molstar
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A comprehensive macromolecular library.
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JavaScript
"use strict";
/**
* Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.350, IHM 1.17, CARB draft.
*
* @author molstar/ciftools package
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.BIRD_Schema = void 0;
var db_1 = require("../../../../mol-data/db");
var Schema = db_1.Column.Schema;
var str = Schema.str;
var float = Schema.float;
var Aliased = Schema.Aliased;
var int = Schema.int;
exports.BIRD_Schema = {
/**
* Data items in the PDBX_REFERENCE_MOLECULE category record
* reference information about small polymer molecules.
*/
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(str),
/**
* Evidence for the assignment of _pdbx_reference_molecule.type
*/
type_evidence_code: str,
/**
* Broadly defines the function of the entity.
*/
class: Aliased(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(str),
/**
* For entities represented as single molecules, the identifier
* corresponding to the chemical definition for the molecule.
*/
chem_comp_id: str,
/**
* Special details about this molecule.
*/
compound_details: 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(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,
},
/**
* Data items in the PDBX_REFERENCE_ENTITY_LIST category record
* the list of entities within each reference molecule.
*/
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: Aliased(str),
/**
* Additional details about this entity.
*/
details: str,
/**
* The component number of this entity within the molecule.
*/
component_id: int,
},
/**
* Data items in the PDBX_REFERENCE_ENTITY_NONPOLY category record
* the list of entities within each reference molecule.
*/
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,
},
/**
* Data items in the PDBX_REFERENCE_ENTITY_LINK category give details about
* the linkages between entities within reference molecules.
*/
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(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(str),
},
/**
* Data items in the PDBX_REFERENCE_ENTITY_POLY_LINK category give details about
* polymer linkages including both standard and non-standard linkages between
* polymer componnents.
*/
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(str),
},
/**
* Data items in the PDBX_REFERENCE_ENTITY_POLY category record details about
* the polymer, such as the type of the polymer, the number of
* monomers and whether it has nonstandard features.
*/
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(str),
/**
* The database code for this source information
*/
db_code: str,
/**
* The database name for this source information
*/
db_name: str,
},
/**
* Data items in the PDBX_REFERENCE_ENTITY_POLY_SEQ category specify the sequence
* of monomers in a polymer.
*/
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(str),
/**
* A flag to indicate that sequence heterogeneity at this monomer position.
*/
hetero: Aliased(str),
},
/**
* Additional features associated with the reference entity.
*/
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: Aliased(str),
/**
* A flag to indicate a non-ribosomal entity.
*/
NRP_flag: Aliased(str),
/**
* The one-letter-code sequence for this entity. Non-standard monomers are represented as 'X'.
*/
one_letter_codes: str,
},
/**
* Data items in the PDBX_REFERENCE_ENTITY_SRC_NAT category record
* details of the source from which the entity was obtained.
*/
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,
},
/**
* Data items in the PDBX_PRD_AUDIT category records
* the status and tracking information for this molecule.
*/
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: Aliased(str),
/**
* The action associated with this audit record.
*/
action_type: Aliased(str),
},
};
;
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