/** * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info. * * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.408, IHM 1.28, MA 1.4.8. * * @author molstar/ciftools package */ import { Database, Column } from '../../../../mol-data/db.js'; import Schema = Column.Schema; export declare 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: Schema.Str; /** * Formula mass in daltons of the entity. */ formula_weight: Schema.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: Schema.Str; /** * Defines the structural classification of the entity. */ type: Schema.Aliased<"non-polymer" | "peptide-like" | "macrolide" | "unknown" | "amino acid" | "aminoglycoside" | "anthracycline" | "anthraquinone" | "ansamycin" | "chalkophore" | "chromophore" | "glycopeptide" | "cyclic depsipeptide" | "cyclic lipopeptide" | "cyclic peptide" | "heterocyclic" | "imino sugar" | "keto acid" | "lipoglycopeptide" | "lipopeptide" | "nucleoside" | "oligopeptide" | "oligosaccharide" | "peptaibol" | "polycyclic" | "polypeptide" | "polysaccharide" | "quinolone" | "thiolactone" | "thiopeptide" | "siderophore" | "chalkophore, polypeptide">; /** * Evidence for the assignment of _pdbx_reference_molecule.type */ type_evidence_code: Schema.Str; /** * Broadly defines the function of the entity. */ class: Schema.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">; /** * Evidence for the assignment of _pdbx_reference_molecule.class */ class_evidence_code: Schema.Str; /** * A name of the entity. */ name: Schema.Str; /** * Defines how this entity is represented in PDB data files. */ represent_as: Schema.Aliased<"polymer" | "branched" | "single molecule">; /** * For entities represented as single molecules, the identifier * corresponding to the chemical definition for the molecule. */ chem_comp_id: Schema.Str; /** * Special details about this molecule. */ compound_details: Schema.Str; /** * Description of this molecule. */ description: Schema.Str; /** * The PDB accession code for the entry containing a representative example of this molecule. */ representative_PDB_id_code: Schema.Str; /** * Defines the current PDB release status for this molecule definition. */ release_status: Schema.Aliased<"wait" | "rel" | "hold" | "obs">; /** * 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: Schema.Str; /** * Assigns the identifier of the reference molecule that has replaced this molecule. */ replaced_by: Schema.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: Schema.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: Schema.Str; /** * Defines the polymer characteristic of the entity. */ type: Schema.Aliased<"non-polymer" | "polymer" | "branched" | "polymer-like">; /** * Additional details about this entity. */ details: Schema.Str; /** * The component number of this entity within the molecule. */ component_id: Schema.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: Schema.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: Schema.Str; /** * A name of the non-polymer entity. */ name: Schema.Str; /** * For non-polymer entities, the identifier corresponding * to the chemical definition for the molecule. */ chem_comp_id: Schema.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: Schema.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: Schema.Str; /** * A description of special aspects of a linkage between * chemical components in the structure. */ details: Schema.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: Schema.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: Schema.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: Schema.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: Schema.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: Schema.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: Schema.Str; /** * The atom identifier/name in the first of the two entities containing the linkage. */ atom_id_1: Schema.Str; /** * The atom identifier/name in the second of the two entities containing the linkage. */ atom_id_2: Schema.Str; /** * The bond order target for the chemical linkage. */ value_order: Schema.Aliased<"sing" | "doub" | "trip" | "quad" | "arom" | "poly" | "delo" | "pi">; /** * The entity component identifier for the first of two entities containing the linkage. */ component_1: Schema.Int; /** * The entity component identifier for the second of two entities containing the linkage. */ component_2: Schema.Int; /** * A code indicating the entity types involved in the linkage. */ link_class: Schema.Aliased<"PP" | "PN" | "NP" | "NN">; }; /** * 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: Schema.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: Schema.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: Schema.Str; /** * The entity component identifier entity containing the linkage. */ component_id: Schema.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: Schema.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: Schema.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: Schema.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: Schema.Str; /** * The atom identifier/name in the first of the two components making * the linkage. */ atom_id_1: Schema.Str; /** * The atom identifier/name in the second of the two components making * the linkage. */ atom_id_2: Schema.Str; /** * The bond order target for the non-standard linkage. */ value_order: Schema.Aliased<"sing" | "doub" | "trip" | "quad" | "arom" | "poly" | "delo" | "pi">; }; /** * 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: Schema.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: Schema.Str; /** * The type of the polymer. */ type: Schema.Aliased<"peptide-like" | "oligosaccharide" | "nucleic-acid-like" | "polysaccharide-like">; /** * The database code for this source information */ db_code: Schema.Str; /** * The database name for this source information */ db_name: Schema.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: Schema.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: Schema.Str; /** * This data item is the chemical component identifier of monomer. */ mon_id: Schema.Str; /** * This data item is the chemical component identifier for the parent component corresponding to this monomer. */ parent_mon_id: Schema.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: Schema.Int; /** * A flag to indicate that this monomer is observed in the instance example. */ observed: Schema.Aliased<"y" | "n">; /** * A flag to indicate that sequence heterogeneity at this monomer position. */ hetero: Schema.Aliased<"y" | "n">; }; /** * 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: Schema.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: Schema.Str; /** * The monomer type for the sequence. */ type: Schema.Aliased<"saccharide" | "peptide-like">; /** * A flag to indicate a non-ribosomal entity. */ NRP_flag: Schema.Aliased<"Y" | "N">; /** * The one-letter-code sequence for this entity. Non-standard monomers are represented as 'X'. */ one_letter_codes: Schema.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: Schema.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: Schema.Str; /** * The value of _pdbx_reference_entity_src_nat.ordinal distinguishes * source details for this entity. */ ordinal: Schema.Int; /** * The scientific name of the organism from which the entity was isolated. */ organism_scientific: Schema.Str; /** * The NCBI TaxId of the organism from which the entity was isolated. */ taxid: Schema.Str; /** * The database code for this source information */ db_code: Schema.Str; /** * The database name for this source information */ db_name: Schema.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: Schema.Str; /** * The date associated with this audit record. */ date: Schema.Str; /** * An identifier for the wwPDB site creating or modifying the molecule. */ processing_site: Schema.Aliased<"RCSB" | "PDBE" | "PDBJ" | "BMRB" | "PDBC">; /** * The action associated with this audit record. */ action_type: Schema.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">; }; }; export type BIRD_Schema = typeof BIRD_Schema; export interface BIRD_Database extends Database { }