name of the software.
+ *
* Examples:
- * thiostrepton
+ * Merlot, O, Xengen, X-plor
+ *
*/
readonly name?: Maybe<Scalars['String']>;
/**
- * The value of _pdbx_molecule_features.prd_id is the PDB accession code for this
- * reference molecule.
+ * The name of the operating system under which the software
+ * runs.
+ *
+ * Examples:
+ * Ultrix, OpenVMS, DOS, Windows 95, Windows NT, Irix, HPUX, DEC Unix
+ *
*/
- readonly prd_id: Scalars['String'];
+ readonly os?: Maybe<Scalars['String']>;
+ /** An ordinal index for this category */
+ readonly pdbx_ordinal: Scalars['Int'];
/**
- * Defines the structural classification of the molecule.
- *
+ * The classification of the software according to the most
+ * common types.
+ *
* Allowable values:
- * Amino acid, Aminoglycoside, Ansamycin, Anthracycline, Anthraquinone, Chalkophore, Chalkophore, Polypeptide, Chromophore, Cyclic depsipeptide, Cyclic lipopeptide, Cyclic peptide, Glycopeptide, Heterocyclic, Imino sugar, Keto acid, Lipoglycopeptide, Lipopeptide, Macrolide, Non-polymer, Nucleoside, Oligopeptide, Oligosaccharide, Peptaibol, Peptide-like, Polycyclic, Polypeptide, Polysaccharide, Quinolone, Siderophore, Thiolactone, Thiopeptide, Unknown
+ * filter, jiffy, library, other, package, program
+ *
*/
readonly type?: Maybe<Scalars['String']>;
-};
-
-export type RcsbEntryContainerIdentifiers = {
- /** List of identifiers for assemblies generated from the entry. */
- readonly assembly_ids?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
- /** List of identifiers for the branched entity constituents for the entry. */
- readonly branched_entity_ids?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
- /**
- * List of EMDB identifiers for the 3D electron microscopy density maps
- * used in the production of the structure model.
- */
- readonly emdb_ids?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
- /** List of identifiers or the entity constituents for the entry. */
- readonly entity_ids?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
- /** Entry identifier for the container. */
- readonly entry_id: Scalars['String'];
- /** List of PDB model identifiers for the entry. */
- readonly model_ids?: Maybe<ReadonlyArray<Maybe<Scalars['Int']>>>;
- /** List of identifiers for the non-polymer entity constituents for the entry. */
- readonly non_polymer_entity_ids?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
- /** List of identifiers for the polymer entity constituents for the entry. */
- readonly polymer_entity_ids?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
- /** Unique integer value assigned to each PubMed record. */
- readonly pubmed_id?: Maybe<Scalars['Int']>;
- /** A unique identifier for each object in this entry container. */
- readonly rcsb_id?: Maybe<Scalars['String']>;
/**
- * List of EMDB identifiers for the 3D electron microscopy density maps
- * related to the structure model.
+ * The version of the software.
+ *
+ * Examples:
+ * v1.0, beta, 3.1-2, unknown
+ *
*/
- readonly related_emdb_ids?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
- /** List of identifiers for the solvent/water entity constituents for the entry. */
- readonly water_entity_ids?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
+ readonly version?: Maybe<Scalars['String']>;
};
-export type PdbxSerialCrystallographySampleDeliveryInjection = {
+export type Struct = {
/**
- * For continuous sample flow experiments, the carrier buffer used
- * to move the sample into the beam. Should include protein
- * concentration.
- *
- * Examples:
- * LCP, grease, liquid
+ * The item indicates whether the entry is a CASP target, a CASD-NMR target,
+ * or similar target participating in methods development experiments.
+ *
+ * Allowable values:
+ * N, Y
+ *
*/
- readonly carrier_solvent?: Maybe<Scalars['String']>;
+ readonly pdbx_CASP_flag?: Maybe<Scalars['String']>;
/**
- * For continuous sample flow experiments, the concentration of
- * crystals in the solution being injected.
- *
- * The concentration is measured in million crystals/ml.
+ * An automatically generated descriptor for an NDB structure or
+ * the unstructured content of the PDB COMPND record.
+ *
+ * Examples:
+ * Cytochrome b5, Regulatory protein RecX, Uridine kinase (E.C.2.7.1.48)
+ *
*/
- readonly crystal_concentration?: Maybe<Scalars['Float']>;
+ readonly pdbx_descriptor?: Maybe<Scalars['String']>;
/**
- * For continuous sample flow experiments, a description of the injector used
- * to move the sample into the beam.
- *
+ * Text description of the methodology which produced this
+ * model structure.
+ *
* Examples:
- * microextrusion injector
+ * This model was produced from a 10 nanosecond Amber/MD simulation
+ * starting from PDB structure ID 1ABC.
+ *
*/
- readonly description?: Maybe<Scalars['String']>;
+ readonly pdbx_model_details?: Maybe<Scalars['String']>;
/**
- * The data item is a pointer to _diffrn.id in the DIFFRN
- * category.
- *
+ * A description of the type of structure model.
+ *
* Examples:
- * 1
+ * MINIMIZED AVERAGE
+ *
*/
- readonly diffrn_id: Scalars['String'];
- /** The size of filter in micrometres in filtering crystals */
- readonly filter_size?: Maybe<Scalars['Float']>;
+ readonly pdbx_model_type_details?: Maybe<Scalars['String']>;
/**
- * For continuous sample flow experiments, the flow rate of
- * solution being injected measured in ul/min.
+ * A title for the data block. The author should attempt to convey
+ * the essence of the structure archived in the CIF in the title,
+ * and to distinguish this structural result from others.
+ *
+ * Examples:
+ * T4 lysozyme mutant - S32A, Rhinovirus 16 polymerase elongation complex (r1_form), Crystal structure of the OXA-10 W154A mutant at pH 9.0, Mutant structure of Thermus thermophilus HB8 uridine-cytidine kinase, Crystal structure of xylanase from Trichoderma longibrachiatum
+ *
*/
- readonly flow_rate?: Maybe<Scalars['Float']>;
+ readonly title?: Maybe<Scalars['String']>;
+};
+
+export type StructKeywords = {
/**
- * For continuous sample flow experiments, the diameter of the
- * injector in micrometres.
+ * Terms characterizing the macromolecular structure.
+ *
+ * Examples:
+ * DNA, RNA, T-RNA, DNA/RNA, RIBOZYME, PROTEIN/DNA, PROTEIN/RNA, PEPTIDE NUCLEIC ACID, PEPTIDE NUCLEIC ACID/DNA, DNA-BINDING PROTEIN, RNA-BINDING PROTEIN
+ *
*/
- readonly injector_diameter?: Maybe<Scalars['Float']>;
+ readonly pdbx_keywords?: Maybe<Scalars['String']>;
/**
- * The type of nozzle to deliver and focus sample jet
- *
+ * Keywords describing this structure.
+ *
* Examples:
- * gas, GDVN
+ * Inhibitor, Complex, Isomerase..., serine protease, inhibited complex, high-resolution refinement
+ *
*/
- readonly injector_nozzle?: Maybe<Scalars['String']>;
+ readonly text?: Maybe<Scalars['String']>;
+};
+
+export type Symmetry = {
/**
- * For continuous sample flow experiments, the mean pressure
- * in kilopascals at which the sample is injected into the beam.
+ * Space-group number from International Tables for Crystallography
+ * Vol. A (2002).
*/
- readonly injector_pressure?: Maybe<Scalars['Float']>;
+ readonly Int_Tables_number?: Maybe<Scalars['Int']>;
/**
- * For continuous sample flow experiments, the temperature in
- * Kelvins of the speciman injected. This may be different from
- * the temperature of the sample.
+ * The cell settings for this space-group symmetry.
+ *
+ * Allowable values:
+ * cubic, hexagonal, monoclinic, orthorhombic, rhombohedral, tetragonal, triclinic, trigonal
+ *
*/
- readonly injector_temperature?: Maybe<Scalars['Float']>;
- /** Diameter in micrometres of jet stream of sample delivery */
- readonly jet_diameter?: Maybe<Scalars['Float']>;
+ readonly cell_setting?: Maybe<Scalars['String']>;
/**
- * Sample deliver driving force, e.g. Gas, Electronic Potential
- *
+ * Used for PDB space group:
+ *
+ * Example: 'C 1 2 1' (instead of C 2)
+ * 'P 1 2 1' (instead of P 2)
+ * 'P 1 21 1' (instead of P 21)
+ * 'P 1 1 21' (instead of P 21 -unique C axis)
+ * 'H 3' (instead of R 3 -hexagonal)
+ * 'H 3 2' (instead of R 3 2 -hexagonal)
+ *
* Examples:
- * syringe, gas, electronic potential
+ * Example: 'C 1 2 1' (instead of C 2)
+ * 'P 1 2 1' (instead of P 2)
+ * 'P 1 21 1' (instead of P 21)
+ * 'P 1 1 21' (instead of P 21 -unique C axis)
+ * 'H 3' (instead of R 3 -hexagonal)
+ * 'H 3 2' (instead of R 3 2 -hexagonal)
+ *
*/
- readonly power_by?: Maybe<Scalars['String']>;
+ readonly pdbx_full_space_group_name_H_M?: Maybe<Scalars['String']>;
/**
- * Details of crystal growth and preparation of the crystals
- *
+ * Hermann-Mauguin space-group symbol. Note that the
+ * Hermann-Mauguin symbol does not necessarily contain complete
+ * information about the symmetry and the space-group origin. If
+ * used, always supply the FULL symbol from International Tables
+ * for Crystallography Vol. A (2002) and indicate the origin and
+ * the setting if it is not implicit. If there is any doubt that
+ * the equivalent positions can be uniquely deduced from this
+ * symbol, specify the _symmetry_equiv.pos_as_xyz or
+ * _symmetry.space_group_name_Hall data items as well. Leave
+ * spaces between symbols referring to
+ * different axes.
+ *
* Examples:
- * Crystals transfered to carrier solvent at room temperature
+ * A 1, A 1 2 1, A 2, B 1 1 2, B 2, B 2 21 2, C 2, C 1 2 1, C 21, C 1 21 1, C 2(A 112), C 2 2 2, C 2 2 21, C 4 21 2, F 2 2 2, F 2 3, F 4 2 2, F 4 3 2, F 41 3 2, I 1 2 1, I 1 21 1, I 2, I 2 2 2, I 2 3, I 21, I 21 3, I 21 21 21, I 4, I 4 2 2, I 4 3 2, I 41, I 41/a, I 41 2 2, I 41 3 2, P 1, P 1-, P 2, P 1 2 1, P 1 1 2, P 2 2 2, P 2 3, P 2 2 21, P 2 21 21, P 21, P 1 21 1, P 1 21/c 1, P 1 1 21, P 21(C), P 21 2 21, P 21 3, P 21 21 2, P 21 21 2 A, P 21 21 21, P 3, P 3 1 2, P 3 2 1, P 31, P 31 1 2, P 31 2 1, P 32, P 32 1 2, P 32 2 1, P 4, P 4 2 2, P 4 3 2, P 4 21 2, P 41, P 41 2 2, P 41 3 2, P 41 21 2, P 42, P 42 2 2, P 42 3 2, P 42 21 2, P 43, P 43 2 2, P 43 3 2, P 43 21 2, P 6, P 6 2 2, P 61, P 61 2 2, P 62, P 62 2 2, P 63, P 63 2 2, P 64, P 64 2 2, P 65, P 65 2 2, H 3, R 3, H 3 2, R 3 2
+ *
*/
- readonly preparation?: Maybe<Scalars['String']>;
-};
-
-export type RcsbPolymerInstanceFeatureFeaturePositions = {
- /** An identifier for the monomer(s) corresponding to the feature assignment. */
- readonly beg_comp_id?: Maybe<Scalars['String']>;
- /** An identifier for the monomer at which this segment of the feature begins. */
- readonly beg_seq_id: Scalars['Int'];
- /** An identifier for the monomer at which this segment of the feature ends. */
- readonly end_seq_id?: Maybe<Scalars['Int']>;
- /** The value of the feature over the monomer segment. */
- readonly value?: Maybe<Scalars['Float']>;
+ readonly space_group_name_H_M?: Maybe<Scalars['String']>;
+ /**
+ * Space-group symbol as described by Hall (1981). This symbol
+ * gives the space-group setting explicitly. Leave spaces between
+ * the separate components of the symbol.
+ *
+ * Ref: Hall, S. R. (1981). Acta Cryst. A37, 517-525; erratum
+ * (1981) A37, 921.
+ *
+ * Examples:
+ * -P 2ac 2n, -R 3 2", P 61 2 2 (0 0 -1)
+ *
+ */
+ readonly space_group_name_Hall?: Maybe<Scalars['String']>;
};
export type AssemblySymmetryQueryVariables = Exact<{
@@ -11340,10 +13144,4 @@ export type AssemblySymmetryQueryVariables = Exact<{
}>;
-export type AssemblySymmetryQuery = { readonly assembly?: Maybe<{ readonly rcsb_struct_symmetry?: Maybe<ReadonlyArray<Maybe<(
- Pick<RcsbStructSymmetry, 'kind' | 'oligomeric_state' | 'stoichiometry' | 'symbol' | 'type'>
- & { readonly clusters: ReadonlyArray<Maybe<(
- Pick<RcsbStructSymmetryClusters, 'avg_rmsd'>
- & { readonly members: ReadonlyArray<Maybe<Pick<ClustersMembers, 'asym_id' | 'pdbx_struct_oper_list_ids'>>> }
- )>>, readonly rotation_axes?: Maybe<ReadonlyArray<Maybe<Pick<RcsbStructSymmetryRotationAxes, 'order' | 'start' | 'end'>>>> }
- )>>> }> };
+export type AssemblySymmetryQuery = { readonly assembly?: Maybe<{ readonly rcsb_struct_symmetry?: Maybe<ReadonlyArray<Maybe<{ readonly kind: string, readonly oligomeric_state: string, readonly stoichiometry: ReadonlyArray<Maybe<string>>, readonly symbol: string, readonly type: string, readonly clusters: ReadonlyArray<Maybe<{ readonly avg_rmsd?: Maybe<number>, readonly members: ReadonlyArray<Maybe<{ readonly asym_id: string, readonly pdbx_struct_oper_list_ids?: Maybe<ReadonlyArray<Maybe<string>>> }>> }>>, readonly rotation_axes?: Maybe<ReadonlyArray<Maybe<{ readonly order?: Maybe<number>, readonly start: ReadonlyArray<Maybe<number>>, readonly end: ReadonlyArray<Maybe<number>> }>>> }>>> }> };