/** * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info. * * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.360, IHM 1.17, MA 1.4.2. * * @author molstar/ciftools package */ import { Database, Column } from '../../../../mol-data/db'; import Schema = Column.Schema; const str = Schema.str; const float = Schema.float; const lstr = Schema.lstr; const Aliased = Schema.Aliased; const int = Schema.int; export const 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<'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'>(lstr), /** * Evidence for the assignment of _pdbx_reference_molecule.type */ type_evidence_code: str, /** * 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' | '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'>(lstr), /** * 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' | 'branched'>(lstr), /** * 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<'rel' | 'hold' | 'obs' | 'wait'>(lstr), /** * 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<'polymer' | 'polymer-like' | 'non-polymer' | 'branched'>(lstr), /** * 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<'sing' | 'doub' | 'trip' | 'quad' | 'arom' | 'poly' | 'delo' | 'pi'>(lstr), /** * 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), }, /** * 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<'sing' | 'doub' | 'trip' | 'quad' | 'arom' | 'poly' | 'delo' | 'pi'>(lstr), }, /** * 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<'peptide-like' | 'nucleic-acid-like' | 'polysaccharide-like' | 'oligosaccharide'>(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<'y' | 'n'>(lstr), /** * A flag to indicate that sequence heterogeneity at this monomer position. */ hetero: Aliased<'y' | 'n'>(lstr), }, /** * 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<'peptide-like' | 'saccharide'>(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, }, /** * 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<'RCSB' | 'PDBE' | 'PDBJ' | 'BMRB' | 'PDBC'>(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), }, }; export type BIRD_Schema = typeof BIRD_Schema; export interface BIRD_Database extends Database {};