diff --git a/src/extensions/rcsb/graphql/types.ts b/src/extensions/rcsb/graphql/types.ts
index d18c006bc99fff7aa846790cbe82ef0be76a1e60..c0efb6f1fbc0fb79e0b6c5059c6759f4ee5ffcf4 100644
--- a/src/extensions/rcsb/graphql/types.ts
+++ b/src/extensions/rcsb/graphql/types.ts
@@ -1,7 +1,7 @@
/* eslint-disable */
export type Maybe<T> = T | null;
-
-// Generated in 2020-05-27T17:35:45-07:00
+export type Exact<T extends { [key: string]: unknown }> = { [K in keyof T]: T[K] };
+// Generated on 2020-09-13T02:52:22-07:00
/** All built-in and custom scalars, mapped to their actual values */
export type Scalars = {
@@ -120,32 +120,40 @@ export type PdbxChemCompAudit = {
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 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 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 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 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 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 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 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 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>;
};
@@ -159,82 +167,108 @@ export type QueryPolymer_Entity_InstanceArgs = {
/** Query root */
-export type QueryAssembliesArgs = {
- assembly_ids: ReadonlyArray<Maybe<Scalars['String']>>;
+export type QueryNonpolymer_EntitiesArgs = {
+ entity_ids: ReadonlyArray<Scalars['String']>;
};
/** Query root */
-export type QueryNonpolymer_EntitiesArgs = {
+export type QueryPolymer_EntitiesArgs = {
entity_ids: ReadonlyArray<Scalars['String']>;
};
/** Query root */
-export type QueryNonpolymer_Entity_InstanceArgs = {
- asym_id: Scalars['String'];
+export type QueryPolymer_EntityArgs = {
+ entity_id: Scalars['String'];
entry_id: Scalars['String'];
};
/** Query root */
-export type QueryPolymer_EntitiesArgs = {
- entity_ids: ReadonlyArray<Scalars['String']>;
+export type QueryPubmedArgs = {
+ pubmed_id: Scalars['Int'];
};
/** Query root */
-export type QueryPolymer_EntityArgs = {
- entity_id: Scalars['String'];
+export type QueryAssemblyArgs = {
+ assembly_id: Scalars['String'];
entry_id: Scalars['String'];
};
/** Query root */
-export type QueryChem_CompArgs = {
- comp_id: Scalars['String'];
+export type QueryBranched_Entity_InstancesArgs = {
+ instance_ids: ReadonlyArray<Maybe<Scalars['String']>>;
};
/** Query root */
-export type QueryEntryArgs = {
+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 QueryEntriesArgs = {
- entry_ids: ReadonlyArray<Scalars['String']>;
+export type QueryBranched_Entity_InstanceArgs = {
+ asym_id: Scalars['String'];
+ entry_id: Scalars['String'];
};
/** Query root */
-export type QueryPubmedArgs = {
- pubmed_id: Scalars['Int'];
+export type QueryNonpolymer_Entity_InstanceArgs = {
+ asym_id: Scalars['String'];
+ entry_id: Scalars['String'];
};
/** Query root */
-export type QueryAssemblyArgs = {
- assembly_id: Scalars['String'];
+export type QueryChem_CompArgs = {
+ comp_id: Scalars['String'];
+};
+
+
+/** Query root */
+export type QueryEntryArgs = {
entry_id: Scalars['String'];
};
/** Query root */
-export type QueryUniprotArgs = {
- uniprot_id: Scalars['String'];
+export type QueryEntriesArgs = {
+ entry_ids: ReadonlyArray<Scalars['String']>;
};
/** Query root */
-export type QueryNonpolymer_Entity_InstancesArgs = {
- instance_ids: ReadonlyArray<Maybe<Scalars['String']>>;
+export type QueryBranched_EntitiesArgs = {
+ entity_ids: ReadonlyArray<Scalars['String']>;
};
/** Query root */
-export type QueryPolymer_Entity_InstancesArgs = {
+export type QueryUniprotArgs = {
+ uniprot_id: Scalars['String'];
+};
+
+
+/** Query root */
+export type QueryNonpolymer_Entity_InstancesArgs = {
instance_ids: ReadonlyArray<Maybe<Scalars['String']>>;
};
@@ -601,7 +635,7 @@ export type RcsbChemCompRelated = {
* The method used to establish the resource correspondence.
*
* Allowable values:
- * assigned by DrugBank resource, assigned by PDB, matching InChIKey in DrugBank, matching InChIKey-prefix in DrugBank, matching by RESID resource
+ * 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']>;
/**
@@ -615,7 +649,7 @@ export type RcsbChemCompRelated = {
* The resource name for the related chemical reference.
*
* Allowable values:
- * CAS, CCDC/CSD, ChEBI, ChEMBL, DrugBank, PubChem, RESID
+ * CAS, CCDC/CSD, ChEBI, ChEMBL, DrugBank, Pharos, PubChem, RESID
*/
readonly resource_name?: Maybe<Scalars['String']>;
};
@@ -699,6 +733,15 @@ export type PdbxAuditRevisionHistory = {
readonly revision_date?: Maybe<Scalars['Date']>;
};
+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 DiffrnSource = {
/** A description of special aspects of the radiation source used. */
readonly details?: Maybe<Scalars['String']>;
@@ -849,6 +892,14 @@ export type RcsbPolymerEntityInstanceContainerIdentifiers = {
readonly asym_id: Scalars['String'];
/** Author instance identifier for this container. */
readonly auth_asym_id?: 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.
+ */
+ 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. */
@@ -860,6 +911,43 @@ export type RcsbPolymerEntityInstanceContainerIdentifiers = {
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']>;
+ /**
+ * Code identifying the individual, organization or program that
+ * assigned the annotation.
+ */
+ 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 = {
/**
* Any additional details about CTF correction
@@ -1256,11 +1344,11 @@ export type RcsbUniprotAlignments = {
};
export type CoreNonpolymerEntity = {
- /** Get PDB entry that contains this molecular entity. */
+ /** 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 molecular entity. */
+ /** 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. */
@@ -1330,8 +1418,13 @@ export type RcsbPolymerEntity = {
* N, Y
*/
readonly rcsb_multiple_source_flag?: Maybe<Scalars['String']>;
- /** The number of biological sources for the polymer entity. */
+ /**
+ * The number of biological sources for the polymer entity. Multiple source contributions
+ * may come from the same organism (taxonomy).
+ */
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']>;
/**
* The method by which the sample for the polymer entity was produced.
* Entities isolated directly from natural sources (tissues, soil
@@ -1394,9 +1487,16 @@ export type RcsbChemCompSynonyms = {
* The provenance of this synonym.
*
* Allowable values:
- * ACDLabs, Author, ChEBI, ChEMBL, DrugBank, GMML, Lexichem, OpenEye OEToolkits, OpenEye/Lexichem, PDB Reference Data, PDB-CARE, PubChem, RESID
+ * ACDLabs, Author, ChEBI, ChEMBL, DrugBank, GMML, Lexichem, OpenEye OEToolkits, OpenEye/Lexichem, PDB Reference Data, PDB Reference Data (Preferred), PDB-CARE, PubChem, RESID
*/
readonly provenance_source?: 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
+ */
+ readonly type?: Maybe<Scalars['String']>;
};
export type PdbxDepositGroup = {
@@ -1739,9 +1839,9 @@ export type RcsbPolymerEntityRcsbEcLineage = {
export type RcsbAssemblyInfo = {
/** Entity identifier for the container. */
readonly assembly_id?: Maybe<Scalars['String']>;
- /** The assembly atomic coordinate count. */
+ /** The assembly non-hydrogen atomic coordinate count. */
readonly atom_count?: Maybe<Scalars['Int']>;
- /** The assembly branched entity atomic coordinate count. */
+ /** 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']>;
@@ -1765,7 +1865,7 @@ export type RcsbAssemblyInfo = {
* DNA (only), DNA/RNA (only), NA-hybrid (only), Other, RNA (only)
*/
readonly na_polymer_entity_types?: Maybe<Scalars['String']>;
- /** The assembly non-polymer entity atomic coordinate count. */
+ /** 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']>;
@@ -1774,7 +1874,7 @@ export type RcsbAssemblyInfo = {
* 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 polymer entity atomic coordinate count. */
+ /** 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.
@@ -1838,7 +1938,7 @@ export type RcsbAssemblyInfo = {
* Nucleic acid (only), Other, Protein (only), Protein/NA
*/
readonly selected_polymer_entity_types?: Maybe<Scalars['String']>;
- /** The assembly solvent atomic coordinate count. */
+ /** 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']>;
@@ -1889,8 +1989,8 @@ export type RcsbBindingAffinity = {
/**
* 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.
*
- * Examples:
- * IC50, EC50, Kd, Ka, Ki
+ * Allowable values:
+ * IC50, EC50, Kd, Ka, Ki, ΔG, ΔH, -TΔS
*/
readonly type: Scalars['String'];
/**
@@ -1904,6 +2004,28 @@ export type RcsbBindingAffinity = {
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']>;
+ /**
+ * Type or category of the feature.
+ *
+ * Allowable values:
+ * mutation
+ */
+ readonly type?: Maybe<Scalars['String']>;
+};
+
export type EmEntityAssembly = {
/**
* Additional details about the component.
@@ -2023,7 +2145,7 @@ export type RcsbChemCompAnnotation = {
* A type or category of the annotation.
*
* Allowable values:
- * ATC, Generating Enzyme, Modification Type, PSI-MOD
+ * ATC, Carbohydrate Anomer, Carbohydrate Isomer, Carbohydrate Primary Carbonyl Group, Carbohydrate Ring, Generating Enzyme, Modification Type, PSI-MOD
*/
readonly type?: Maybe<Scalars['String']>;
};
@@ -2100,6 +2222,39 @@ export type ExptlCrystalGrow = {
readonly temp_details?: 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>>>;
+ /**
+ * A unique identifier for each object in this entity instance container formed by
+ * an 'dot' (.) separated concatenation of entry and entity instance identifiers.
+ */
+ 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']>;
+ /**
+ * The number of molecules of the branched entity in the entry.
+ *
+ * Examples:
+ * 1, 2, 3
+ */
+ 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']>;
@@ -2215,6 +2370,8 @@ 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>>>;
@@ -2583,9 +2740,14 @@ export type RcsbPolymerEntityNameCom = {
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['String'];
+ 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 */
@@ -2631,6 +2793,8 @@ export type RcsbEntryInfo = {
* per deposited structure model.
*/
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 unmodeled polymer monomers in the deposited coordinate data. This is
* the total count of monomers with unreported coordinate data for all polymer
@@ -2641,6 +2805,7 @@ export type RcsbEntryInfo = {
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. */
@@ -2704,7 +2869,7 @@ export type RcsbEntryInfo = {
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. */
+ /** Combined estimates of experimental resolution contributing to the refined structural model. */
readonly resolution_combined?: Maybe<ReadonlyArray<Maybe<Scalars['Float']>>>;
/**
* Selected polymer entity type categories describing the entry.
@@ -2737,8 +2902,8 @@ export type PdbxChemCompFeature = {
/**
* The component feature type.
*
- * Examples:
- * FUNCTION, ENZYME INHIBITED, STRUCTURE IMAGE URL, CARBOHYDRATE ANOMER, CARBOHYDRATE ISOMER, CARBOHYDRATE RING
+ * Allowable values:
+ * CARBOHYDRATE ANOMER, CARBOHYDRATE ISOMER, CARBOHYDRATE PRIMARY CARBONYL GROUP, CARBOHYDRATE RING
*/
readonly type: Scalars['String'];
/** The component feature value. */
@@ -2794,6 +2959,74 @@ export type RcsbMembraneLineage = {
readonly name?: Maybe<Scalars['String']>;
};
+export type RcsbBranchedStructConnConnectTarget = {
+ /**
+ * 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 auth_asym_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_seq_id in the
+ * ATOM_SITE category.
+ */
+ readonly auth_seq_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.label_alt_id in the
+ * ATOM_SITE category.
+ */
+ readonly label_alt_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.label_asym_id in the
+ * ATOM_SITE category.
+ */
+ readonly label_asym_id: 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.
+ */
+ readonly label_atom_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.label_comp_id in the
+ * ATOM_SITE category.
+ */
+ readonly label_comp_id: 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.
+ */
+ 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.label* to generate the
+ * target of the structure connection.
+ *
+ * Examples:
+ * 1_555, 7_645
+ */
+ readonly symmetry?: Maybe<Scalars['String']>;
+};
+
export type PdbxNmrRefine = {
/**
* Additional details about the NMR refinement.
@@ -3222,6 +3455,40 @@ export type RefineAnalyze = {
readonly pdbx_refine_id: 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'];
+ /**
+ * Code identifying the individual, organization or program that
+ * assigned the feature.
+ */
+ 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, 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
+ */
+ 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']>;
@@ -3312,6 +3579,34 @@ export type PdbxDatabaseStatus = {
readonly status_code_sf?: Maybe<Scalars['String']>;
};
+export type PdbxEntityBranchDescriptor = {
+ /**
+ * 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']>;
+ /**
+ * This data item contains the version of the program
+ * or library used to compute the descriptor.
+ */
+ 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']>;
@@ -3464,6 +3759,33 @@ export type RcsbNonpolymerStructConnConnectTarget = {
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>>>;
+ /**
+ * A unique identifier for each object in this entity container formed by
+ * an underscore separated concatenation of entry and entity identifiers.
+ */
+ 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']>;
@@ -3492,6 +3814,17 @@ export type Em3dCrystalEntity = {
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']>;
+};
+
export type GeneName = {
/**
* Allowable values:
@@ -4084,6 +4417,16 @@ export type RcsbUniprotKeyword = {
readonly value?: Maybe<Scalars['String']>;
};
+export type RcsbBranchedEntityNameCom = {
+ /**
+ * A common name for the branched entity.
+ *
+ * Examples:
+ * HIV protease monomer, hemoglobin alpha chain
+ */
+ readonly name?: Maybe<Scalars['String']>;
+};
+
export type RcsbGenomicLineage = {
/** Classification hierarchy depth. */
readonly depth?: Maybe<Scalars['Int']>;
@@ -4124,22 +4467,50 @@ export type DiffrnDetector = {
* Examples:
* 1996-12-25
*/
- 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 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'];
+};
+
+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'];
+ /**
+ * 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:
+ * CATH, SCOP
+ */
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'];
-};
-
export type CorePfam = {
/** Accession number of Pfam entry. */
readonly rcsb_id: Scalars['String'];
@@ -4312,6 +4683,15 @@ export type RcsbBirdCitation = {
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']>;
@@ -5813,6 +6193,44 @@ export type PdbxChemCompIdentifier = {
readonly type: Scalars['String'];
};
+export type RcsbBranchedStructConn = {
+ readonly connect_partner?: Maybe<RcsbBranchedStructConnConnectPartner>;
+ readonly connect_target?: Maybe<RcsbBranchedStructConnConnectTarget>;
+ /**
+ * 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. */
+ 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 RcsbPolymerInstanceFeature = {
/** Identifies the version of the feature assignment. */
readonly assignment_version?: Maybe<Scalars['String']>;
@@ -6724,8 +7142,7 @@ export type PdbxVrptSummary = {
readonly Babinet_b?: Maybe<Scalars['Float']>;
/**
* 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.
+ * Example: X-ray entry specific, obtained in the eds step from REFMAC calculation.
*/
readonly Babinet_k?: Maybe<Scalars['Float']>;
/**
@@ -6766,21 +7183,29 @@ export type PdbxVrptSummary = {
*/
readonly EDS_resolution_low?: Maybe<Scalars['Float']>;
/**
- * Fo,Fc correlation: The difference between the observed structure factors (Fo) and the
+ * 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 EMDB_deposition_date?: Maybe<Scalars['Date']>;
+ /** Either a decimal number or the string "NotAvailable". */
+ readonly EMDB_resolution?: Maybe<Scalars['Float']>;
+ /**
+ * 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.
+ * experimental data.
* Example: X-ray entry specific, obtained in the eds step from REFMAC calculation.
*/
readonly Fo_Fc_correlation?: Maybe<Scalars['Float']>;
/**
- * Each reflection has an intensity (I) and an uncertainty in measurement
+ * 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.
+ * estimate before calculating the metric.
* Example X-ray entry specific, calculated by Phenix Xtriage program.
*/
readonly I_over_sigma?: Maybe<Scalars['String']>;
@@ -6790,8 +7215,8 @@ export type PdbxVrptSummary = {
readonly PDB_Rfree?: Maybe<Scalars['Float']>;
/**
* 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 depositon process should not have this item.
+ * 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 PDB_deposition_date?: Maybe<Scalars['Date']>;
@@ -6819,105 +7244,131 @@ export type PdbxVrptSummary = {
*/
readonly RNA_suiteness?: Maybe<Scalars['Float']>;
/**
- * Result of absolute likelihood based Wilson scaling,
- * The anisotropic B value of the data is determined using a likelihood based approach.
+ * 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.
+ * A large spread in (especially the diagonal) values indicates anisotropy.
+ * Example: X-ray entry specific, calculated by Phenix Xtriage program.
*/
readonly Wilson_B_aniso?: Maybe<Scalars['String']>;
/**
- * An estimate of the overall B-value of the structure, calculated from the diffraction data.
+ * 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
+ * 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 Wilson_B_estimate?: 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
+ * 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 absolute_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
+ * 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 absolute_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
+ * 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 absolute_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
+ * 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 absolute_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
+ * 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 absolute_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
+ * 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 absolute_percentile_percent_rotamer_outliers?: Maybe<Scalars['Float']>;
/**
- * The number of acentric reflections that Xtriage identifies as outliers on the basis
- * of Wilson statistics. Note that if pseudo translational symmetry is present,
+ * 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 acentric_outliers?: Maybe<Scalars['Int']>;
/**
- * The overall root mean square of the Z-score for deviations of bond angles in comparison to
+ * 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.
+ * 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 overall root mean square of the Z-score for deviations of bond lengths in comparison to
+ /** 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']>;
+ /**
+ * 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
+ * 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.
+ * 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
+ * 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 0.143. */
+ 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']>;
/**
* The version of CCP4 suite pdbx_vrpt_sotfware_notused used in the analysis.
* Example: X-ray entry specific, obtained from the eds step.
@@ -6929,12 +7380,12 @@ export type PdbxVrptSummary = {
*/
readonly centric_outliers?: Maybe<Scalars['Float']>;
/**
- * Overall completeness of the chemical shift assignments for the well-defined
+ * 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
+ * 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).
*/
@@ -6945,21 +7396,23 @@ export type PdbxVrptSummary = {
*/
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.
+ * 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
+ * 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
+ * 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']>;
@@ -6968,8 +7421,8 @@ export type PdbxVrptSummary = {
/** 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.
+ * 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.
*/
@@ -6977,17 +7430,22 @@ export type PdbxVrptSummary = {
/** A percentage, Normally percent proportion of the total number. Between 0% and 100%. */
readonly data_completeness?: Maybe<Scalars['Float']>;
/**
- * 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
+ * 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
+ * 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.
@@ -6995,35 +7453,35 @@ export type PdbxVrptSummary = {
*/
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
+ * 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
+ * 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
+ * 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
+ * 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.
@@ -7037,17 +7495,17 @@ export type PdbxVrptSummary = {
*/
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
+ * 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
+ * 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.
@@ -7055,49 +7513,49 @@ export type PdbxVrptSummary = {
*/
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
+ * 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
+ * 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
+ * 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
+ * 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 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
+ * 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']>;
@@ -7131,7 +7589,7 @@ export type PdbxVrptSummary = {
*/
readonly no_ligands_for_mogul?: Maybe<Scalars['String']>;
/**
- * Will be set to "true" if no property was found to do percentile analysis on.
+ * 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']>;
@@ -7141,34 +7599,33 @@ export type PdbxVrptSummary = {
*/
readonly num_H_reduce?: Maybe<Scalars['Float']>;
/**
- * The number of PDB depositions used in the comparison when calculating the attribute
+ * 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.
+ * 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
+ * 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
+ * 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
+ * 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_ramachandran_outliers"
+ * 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']>;
@@ -7179,39 +7636,38 @@ export type PdbxVrptSummary = {
*/
readonly num_PDBids_absolute_percentile_percent_rotamer_outliers?: Maybe<Scalars['Int']>;
/**
- * The number of PDB depositions used in the comparison when calculating the attribute
+ * 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.
+ * 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
+ * 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
+ * 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
+ * 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
+ * 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
+ * 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.
*/
@@ -7229,7 +7685,7 @@ export type PdbxVrptSummary = {
*/
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.
+ * 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']>;
@@ -7256,8 +7712,8 @@ export type PdbxVrptSummary = {
/**
* 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
+ * 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.
@@ -7268,7 +7724,7 @@ export type PdbxVrptSummary = {
* 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.
+ * Normally the entity.id's are integer numbers but not necessarily so.
* Example
*/
readonly protein_DNA_RNA_entities?: Maybe<Scalars['String']>;
@@ -7280,77 +7736,77 @@ export type PdbxVrptSummary = {
*/
readonly reflections_input_filename?: Maybe<Scalars['String']>;
/**
- * Version of the REFMAC pdbx_vrpt_software used in the EDS step.
+ * 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
+ * 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
+ * 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
+ * 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
+ * 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
+ * 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
+ * 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 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
+ * 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
+ * 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
+ * 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
+ * Version of the software for chemical shift outlier detection - currently
* same as revision number of the validation pipeline.
*/
readonly shiftchecker_version?: Maybe<Scalars['String']>;
@@ -7361,20 +7817,20 @@ export type PdbxVrptSummary = {
*/
readonly trans_NSC?: Maybe<Scalars['String']>;
/**
- * Padilla and Yeates twinning parameter <|L|>.
+ * 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|>.
+ * 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
+ * list of operators with fractions is givens
* Example: X-ray entry specific, obtained from the Xtriage program.
*/
readonly twin_fraction?: Maybe<Scalars['String']>;
@@ -7438,7 +7894,7 @@ export type RcsbPolymerStructConn = {
* The chemical or structural role of the interaction
*
* Allowable values:
- * C-Mannosylation, N-Glycosylation, O-Glycosylation
+ * C-Mannosylation, N-Glycosylation, O-Glycosylation, S-Glycosylation
*/
readonly role?: Maybe<Scalars['String']>;
/**
@@ -7549,6 +8005,26 @@ export type PdbxStructAssembly = {
readonly rcsb_details?: 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']>>>;
+ /** 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']>;
+ /**
+ * A unique identifier for each object in this entity container formed by
+ * an underscore separated concatenation of entry and entity identifiers.
+ */
+ readonly rcsb_id?: Maybe<Scalars['String']>;
+};
+
export type RcsbRepositoryHoldingsCurrentEntryContainerIdentifiers = {
/** The assembly id codes. */
readonly assembly_ids?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
@@ -7721,7 +8197,7 @@ export type ChemComp = {
* 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 1,4 and 1,4 linking, D-saccharide 1,4 and 1,6 linking, 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 1,4 and 1,4 linking, L-saccharide 1,4 and 1,6 linking, 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
+ * 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']>;
};
@@ -7755,7 +8231,7 @@ export type PdbxReferenceEntityPoly = {
* The type of the polymer.
*
* Allowable values:
- * nucleic-acid-like, peptide-like, polysaccharide-like
+ * nucleic-acid-like, oligosaccharide, peptide-like, polysaccharide-like
*/
readonly type?: Maybe<Scalars['String']>;
};
@@ -7776,13 +8252,23 @@ export type RcsbStructSymmetry = {
* Global Symmetry, Pseudo Symmetry, Local Symmetry
*/
readonly kind: Scalars['String'];
- /** 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'. */
+ /**
+ * 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. */
+ /**
+ * 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.
@@ -8129,9 +8615,9 @@ export type PdbxReferenceMolecule = {
* Broadly defines the function of the entity.
*
* Allowable values:
- * Antagonist, Anthelmintic, Antibiotic, Anticancer, Anticoagulant, Antifungal, Antiinflammatory, Antimicrobial, Antineoplastic, Antiparasitic, Antiretroviral, Antithrombotic, Antitumor, Antiviral, CASPASE inhibitor, Chaperone binding, Enzyme inhibitor, Growth factor, Immunosuppressant, Inhibitor, Lantibiotic, Metabolism, Metal transport, Oxidation-reduction, RNA synthesis Inhibitor, Receptor, Synthetic opioid, Thrombin inhibitor, Toxin, Transition state mimetic, Transport activator, Trypsin inhibitor, Unknown
+ * 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 class?: Maybe<ReadonlyArray<Maybe<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. */
@@ -8208,9 +8694,9 @@ export type PdbxReferenceMolecule = {
* 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, Tricyclic pentaglycosidic antineoplastic antibiotic, Unknown
+ * 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<ReadonlyArray<Maybe<Scalars['String']>>>;
+ readonly type?: Maybe<Scalars['String']>;
/** Evidence for the assignment of _pdbx_reference_molecule.type */
readonly type_evidence_code?: Maybe<Scalars['String']>;
};
@@ -8695,13 +9181,35 @@ export type PdbxStructAssemblyAuthEvidence = {
* Provides the experimental method to determine the state of this assembly
*
* Allowable values:
- * 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
+ * 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
*/
readonly experimental_support?: Maybe<Scalars['String']>;
/** Identifies a unique record in pdbx_struct_assembly_auth_evidence. */
readonly id: Scalars['String'];
};
+export type RcsbBranchedInstanceFeatureSummary = {
+ /** 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']>;
+ /**
+ * 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
+ */
+ readonly type?: Maybe<Scalars['String']>;
+};
+
export type RcsbNonpolymerInstanceAnnotation = {
/** An identifier for the annotation. */
readonly annotation_id?: Maybe<Scalars['String']>;
@@ -8861,7 +9369,7 @@ export type RcsbNonpolymerStructConn = {
* The chemical or structural role of the interaction
*
* Allowable values:
- * C-Mannosylation, N-Glycosylation, O-Glycosylation
+ * C-Mannosylation, N-Glycosylation, O-Glycosylation, S-Glycosylation
*/
readonly role?: Maybe<Scalars['String']>;
/**
@@ -9055,6 +9563,18 @@ export type RcsbClusterFlexibility = {
readonly provenance_code?: Maybe<Scalars['String']>;
};
+export type RcsbEntryInfoDiffrnResolutionHigh = {
+ /**
+ * 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 provenance_source?: Maybe<Scalars['String']>;
+ /** The high resolution limit of data collection. */
+ readonly value?: Maybe<Scalars['Float']>;
+};
+
export type RcsbNonpolymerEntityContainerIdentifiers = {
/** Instance identifiers corresponding to copies of the entity in this container. */
readonly asym_ids?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
@@ -9145,7 +9665,7 @@ export type PdbxAuditRevisionDetails = {
* A type classification of the revision
*
* Allowable values:
- * Coordinate replacement, Initial release, Obsolete
+ * Coordinate replacement, Initial release, Obsolete, Remediation
*/
readonly type?: Maybe<Scalars['String']>;
};
@@ -9231,6 +9751,26 @@ export type Struct = {
readonly title?: Maybe<Scalars['String']>;
};
+export type RcsbBranchedInstanceFeatureFeatureValue = {
+ /** 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']>;
+ /**
+ * The type of estimated uncertainty for the reported feature value.
+ *
+ * Allowable values:
+ * Z-Score
+ */
+ readonly uncertainty_estimate_type?: Maybe<Scalars['String']>;
+};
+
export type RcsbNonpolymerStructConnConnectPartner = {
/**
* A component of the identifier for the partner in the structure
@@ -9488,6 +10028,22 @@ export type RcsbNonpolymerEntity = {
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'];
+ /**
+ * A unique identifier for each object in this entity instance container formed by
+ * an 'dot' (.) separated concatenation of entry and entity instance identifiers.
+ */
+ readonly rcsb_id?: Maybe<Scalars['String']>;
+};
+
export type EntitySrcGen = {
/**
* A unique identifier for the expression system. This
@@ -10000,6 +10556,18 @@ export type EmSoftware = {
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']>;
+ /**
+ * The type of this branched oligosaccharide.
+ *
+ * Allowable values:
+ * oligosaccharide
+ */
+ readonly type?: Maybe<Scalars['String']>;
+};
+
export type RcsbAccessionInfo = {
/** The entry deposition date. */
readonly deposit_date?: Maybe<Scalars['Date']>;
@@ -10516,6 +11084,89 @@ export type PdbxSerialCrystallographyMeasurement = {
readonly xfel_pulse_repetition_rate?: Maybe<Scalars['Float']>;
};
+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 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_branched_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 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']>;
+ /**
+ * Code identifying the individual, organization or program that
+ * assigned the feature.
+ */
+ readonly provenance_source?: Maybe<Scalars['String']>;
+ /**
+ * Code residue coordinate system for the assigned feature.
+ *
+ * Allowable values:
+ * 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 RcsbRepositoryHoldingsCurrent = {
/**
* The list of content types associated with this entry.
@@ -10532,7 +11183,7 @@ export type PdbxMoleculeFeatures = {
* Broadly defines the function of the molecule.
*
* Allowable values:
- * Antagonist, Anthelmintic, Antibiotic, Antibiotic, Anthelmintic, Antibiotic, Antimicrobial, Antibiotic, Antineoplastic, Anticancer, Anticoagulant, Anticoagulant, Antithrombotic, Antifungal, Antiinflammatory, Antimicrobial, Antimicrobial, Antiparasitic, Antibiotic, Antimicrobial, Antiretroviral, Antimicrobial, Antitumor, Antineoplastic, Antiparasitic, Antiretroviral, Antithrombotic, Antitumor, Antiviral, CASPASE inhibitor, Chaperone binding, Enzyme inhibitor, Growth factor, Immunosuppressant, Inhibitor, Lantibiotic, Metabolism, Metal transport, Oxidation-reduction, Receptor, Thrombin inhibitor, Thrombin inhibitor, Trypsin inhibitor, Toxin, Transport activator, Trypsin inhibitor, Unknown
+ * 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 class?: Maybe<Scalars['String']>;
/** Additional details describing the molecule. */
@@ -10683,10 +11334,10 @@ export type RcsbPolymerInstanceFeatureFeaturePositions = {
readonly value?: Maybe<Scalars['Float']>;
};
-export type AssemblySymmetryQueryVariables = {
+export type AssemblySymmetryQueryVariables = Exact<{
assembly_id: Scalars['String'];
entry_id: Scalars['String'];
-};
+}>;
export type AssemblySymmetryQuery = { readonly assembly?: Maybe<{ readonly rcsb_struct_symmetry?: Maybe<ReadonlyArray<Maybe<(
diff --git a/src/mol-io/reader/cif/schema/bird.ts b/src/mol-io/reader/cif/schema/bird.ts
index fca6e4ec39dab0f4ff8be104943fc433112f9027..ab1c7fa88c38e24ff992a28710c1925396e9f8e2 100644
--- a/src/mol-io/reader/cif/schema/bird.ts
+++ b/src/mol-io/reader/cif/schema/bird.ts
@@ -1,7 +1,7 @@
/**
* Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
- * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.326, IHM 1.09, CARB draft.
+ * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.333, IHM 1.12, CARB draft.
*
* @author molstar/ciftools package
*/
@@ -66,7 +66,7 @@ export const BIRD_Schema = {
/**
* Broadly defines the function of the entity.
*/
- class: Aliased<'Antagonist' | 'Antibiotic' | 'Anticancer' | 'Anticoagulant' | 'Antifungal' | 'Antigen' | 'Antiinflammatory' | 'Antimicrobial' | 'Antineoplastic' | 'Antiparasitic' | 'Antiretroviral' | 'Anthelmintic' | 'Antithrombotic' | 'Antitumor' | 'Antiviral' | 'CASPASE inhibitor' | 'Chaperone binding' | 'Enzyme inhibitor' | 'Drug delivery' | 'Glycan component' | 'Growth factor' | 'Immunosuppressant' | 'Inducer' | 'Inhibitor' | 'Lantibiotic' | 'Metabolism' | 'Metal transport' | 'Nutrient' | 'Oxidation-reduction' | 'Protein binding' | 'Receptor' | 'Substrate analog' | 'Thrombin inhibitor' | 'Trypsin inhibitor' | 'Toxin' | 'Unknown' | 'Water retention' | 'Anticoagulant, Antithrombotic' | 'Antibiotic, Antimicrobial' | 'Antibiotic, Anthelmintic' | 'Antibiotic, Antineoplastic' | 'Antimicrobial, Antiretroviral' | 'Antimicrobial, Antitumor' | 'Antimicrobial, Antiparasitic, Antibiotic' | 'Thrombin inhibitor, Trypsin inhibitor'>(str),
+ class: Aliased<'Antagonist' | 'Antibiotic' | 'Anticancer' | 'Anticoagulant' | 'Antifungal' | 'Antigen' | 'Antiinflammatory' | 'Antimicrobial' | 'Antineoplastic' | 'Antiparasitic' | 'Antiretroviral' | 'Anthelmintic' | 'Antithrombotic' | 'Antitumor' | 'Antiviral' | 'CASPASE inhibitor' | 'Chaperone binding' | 'Enzyme inhibitor' | 'Drug delivery' | 'Glycan component' | 'Growth factor' | 'Immunosuppressant' | 'Inducer' | 'Inhibitor' | 'Lantibiotic' | 'Metabolism' | 'Metal transport' | 'Nutrient' | 'Oxidation-reduction' | 'Protein binding' | 'Receptor' | 'Substrate analog' | 'Synthetic opioid' | 'Thrombin inhibitor' | 'Transition state mimetic' | 'Transport activator' | 'Trypsin inhibitor' | 'Toxin' | 'Unknown' | 'Water retention' | 'Anticoagulant, Antithrombotic' | 'Antibiotic, Antimicrobial' | 'Antibiotic, Anthelmintic' | 'Antibiotic, Antineoplastic' | 'Antimicrobial, Antiretroviral' | 'Antimicrobial, Antitumor' | 'Antimicrobial, Antiparasitic, Antibiotic' | 'Thrombin inhibitor, Trypsin inhibitor'>(str),
/**
* Evidence for the assignment of _pdbx_reference_molecule.class
*/
diff --git a/src/mol-io/reader/cif/schema/ccd.ts b/src/mol-io/reader/cif/schema/ccd.ts
index 18b3a253020f6ced8753e2821fcb8fd09d24a183..6f70b529913f9f7dd1bc480b4642f4bb1507de68 100644
--- a/src/mol-io/reader/cif/schema/ccd.ts
+++ b/src/mol-io/reader/cif/schema/ccd.ts
@@ -1,7 +1,7 @@
/**
* Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
- * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.326, IHM 1.09, CARB draft.
+ * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.333, IHM 1.12, CARB draft.
*
* @author molstar/ciftools package
*/
@@ -103,7 +103,7 @@ export const CCD_Schema = {
* linking monomers, monomers with some type of N-terminal (or 5')
* cap and monomers with some type of C-terminal (or 3') cap.
*/
- type: Aliased<'D-peptide linking' | 'L-peptide linking' | 'D-peptide NH3 amino terminus' | 'L-peptide NH3 amino terminus' | 'D-peptide COOH carboxy terminus' | 'L-peptide COOH carboxy terminus' | 'DNA linking' | 'RNA linking' | 'L-RNA linking' | 'L-DNA linking' | 'DNA OH 5 prime terminus' | 'RNA OH 5 prime terminus' | 'DNA OH 3 prime terminus' | 'RNA OH 3 prime terminus' | 'D-saccharide 1,4 and 1,4 linking' | 'L-saccharide 1,4 and 1,4 linking' | 'D-saccharide 1,4 and 1,6 linking' | 'L-saccharide 1,4 and 1,6 linking' | 'D-saccharide, beta linking' | 'D-saccharide, alpha linking' | 'L-saccharide, beta linking' | 'L-saccharide, alpha linking' | 'L-saccharide' | 'D-saccharide' | 'saccharide' | 'non-polymer' | 'peptide linking' | 'peptide-like' | 'L-gamma-peptide, C-delta linking' | 'D-gamma-peptide, C-delta linking' | 'L-beta-peptide, C-gamma linking' | 'D-beta-peptide, C-gamma linking' | 'other'>(str),
+ type: Aliased<'D-peptide linking' | 'L-peptide linking' | 'D-peptide NH3 amino terminus' | 'L-peptide NH3 amino terminus' | 'D-peptide COOH carboxy terminus' | 'L-peptide COOH carboxy terminus' | 'DNA linking' | 'RNA linking' | 'L-RNA linking' | 'L-DNA linking' | 'DNA OH 5 prime terminus' | 'RNA OH 5 prime terminus' | 'DNA OH 3 prime terminus' | 'RNA OH 3 prime terminus' | 'D-saccharide, beta linking' | 'D-saccharide, alpha linking' | 'L-saccharide, beta linking' | 'L-saccharide, alpha linking' | 'L-saccharide' | 'D-saccharide' | 'saccharide' | 'non-polymer' | 'peptide linking' | 'peptide-like' | 'L-gamma-peptide, C-delta linking' | 'D-gamma-peptide, C-delta linking' | 'L-beta-peptide, C-gamma linking' | 'D-beta-peptide, C-gamma linking' | 'other'>(str),
/**
* Synonym list for the component.
*/
diff --git a/src/mol-io/reader/cif/schema/cif-core.ts b/src/mol-io/reader/cif/schema/cif-core.ts
index e99979935b9ddb7691efc05a052d383d543eb77b..711bcd0fd37a8aea863079e39b0a06acf906e8ba 100644
--- a/src/mol-io/reader/cif/schema/cif-core.ts
+++ b/src/mol-io/reader/cif/schema/cif-core.ts
@@ -1,7 +1,7 @@
/**
* Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
- * Code-generated 'CifCore' schema file. Dictionary versions: CifCore 3.0.13.
+ * Code-generated 'CifCore' schema file. Dictionary versions: CifCore 3.0.14.
*
* @author molstar/ciftools package
*/
diff --git a/src/mol-io/reader/cif/schema/mmcif.ts b/src/mol-io/reader/cif/schema/mmcif.ts
index 5013868708b3924b87c7d1de43bd62d014bf4db9..6f877144a7477758dd5602de71a994f55a189467 100644
--- a/src/mol-io/reader/cif/schema/mmcif.ts
+++ b/src/mol-io/reader/cif/schema/mmcif.ts
@@ -1,7 +1,7 @@
/**
* Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
- * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.326, IHM 1.09, CARB draft.
+ * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.333, IHM 1.12, CARB draft.
*
* @author molstar/ciftools package
*/
@@ -139,6 +139,10 @@ export const mmCIF_Schema = {
* introduced that was independent of the different modes of
* identifying the atoms. For compatibility with older CIFs,
* _atom_site_label is aliased to _atom_site.id.
+ *
+ * In general, this aggregate identifier does not uniquely
+ * identify an atom site as for non-polymers _atom_site.label_seq_id
+ * is '.'.
*/
id: int,
/**
@@ -492,7 +496,7 @@ export const mmCIF_Schema = {
* linking monomers, monomers with some type of N-terminal (or 5')
* cap and monomers with some type of C-terminal (or 3') cap.
*/
- type: Aliased<'D-peptide linking' | 'L-peptide linking' | 'D-peptide NH3 amino terminus' | 'L-peptide NH3 amino terminus' | 'D-peptide COOH carboxy terminus' | 'L-peptide COOH carboxy terminus' | 'DNA linking' | 'RNA linking' | 'L-RNA linking' | 'L-DNA linking' | 'DNA OH 5 prime terminus' | 'RNA OH 5 prime terminus' | 'DNA OH 3 prime terminus' | 'RNA OH 3 prime terminus' | 'D-saccharide 1,4 and 1,4 linking' | 'L-saccharide 1,4 and 1,4 linking' | 'D-saccharide 1,4 and 1,6 linking' | 'L-saccharide 1,4 and 1,6 linking' | 'D-saccharide, beta linking' | 'D-saccharide, alpha linking' | 'L-saccharide, beta linking' | 'L-saccharide, alpha linking' | 'L-saccharide' | 'D-saccharide' | 'saccharide' | 'non-polymer' | 'peptide linking' | 'peptide-like' | 'L-gamma-peptide, C-delta linking' | 'D-gamma-peptide, C-delta linking' | 'L-beta-peptide, C-gamma linking' | 'D-beta-peptide, C-gamma linking' | 'other'>(str),
+ type: Aliased<'D-peptide linking' | 'L-peptide linking' | 'D-peptide NH3 amino terminus' | 'L-peptide NH3 amino terminus' | 'D-peptide COOH carboxy terminus' | 'L-peptide COOH carboxy terminus' | 'DNA linking' | 'RNA linking' | 'L-RNA linking' | 'L-DNA linking' | 'DNA OH 5 prime terminus' | 'RNA OH 5 prime terminus' | 'DNA OH 3 prime terminus' | 'RNA OH 3 prime terminus' | 'D-saccharide, beta linking' | 'D-saccharide, alpha linking' | 'L-saccharide, beta linking' | 'L-saccharide, alpha linking' | 'L-saccharide' | 'D-saccharide' | 'saccharide' | 'non-polymer' | 'peptide linking' | 'peptide-like' | 'L-gamma-peptide, C-delta linking' | 'D-gamma-peptide, C-delta linking' | 'L-beta-peptide, C-gamma linking' | 'D-beta-peptide, C-gamma linking' | 'other'>(str),
/**
* Synonym list for the component.
*/
@@ -1407,10 +1411,9 @@ export const mmCIF_Schema = {
* The value of _struct_ncs_oper.id must uniquely identify a
* record in the STRUCT_NCS_OPER list.
*
- * Note that this item need not be a number; it can be any unique
- * identifier.
+ * Note that for PDB _struct_ncs_oper.id must be a number.
*/
- id: str,
+ id: int,
/**
* The elements of the 3x3 matrix component of a
* noncrystallographic symmetry operation.
@@ -2408,7 +2411,7 @@ export const mmCIF_Schema = {
/**
* Broadly defines the function of the molecule.
*/
- class: Aliased<'Antagonist' | 'Antibiotic' | 'Anticancer' | 'Anticoagulant' | 'Antifungal' | 'Antiinflammatory' | 'Antimicrobial' | 'Antineoplastic' | 'Antiparasitic' | 'Antiretroviral' | 'Anthelmintic' | 'Antithrombotic' | 'Antitumor' | 'Antiviral' | 'CASPASE inhibitor' | 'Chaperone binding' | 'Enzyme inhibitor' | 'Growth factor' | 'Immunosuppressant' | 'Inhibitor' | 'Lantibiotic' | 'Metabolism' | 'Metal transport' | 'Oxidation-reduction' | 'Receptor' | 'Thrombin inhibitor' | 'Trypsin inhibitor' | 'Toxin' | 'Transport activator' | 'Unknown' | 'Anticoagulant, Antithrombotic' | 'Antibiotic, Antimicrobial' | 'Antibiotic, Anthelmintic' | 'Antibiotic, Antineoplastic' | 'Antimicrobial, Antiretroviral' | 'Antimicrobial, Antitumor' | 'Antimicrobial, Antiparasitic, Antibiotic' | 'Thrombin inhibitor, Trypsin inhibitor'>(str),
+ class: Aliased<'Antagonist' | 'Antibiotic' | 'Anticancer' | 'Anticoagulant' | 'Antifungal' | 'Antigen' | 'Antiinflammatory' | 'Antimicrobial' | 'Antineoplastic' | 'Antiparasitic' | 'Antiretroviral' | 'Anthelmintic' | 'Antithrombotic' | 'Antitumor' | 'Antiviral' | 'CASPASE inhibitor' | 'Chaperone binding' | 'Enzyme inhibitor' | 'Drug delivery' | 'Glycan component' | 'Growth factor' | 'Immunosuppressant' | 'Inducer' | 'Inhibitor' | 'Lantibiotic' | 'Metabolism' | 'Metal transport' | 'Nutrient' | 'Oxidation-reduction' | 'Protein binding' | 'Receptor' | 'Substrate analog' | 'Synthetic opioid' | 'Thrombin inhibitor' | 'Transition state mimetic' | 'Transport activator' | 'Trypsin inhibitor' | 'Toxin' | 'Unknown' | 'Water retention' | 'Anticoagulant, Antithrombotic' | 'Antibiotic, Antimicrobial' | 'Antibiotic, Anthelmintic' | 'Antibiotic, Antineoplastic' | 'Antimicrobial, Antiretroviral' | 'Antimicrobial, Antitumor' | 'Antimicrobial, Antiparasitic, Antibiotic' | 'Thrombin inhibitor, Trypsin inhibitor'>(str),
/**
* Defines the structural classification of the molecule.
*/
@@ -2799,6 +2802,27 @@ export const mmCIF_Schema = {
*/
auth_mon_id: str,
},
+ /**
+ * PDBX_CHEM_COMP_RELATED describes the relationship between two chemical components.
+ */
+ pdbx_chem_comp_related: {
+ /**
+ * The chemical component for which this relationship applies.
+ */
+ comp_id: str,
+ /**
+ * The related chemical component for which this chemical component is based.
+ */
+ related_comp_id: str,
+ /**
+ * Describes the type of relationship
+ */
+ relationship_type: Aliased<'Carbohydrate core' | 'Precursor'>(str),
+ /**
+ * Describes the type of relationship
+ */
+ details: str,
+ },
/**
* Data items in the IHM_STARTING_MODEL_DETAILS category records the
* details about structural models used as starting inputs in
@@ -3497,7 +3521,7 @@ export const mmCIF_Schema = {
/**
* The type of data held in the dataset.
*/
- data_type: Aliased<'NMR data' | '3DEM volume' | '2DEM class average' | 'EM raw micrographs' | 'SAS data' | 'CX-MS data' | 'Mass Spectrometry data' | 'EPR data' | 'H/D exchange data' | 'Single molecule FRET data' | 'Experimental model' | 'Comparative model' | 'Integrative model' | 'De Novo model' | 'Predicted contacts' | 'Mutagenesis data' | 'DNA footprinting data' | 'Hydroxyl radical footprinting data' | 'Yeast two-hybrid screening data' | 'Quantitative measurements of genetic interactions' | 'Other'>(str),
+ data_type: Aliased<'NMR data' | '3DEM volume' | '2DEM class average' | 'EM raw micrographs' | 'X-ray diffraction data' | 'SAS data' | 'CX-MS data' | 'Mass Spectrometry data' | 'EPR data' | 'H/D exchange data' | 'Single molecule FRET data' | 'Experimental model' | 'Comparative model' | 'Integrative model' | 'De Novo model' | 'Predicted contacts' | 'Mutagenesis data' | 'DNA footprinting data' | 'Hydroxyl radical footprinting data' | 'Yeast two-hybrid screening data' | 'Quantitative measurements of genetic interactions' | 'Other'>(str),
/**
* A flag that indicates whether the dataset is archived in
* an IHM related database or elsewhere.
@@ -3906,7 +3930,7 @@ export const mmCIF_Schema = {
/**
* The type of crosslinker used.
*/
- linker_type: Aliased<'EDC' | 'DSS' | 'EGS' | 'BS3' | 'BS2G' | 'DST' | 'sulfo-SDA' | 'sulfo-SMCC' | 'DSSO' | 'DSG' | 'BSP' | 'BMSO' | 'DHSO' | 'CYS' | 'Other'>(str),
+ linker_type: Aliased<'EDC' | 'DSS' | 'EGS' | 'BS3' | 'BS2G' | 'DST' | 'sulfo-SDA' | 'sulfo-SMCC' | 'DSSO' | 'DSG' | 'BSP' | 'BMSO' | 'DHSO' | 'CYS' | 'SDA' | 'DSA' | 'Other'>(str),
/**
* Identifier to the crosslinking dataset.
* This data item is a pointer to the _ihm_dataset_list.id in the
@@ -4646,7 +4670,7 @@ export const mmCIF_Schema = {
/**
* The type of distance restraint applied.
*/
- restraint_type: Aliased<'lower bound' | 'upper bound' | 'lower and upper bound'>(str),
+ restraint_type: Aliased<'lower bound' | 'upper bound' | 'lower and upper bound' | 'harmonic'>(str),
/**
* Identifier to the input data from which the distance restraint is derived.
* This data item is a pointer to the _ihm_dataset_list.id in the
@@ -4658,27 +4682,6 @@ export const mmCIF_Schema = {
*/
dataset_list_id: int,
},
- /**
- * PDBX_CHEM_COMP_RELATED describes the relationship between two chemical components.
- */
- pdbx_chem_comp_related: {
- /**
- * The chemical component for which this relationship applies.
- */
- comp_id: str,
- /**
- * The related chemical component for which this chemical component is based.
- */
- related_comp_id: str,
- /**
- * Describes the type of relationship
- */
- relationship_type: Aliased<'Carbohydrate core' | 'Precursor'>(str),
- /**
- * Describes the type of relationship
- */
- details: str,
- },
};
export type mmCIF_Schema = typeof mmCIF_Schema;
diff --git a/src/mol-math/geometry/symmetry-operator.ts b/src/mol-math/geometry/symmetry-operator.ts
index 0b644438aa074c2e1c2249059ff365c87c73c802..00c14df63a6098fa59a2b14ebd467e4b605e2f60 100644
--- a/src/mol-math/geometry/symmetry-operator.ts
+++ b/src/mol-math/geometry/symmetry-operator.ts
@@ -20,8 +20,8 @@ interface SymmetryOperator {
readonly operId: number
},
- /** pointer to `struct_ncs_oper.id` or empty string */
- readonly ncsId: string,
+ /** pointer to `struct_ncs_oper.id` or -1 */
+ readonly ncsId: number,
readonly hkl: Vec3,
/** spacegroup symmetry operator index, -1 if not applicable */
@@ -48,12 +48,12 @@ namespace SymmetryOperator {
export const RotationTranslationEpsilon = 0.005;
- export type CreateInfo = { assembly?: SymmetryOperator['assembly'], ncsId?: string, hkl?: Vec3, spgrOp?: number }
+ export type CreateInfo = { assembly?: SymmetryOperator['assembly'], ncsId?: number, hkl?: Vec3, spgrOp?: number }
export function create(name: string, matrix: Mat4, info?: CreateInfo): SymmetryOperator {
let { assembly, ncsId, hkl, spgrOp } = info || { };
const _hkl = hkl ? Vec3.clone(hkl) : Vec3.zero();
spgrOp = defaults(spgrOp, -1);
- ncsId = ncsId || '';
+ ncsId = ncsId || -1;
const suffix = getSuffix(info);
if (Mat4.isIdentity(matrix)) return { name, assembly, matrix, inverse: Mat4.identity(), isIdentity: true, hkl: _hkl, spgrOp, ncsId, suffix };
if (!Mat4.isRotationAndTranslation(matrix, RotationTranslationEpsilon)) throw new Error(`Symmetry operator (${name}) must be a composition of rotation and translation.`);
@@ -72,7 +72,7 @@ namespace SymmetryOperator {
return `-${info.spgrOp + 1}_${5 + i}${5 + j}${5 + k}`;
}
- if (info.ncsId) {
+ if (info.ncsId !== -1) {
return `_${info.ncsId}`;
}
@@ -90,7 +90,7 @@ namespace SymmetryOperator {
return Mat4.isRotationAndTranslation(matrix, RotationTranslationEpsilon);
}
- export function ofRotationAndOffset(name: string, rot: Mat3, offset: Vec3, ncsId?: string) {
+ export function ofRotationAndOffset(name: string, rot: Mat3, offset: Vec3, ncsId?: number) {
const t = Mat4.identity();
for (let i = 0; i < 3; i++) {
for (let j = 0; j < 3; j++) {
diff --git a/src/mol-model/structure/export/categories/atom_site_operator_mapping.ts b/src/mol-model/structure/export/categories/atom_site_operator_mapping.ts
index ae09e71c0a493b45c70a0913dadc1438c5be8277..e1ea1e8776167dc61c19c178d17144d693d9f378 100644
--- a/src/mol-model/structure/export/categories/atom_site_operator_mapping.ts
+++ b/src/mol-model/structure/export/categories/atom_site_operator_mapping.ts
@@ -37,7 +37,7 @@ export const AtomSiteOperatorMappingSchema = {
symmetry_hkl: Column.Schema.Vector(3),
// NCS
- ncs_id: Column.Schema.Str(),
+ ncs_id: Column.Schema.Int(),
}
};
@@ -57,7 +57,7 @@ const Fields = CifWriter.fields<number, Entry[], keyof (typeof AtomSiteOperatorM
.int('symmetry_operator_index', (i, xs) => xs[i].operator.spgrOp, { valueKind: symmetryValueKind })
.vec('symmetry_hkl', [(i, xs) => xs[i].operator.hkl[0], (i, xs) => xs[i].operator.hkl[1], (i, xs) => xs[i].operator.hkl[2]], { valueKind: symmetryValueKind })
// NCS
- .str('ncs_id', (i, xs) => xs[i].operator.ncsId || '', { valueKind: (i, xs) => !xs[i].operator.ncsId ? Column.ValueKind.NotPresent : Column.ValueKind.Present })
+ .int('ncs_id', (i, xs) => xs[i].operator.ncsId, { valueKind: symmetryValueKind })
.getFields();
const Category: CifWriter.Category<Entry[]> = {