diff --git a/src/mol-io/reader/cif/schema/bird.ts b/src/mol-io/reader/cif/schema/bird.ts
index 23b184e954e1ff0fbbdc12d8a95e5844adcfe034..e50ae25be452619e817f76e65107f94badc49a58 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) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
- * Code-generated 'BIRD' schema file
+ * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.298, IHM 0.134.
*
* @author mol-star package (src/apps/schema-generator/generate)
*/
@@ -22,101 +22,435 @@ const Aliased = Schema.Aliased;
export const BIRD_Schema = {
pdbx_reference_molecule: {
+ /**
+ * The value of _pdbx_reference_molecule.prd_id is the unique identifier
+ * for the reference molecule in this family.
+ *
+ * By convention this ID uniquely identifies the reference molecule in
+ * in the PDB reference dictionary.
+ *
+ * The ID has the template form PRD_dddddd (e.g. PRD_000001)
+ */
prd_id: str,
+ /**
+ * Formula mass in daltons of the entity.
+ */
formula_weight: float,
+ /**
+ * The formula for the reference entity. Formulae are written
+ * according to the rules:
+ *
+ * 1. Only recognised element symbols may be used.
+ *
+ * 2. Each element symbol is followed by a 'count' number. A count
+ * of '1' may be omitted.
+ *
+ * 3. A space or parenthesis must separate each element symbol and
+ * its count, but in general parentheses are not used.
+ *
+ * 4. The order of elements depends on whether or not carbon is
+ * present. If carbon is present, the order should be: C, then
+ * H, then the other elements in alphabetical order of their
+ * symbol. If carbon is not present, the elements are listed
+ * purely in alphabetic order of their symbol. This is the
+ * 'Hill' system used by Chemical Abstracts.
+ */
formula: str,
+ /**
+ * Defines the structural classification of the entity.
+ */
type: Aliased<'Amino acid' | 'Aminoglycoside' | 'Anthracycline' | 'Anthraquinone' | 'Ansamycin' | 'Chalkophore' | 'Chromophore' | 'Glycopeptide' | 'Cyclic depsipeptide' | 'Cyclic lipopeptide' | 'Cyclic peptide' | 'Heterocyclic' | 'Imino sugar' | 'Keto acid' | 'Lipoglycopeptide' | 'Lipopeptide' | 'Macrolide' | 'Non-polymer' | 'Nucleoside' | 'Oligopeptide' | 'Oligosaccharide' | 'Peptaibol' | 'Peptide-like' | 'Polycyclic' | 'Polypeptide' | 'Polysaccharide' | 'Quinolone' | 'Thiolactone' | 'Thiopeptide' | 'Siderophore' | 'Unknown' | 'Chalkophore, Polypeptide'>(str),
+ /**
+ * Evidence for the assignment of _pdbx_reference_molecule.type
+ */
type_evidence_code: str,
- 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' | 'Unknown' | 'Anticoagulant, Antithrombotic' | 'Antibiotic, Antimicrobial' |'Antibiotic, Anthelmintic' | 'Antibiotic, Antineoplastic' | 'Antimicrobial, Antiretroviral' | 'Antimicrobial, Antitumor' | 'Antimicrobial, Antiparasitic, Antibiotic' | 'Thrombin inhibitor, Trypsin inhibitor'>(str),
+ /**
+ * Broadly defines the function of the entity.
+ */
+ 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' | 'Unknown' | '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
+ */
class_evidence_code: str,
+ /**
+ * A name of the entity.
+ */
name: str,
+ /**
+ * Defines how this entity is represented in PDB data files.
+ */
represent_as: Aliased<'polymer' | 'single molecule'>(str),
+ /**
+ * For entities represented as single molecules, the identifier
+ * corresponding to the chemical definition for the molecule.
+ */
chem_comp_id: str,
+ /**
+ * Description of this molecule.
+ */
description: str,
+ /**
+ * The PDB accession code for the entry containing a representative example of this molecule.
+ */
representative_PDB_id_code: str,
+ /**
+ * Defines the current PDB release status for this molecule definition.
+ */
release_status: Aliased<'REL' | 'HOLD' | 'OBS' | 'WAIT'>(str),
+ /**
+ * Assigns the identifier for the reference molecule which have been replaced
+ * by this reference molecule.
+ * Multiple molecule identifier codes should be separated by commas.
+ */
replaces: str,
+ /**
+ * Assigns the identifier of the reference molecule that has replaced this molecule.
+ */
replaced_by: str,
},
pdbx_reference_entity_list: {
+ /**
+ * The value of _pdbx_reference_entity_list.prd_id is a reference
+ * _pdbx_reference_molecule.prd_id in the PDBX_REFERENCE_MOLECULE category.
+ */
prd_id: str,
+ /**
+ * The value of _pdbx_reference_entity_list.ref_entity_id is a unique identifier
+ * the a constituent entity within this reference molecule.
+ */
ref_entity_id: str,
+ /**
+ * Defines the polymer characteristic of the entity.
+ */
type: str,
+ /**
+ * Additional details about this entity.
+ */
details: str,
+ /**
+ * The component number of this entity within the molecule.
+ */
component_id: int,
},
pdbx_reference_entity_nonpoly: {
+ /**
+ * The value of _pdbx_reference_entity_nonpoly.prd_id is a reference
+ * _pdbx_reference_entity_list.prd_id in the PDBX_REFERENCE_ENTITY_LIST category.
+ */
prd_id: str,
+ /**
+ * The value of _pdbx_reference_entity_nonpoly.ref_entity_id is a reference
+ * to _pdbx_reference_entity_list.ref_entity_id in PDBX_REFERENCE_ENTITY_LIST category.
+ */
ref_entity_id: str,
+ /**
+ * A name of the non-polymer entity.
+ */
name: str,
+ /**
+ * For non-polymer entities, the identifier corresponding
+ * to the chemical definition for the molecule.
+ */
chem_comp_id: str,
},
pdbx_reference_entity_link: {
+ /**
+ * The value of _pdbx_reference_entity_link.link_id uniquely identifies
+ * linkages between entities with a molecule.
+ */
link_id: int,
+ /**
+ * The value of _pdbx_reference_entity_link.prd_id is a reference
+ * _pdbx_reference_entity_list.prd_id in the PDBX_REFERENCE_ENTITY_LIST category.
+ */
prd_id: str,
+ /**
+ * A description of special aspects of a linkage between
+ * chemical components in the structure.
+ */
details: str,
+ /**
+ * The reference entity id of the first of the two entities joined by the
+ * linkage.
+ *
+ * This data item is a pointer to _pdbx_reference_entity_list.ref_entity_id
+ * in the PDBX_REFERENCE_ENTITY_LIST category.
+ */
ref_entity_id_1: str,
+ /**
+ * The reference entity id of the second of the two entities joined by the
+ * linkage.
+ *
+ * This data item is a pointer to _pdbx_reference_entity_list.ref_entity_id
+ * in the PDBX_REFERENCE_ENTITY_LIST category.
+ */
ref_entity_id_2: str,
+ /**
+ * For a polymer entity, the sequence number in the first of
+ * the two entities containing the linkage.
+ *
+ * This data item is a pointer to _pdbx_reference_entity_poly_seq.num
+ * in the PDBX_REFERENCE_ENTITY_POLY_SEQ category.
+ */
entity_seq_num_1: int,
+ /**
+ * For a polymer entity, the sequence number in the second of
+ * the two entities containing the linkage.
+ *
+ * This data item is a pointer to _pdbx_reference_entity_poly_seq.num
+ * in the PDBX_REFERENCE_ENTITY_POLY_SEQ category.
+ */
entity_seq_num_2: int,
+ /**
+ * The component identifier in the first of the two entities containing the linkage.
+ *
+ * For polymer entities, this data item is a pointer to _pdbx_reference_entity_poly_seq.mon_id
+ * in the PDBX_REFERENCE_ENTITY_POLY_SEQ category.
+ *
+ * For non-polymer entities, this data item is a pointer to
+ * _pdbx_reference_entity_nonpoly.chem_comp_id in the
+ * PDBX_REFERENCE_ENTITY_NONPOLY category.
+ */
comp_id_1: str,
+ /**
+ * The component identifier in the second of the two entities containing the linkage.
+ *
+ * For polymer entities, this data item is a pointer to _pdbx_reference_entity_poly_seq.mon_id
+ * in the PDBX_REFERENCE_ENTITY_POLY_SEQ category.
+ *
+ * For non-polymer entities, this data item is a pointer to
+ * _pdbx_reference_entity_nonpoly.chem_comp_id in the
+ * PDBX_REFERENCE_ENTITY_NONPOLY category.
+ */
comp_id_2: str,
+ /**
+ * The atom identifier/name in the first of the two entities containing the linkage.
+ */
atom_id_1: str,
+ /**
+ * The atom identifier/name in the second of the two entities containing the linkage.
+ */
atom_id_2: str,
+ /**
+ * The bond order target for the chemical linkage.
+ */
value_order: Aliased<'sing' | 'doub' | 'trip' | 'quad' | 'arom' | 'poly' | 'delo' | 'pi'>(str),
+ /**
+ * The entity component identifier for the first of two entities containing the linkage.
+ */
component_1: int,
+ /**
+ * The entity component identifier for the second of two entities containing the linkage.
+ */
component_2: int,
+ /**
+ * A code indicating the entity types involved in the linkage.
+ */
link_class: Aliased<'PP' | 'PN' | 'NP' | 'NN'>(str),
},
pdbx_reference_entity_poly_link: {
+ /**
+ * The value of _pdbx_reference_entity_poly_link.link_id uniquely identifies
+ * a linkage within a polymer entity.
+ */
link_id: int,
+ /**
+ * The value of _pdbx_reference_entity_poly_link.prd_id is a reference
+ * _pdbx_reference_entity_list.prd_id in the PDBX_REFERENCE_ENTITY_POLY category.
+ */
prd_id: str,
+ /**
+ * The reference entity id of the polymer entity containing the linkage.
+ *
+ * This data item is a pointer to _pdbx_reference_entity_poly.ref_entity_id
+ * in the PDBX_REFERENCE_ENTITY_POLY category.
+ */
ref_entity_id: str,
+ /**
+ * The entity component identifier entity containing the linkage.
+ */
component_id: int,
+ /**
+ * For a polymer entity, the sequence number in the first of
+ * the two components making the linkage.
+ *
+ * This data item is a pointer to _pdbx_reference_entity_poly_seq.num
+ * in the PDBX_REFERENCE_ENTITY_POLY_SEQ category.
+ */
entity_seq_num_1: int,
+ /**
+ * For a polymer entity, the sequence number in the second of
+ * the two components making the linkage.
+ *
+ * This data item is a pointer to _pdbx_reference_entity_poly_seq.num
+ * in the PDBX_REFERENCE_ENTITY_POLY_SEQ category.
+ */
entity_seq_num_2: int,
+ /**
+ * The component identifier in the first of the two components making the
+ * linkage.
+ *
+ * This data item is a pointer to _pdbx_reference_entity_poly_seq.mon_id
+ * in the PDBX_REFERENCE_ENTITY_POLY_SEQ category.
+ */
comp_id_1: str,
+ /**
+ * The component identifier in the second of the two components making the
+ * linkage.
+ *
+ * This data item is a pointer to _pdbx_reference_entity_poly_seq.mon_id
+ * in the PDBX_REFERENCE_ENTITY_POLY_SEQ category.
+ */
comp_id_2: str,
+ /**
+ * The atom identifier/name in the first of the two components making
+ * the linkage.
+ */
atom_id_1: str,
+ /**
+ * The atom identifier/name in the second of the two components making
+ * the linkage.
+ */
atom_id_2: str,
+ /**
+ * The bond order target for the non-standard linkage.
+ */
value_order: Aliased<'sing' | 'doub' | 'trip' | 'quad' | 'arom' | 'poly' | 'delo' | 'pi'>(str),
},
pdbx_reference_entity_poly: {
+ /**
+ * The value of _pdbx_reference_entity_poly.prd_id is a reference
+ * _pdbx_reference_entity_list.prd_id in the PDBX_REFERENCE_ENTITY_LIST category.
+ */
prd_id: str,
+ /**
+ * The value of _pdbx_reference_entity_poly.ref_entity_id is a reference
+ * to _pdbx_reference_entity_list.ref_entity_id in PDBX_REFERENCE_ENTITY_LIST category.
+ */
ref_entity_id: str,
+ /**
+ * The type of the polymer.
+ */
type: Aliased<'peptide-like' | 'nucleic-acid-like' | 'polysaccharide-like'>(str),
+ /**
+ * The database code for this source information
+ */
db_code: str,
+ /**
+ * The database name for this source information
+ */
db_name: str,
},
pdbx_reference_entity_poly_seq: {
+ /**
+ * The value of _pdbx_reference_entity_poly_seq.prd_id is a reference
+ * _pdbx_reference_entity_poly.prd_id in the PDBX_REFERENCE_ENTITY_POLY category.
+ */
prd_id: str,
+ /**
+ * The value of _pdbx_reference_entity_poly_seq.ref_entity_id is a reference
+ * to _pdbx_reference_entity_poly.ref_entity_id in PDBX_REFERENCE_ENTITY_POLY category.
+ */
ref_entity_id: str,
+ /**
+ * This data item is the chemical component identifier of monomer.
+ */
mon_id: str,
+ /**
+ * This data item is the chemical component identifier for the parent component corresponding to this monomer.
+ */
parent_mon_id: str,
+ /**
+ * The value of _pdbx_reference_entity_poly_seq.num must uniquely and sequentially
+ * identify a record in the PDBX_REFERENCE_ENTITY_POLY_SEQ list.
+ *
+ * This value is conforms to author numbering conventions and does not map directly
+ * to the numbering conventions used for _entity_poly_seq.num.
+ */
num: int,
+ /**
+ * A flag to indicate that this monomer is observed in the instance example.
+ */
observed: Aliased<'Y' | 'N'>(str),
+ /**
+ * A flag to indicate that sequence heterogeneity at this monomer position.
+ */
hetero: Aliased<'Y' | 'N'>(str),
},
pdbx_reference_entity_sequence: {
+ /**
+ * The value of _pdbx_reference_entity_sequence.prd_id is a reference
+ * _pdbx_reference_entity_list.prd_id in the PDBX_REFERENCE_ENTITY_LIST category.
+ */
prd_id: str,
+ /**
+ * The value of _pdbx_reference_entity_sequence.ref_entity_id is a reference
+ * to _pdbx_reference_entity_list.ref_entity_id in PDBX_REFERENCE_ENTITY_LIST category.
+ */
ref_entity_id: str,
+ /**
+ * The monomer type for the sequence.
+ */
type: str,
+ /**
+ * A flag to indicate a non-ribosomal entity.
+ */
NRP_flag: Aliased<'Y' | 'N'>(str),
+ /**
+ * The one-letter-code sequence for this entity. Non-standard monomers are represented as 'X'.
+ */
one_letter_codes: str,
},
pdbx_reference_entity_src_nat: {
+ /**
+ * The value of _pdbx_reference_entity_src_nat.prd_id is a reference
+ * _pdbx_reference_entity_list.prd_id in the PDBX_REFERENCE_ENTITY_LIST category.
+ */
prd_id: str,
+ /**
+ * The value of _pdbx_reference_entity_src_nat.ref_entity_id is a reference
+ * to _pdbx_reference_entity_list.ref_entity_id in PDBX_REFERENCE_ENTITY_LIST category.
+ */
ref_entity_id: str,
+ /**
+ * The value of _pdbx_reference_entity_src_nat.ordinal distinguishes
+ * source details for this entity.
+ */
ordinal: int,
+ /**
+ * The scientific name of the organism from which the entity was isolated.
+ */
organism_scientific: str,
+ /**
+ * The NCBI TaxId of the organism from which the entity was isolated.
+ */
taxid: str,
+ /**
+ * The database code for this source information
+ */
db_code: str,
+ /**
+ * The database name for this source information
+ */
db_name: str,
},
pdbx_prd_audit: {
+ /**
+ * This data item is a pointer to _pdbx_reference_molecule.prd_id in the
+ * pdbx_reference_molecule category.
+ */
prd_id: str,
+ /**
+ * The date associated with this audit record.
+ */
date: str,
+ /**
+ * An identifier for the wwPDB site creating or modifying the molecule.
+ */
processing_site: str,
+ /**
+ * The action associated with this audit record.
+ */
action_type: Aliased<'Initial release' | 'Create molecule' | 'Modify type' | 'Modify class' | 'Modify molecule name' | 'Modify representation' | 'Modify sequence' | 'Modify linkage' | 'Modify taxonomy organism' | 'Modify audit' | 'Other modification' | 'Obsolete molecule'>(str),
},
}
diff --git a/src/mol-io/reader/cif/schema/ccd.ts b/src/mol-io/reader/cif/schema/ccd.ts
index 5e8ff5b8f74fec9f4fe03265b06a596b0442554f..0149ed58fa59be1b992e6eda99343fe3823b566d 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) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
- * Code-generated 'CCD' schema file
+ * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.298, IHM 0.134.
*
* @author mol-star package (src/apps/schema-generator/generate)
*/
@@ -22,68 +22,344 @@ const List = Schema.List;
export const CCD_Schema = {
chem_comp: {
+ /**
+ * The formula for the chemical component. Formulae are written
+ * according to the following rules:
+ *
+ * (1) Only recognized element symbols may be used.
+ *
+ * (2) Each element symbol is followed by a 'count' number. A count
+ * of '1' may be omitted.
+ *
+ * (3) A space or parenthesis must separate each cluster of
+ * (element symbol + count), but in general parentheses are
+ * not used.
+ *
+ * (4) The order of elements depends on whether carbon is
+ * present or not. If carbon is present, the order should be:
+ * C, then H, then the other elements in alphabetical order
+ * of their symbol. If carbon is not present, the elements
+ * are listed purely in alphabetic order of their symbol. This
+ * is the 'Hill' system used by Chemical Abstracts.
+ */
formula: str,
+ /**
+ * Formula mass in daltons of the chemical component.
+ */
formula_weight: float,
+ /**
+ * The value of _chem_comp.id must uniquely identify each item in
+ * the CHEM_COMP list.
+ *
+ * For protein polymer entities, this is the three-letter code for
+ * the amino acid.
+ *
+ * For nucleic acid polymer entities, this is the one-letter code
+ * for the base.
+ */
id: str,
+ /**
+ * The identifier for the parent component of the nonstandard
+ * component. May be be a comma separated list if this component
+ * is derived from multiple components.
+ *
+ * Items in this indirectly point to _chem_comp.id in
+ * the CHEM_COMP category.
+ */
mon_nstd_parent_comp_id: List(',', x => x),
+ /**
+ * The full name of the component.
+ */
name: str,
+ /**
+ * For standard polymer components, the one-letter code for
+ * the component. For non-standard polymer components, the
+ * one-letter code for parent component if this exists;
+ * otherwise, the one-letter code should be given as 'X'.
+ *
+ * Components that derived from multiple parents components
+ * are described by a sequence of one-letter-codes.
+ */
one_letter_code: str,
+ /**
+ * For standard polymer components, the common three-letter code for
+ * the component. Non-standard polymer components and non-polymer
+ * components are also assigned three-letter-codes.
+ *
+ * For ambiguous polymer components three-letter code should
+ * be given as 'UNK'. Ambiguous ions are assigned the code 'UNX'.
+ * Ambiguous non-polymer components are assigned the code 'UNL'.
+ */
three_letter_code: str,
+ /**
+ * For standard polymer components, the type of the monomer.
+ * Note that monomers that will form polymers are of three types:
+ * linking monomers, monomers with some type of N-terminal (or 5')
+ * cap and monomers with some type of C-terminal (or 3') cap.
+ */
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' | '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),
- pdbx_synonyms: str,
+ /**
+ * Synonym list for the component.
+ */
+ pdbx_synonyms: List(';', x => x),
+ /**
+ * A preliminary classification used by PDB.
+ */
pdbx_type: str,
+ /**
+ * A preliminary classification used by PDB to indicate
+ * that the chemistry of this component while described
+ * as clearly as possible is still ambiguous. Software
+ * tools may not be able to process this component
+ * definition.
+ */
pdbx_ambiguous_flag: str,
+ /**
+ * Identifies the _chem_comp.id of the component that
+ * has replaced this component.
+ */
pdbx_replaced_by: str,
+ /**
+ * Identifies the _chem_comp.id's of the components
+ * which have been replaced by this component.
+ * Multiple id codes should be separated by commas.
+ */
pdbx_replaces: str,
+ /**
+ * The net integer charge assigned to this component. This is the
+ * formal charge assignment normally found in chemical diagrams.
+ */
pdbx_formal_charge: int,
+ /**
+ * This data item provides additional details about the model coordinates
+ * in the component definition.
+ */
pdbx_model_coordinates_details: str,
+ /**
+ * This data item identifies the PDB database code from which the heavy
+ * atom model coordinates were obtained.
+ */
pdbx_model_coordinates_db_code: str,
+ /**
+ * This data item identifies the source of the ideal coordinates in the
+ * component definition.
+ */
pdbx_ideal_coordinates_details: str,
+ /**
+ * This data item identifies if ideal coordinates are missing in this definition.
+ */
pdbx_ideal_coordinates_missing_flag: Aliased<'Y' | 'N'>(str),
+ /**
+ * This data item identifies if model coordinates are missing in this definition.
+ */
pdbx_model_coordinates_missing_flag: Aliased<'Y' | 'N'>(str),
+ /**
+ * Date component was added to database.
+ */
pdbx_initial_date: str,
+ /**
+ * Date component was last modified.
+ */
pdbx_modified_date: str,
+ /**
+ * This data item identifies the deposition site that processed
+ * this chemical component defintion.
+ */
pdbx_processing_site: Aliased<'PDBE' | 'EBI' | 'PDBJ' | 'RCSB'>(str),
},
chem_comp_atom: {
+ /**
+ * An alternative identifier for the atom. This data item would be
+ * used in cases where alternative nomenclatures exist for labelling
+ * atoms in a group.
+ */
alt_atom_id: str,
+ /**
+ * The value of _chem_comp_atom.atom_id must uniquely identify
+ * each atom in each monomer in the CHEM_COMP_ATOM list.
+ *
+ * The atom identifiers need not be unique over all atoms in the
+ * data block; they need only be unique for each atom in a
+ * component.
+ *
+ * Note that this item need not be a number; it can be any unique
+ * identifier.
+ */
atom_id: str,
+ /**
+ * The net integer charge assigned to this atom. This is the
+ * formal charge assignment normally found in chemical diagrams.
+ */
charge: int,
+ /**
+ * The x component of the coordinates for this atom in this
+ * component specified as orthogonal angstroms. The choice of
+ * reference axis frame for the coordinates is arbitrary.
+ *
+ * The set of coordinates input for the entity here is intended to
+ * correspond to the atomic model used to generate restraints for
+ * structure refinement, not to atom sites in the ATOM_SITE
+ * list.
+ */
model_Cartn_x: coord,
+ /**
+ * The y component of the coordinates for this atom in this
+ * component specified as orthogonal angstroms. The choice of
+ * reference axis frame for the coordinates is arbitrary.
+ *
+ * The set of coordinates input for the entity here is intended to
+ * correspond to the atomic model used to generate restraints for
+ * structure refinement, not to atom sites in the ATOM_SITE
+ * list.
+ */
model_Cartn_y: coord,
+ /**
+ * The z component of the coordinates for this atom in this
+ * component specified as orthogonal angstroms. The choice of
+ * reference axis frame for the coordinates is arbitrary.
+ *
+ * The set of coordinates input for the entity here is intended to
+ * correspond to the atomic model used to generate restraints for
+ * structure refinement, not to atom sites in the ATOM_SITE
+ * list.
+ */
model_Cartn_z: coord,
+ /**
+ * This data item is a pointer to _chem_comp.id in the CHEM_COMP
+ * category.
+ */
comp_id: str,
+ /**
+ * The code used to identify the atom species representing
+ * this atom type. Normally this code is the element
+ * symbol.
+ */
type_symbol: str,
+ /**
+ * Atom name alignment offset in PDB atom field.
+ */
pdbx_align: int,
+ /**
+ * Ordinal index for the component atom list.
+ */
pdbx_ordinal: int,
+ /**
+ * An alternative x component of the coordinates for this atom in this
+ * component specified as orthogonal angstroms.
+ */
pdbx_model_Cartn_x_ideal: coord,
+ /**
+ * An alternative y component of the coordinates for this atom in this
+ * component specified as orthogonal angstroms.
+ */
pdbx_model_Cartn_y_ideal: coord,
+ /**
+ * An alternative z component of the coordinates for this atom in this
+ * component specified as orthogonal angstroms.
+ */
pdbx_model_Cartn_z_ideal: coord,
+ /**
+ * The chiral configuration of the atom that is a chiral center.
+ */
pdbx_stereo_config: Aliased<'R' | 'S' | 'N'>(str),
+ /**
+ * A flag indicating an aromatic atom.
+ */
pdbx_aromatic_flag: Aliased<'Y' | 'N'>(str),
+ /**
+ * A flag indicating a leaving atom.
+ */
pdbx_leaving_atom_flag: Aliased<'Y' | 'N'>(str),
},
chem_comp_bond: {
+ /**
+ * The ID of the first of the two atoms that define the bond.
+ *
+ * This data item is a pointer to _chem_comp_atom.atom_id in the
+ * CHEM_COMP_ATOM category.
+ */
atom_id_1: str,
+ /**
+ * The ID of the second of the two atoms that define the bond.
+ *
+ * This data item is a pointer to _chem_comp_atom.atom_id in the
+ * CHEM_COMP_ATOM category.
+ */
atom_id_2: str,
+ /**
+ * This data item is a pointer to _chem_comp.id in the CHEM_COMP
+ * category.
+ */
comp_id: str,
+ /**
+ * The value that should be taken as the target for the chemical
+ * bond associated with the specified atoms, expressed as a bond
+ * order.
+ */
value_order: Aliased<'sing' | 'doub' | 'trip' | 'quad' | 'arom' | 'poly' | 'delo' | 'pi'>(str),
+ /**
+ * Ordinal index for the component bond list.
+ */
pdbx_ordinal: int,
+ /**
+ * Stereochemical configuration across a double bond.
+ */
pdbx_stereo_config: Aliased<'E' | 'Z' | 'N'>(str),
+ /**
+ * A flag indicating an aromatic bond.
+ */
pdbx_aromatic_flag: Aliased<'Y' | 'N'>(str),
},
pdbx_chem_comp_descriptor: {
+ /**
+ * This data item is a pointer to _chem_comp.id in the CHEM_COMP
+ * category.
+ */
comp_id: str,
+ /**
+ * This data item contains the descriptor value for this
+ * component.
+ */
descriptor: str,
+ /**
+ * This data item contains the descriptor type.
+ */
type: Aliased<'SMILES_CANNONICAL' | 'SMILES_CANONICAL' | 'SMILES' | 'SMILES' | 'InChI' | 'InChI_MAIN' | 'InChI_MAIN_FORMULA' | 'InChI_MAIN_CONNECT' | 'InChI_MAIN_HATOM' | 'InChI_CHARGE' | 'InChI_STEREO' | 'InChI_ISOTOPE' | 'InChI_FIXEDH' | 'InChI_RECONNECT' | 'InChIKey'>(str),
+ /**
+ * This data item contains the name of the program
+ * or library used to compute the descriptor.
+ */
program: str,
+ /**
+ * This data item contains the version of the program
+ * or library used to compute the descriptor.
+ */
program_version: str,
},
pdbx_chem_comp_identifier: {
+ /**
+ * This data item is a pointer to _chem_comp.id in the CHEM_COMP
+ * category.
+ */
comp_id: str,
+ /**
+ * This data item contains the identifier value for this
+ * component.
+ */
identifier: str,
+ /**
+ * This data item contains the identifier type.
+ */
type: Aliased<'COMMON NAME' | 'SYSTEMATIC NAME' | 'CAS REGISTRY NUMBER' | 'PUBCHEM Identifier' | 'MDL Identifier' | 'SYNONYM'>(str),
+ /**
+ * This data item contains the name of the program
+ * or library used to compute the identifier.
+ */
program: str,
+ /**
+ * This data item contains the version of the program
+ * or library used to compute the identifier.
+ */
program_version: str,
},
}