molstar 3.0.0-dev.7 → 3.0.1

package/lib/commonjs/mol-io/reader/cif/schema/bird.d.ts

@@ -1,491 +0,0 @@
-/**
- * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.352, IHM 1.17, CARB draft.
- *
- * @author molstar/ciftools package
- */
-import { Database, Column } from '../../../../mol-data/db';
-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<"Unknown" | "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" | "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<"N" | "Y">;
-        /**
-         * A flag to indicate that sequence heterogeneity at this monomer position.
-         */
-        hetero: Schema.Aliased<"N" | "Y">;
-    };
-    /**
-     * 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<"N" | "Y">;
-        /**
-         * 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" | "BMRB" | "PDBJ" | "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 declare type BIRD_Schema = typeof BIRD_Schema;
-export interface BIRD_Database extends Database<BIRD_Schema> {
-}