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Commit 27d26fa4 authored by Alexander Rose's avatar Alexander Rose
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added description from dictionary to CCD and BIRD schemas

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src/mol-io/reader/cif/schema/bird.ts
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/**
* 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),
},
}
......
src/mol-io/reader/cif/schema/ccd.ts
+ 278
− 2
View file @ 27d26fa4
/**
* 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,
},
}
......
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