TmMolStar/src/mol-io/reader/cif/schema/bird.ts

/**
 * 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<BIRD_Schema> {};