molstar 3.0.0 → 3.0.1

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

@@ -1,497 +0,0 @@
-"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 5.354, IHM 1.17, MA 1.3.3.
- *
- * @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),
-    },
-};
-;
-//# sourceMappingURL=bird.js.map

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

@@ -1,12 +0,0 @@
-/**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-export declare const ccd_chemCompAtom_schema: {
-    comp_id: import("../../../../mol-data/db/column").Column.Schema.Str;
-    atom_id: import("../../../../mol-data/db/column").Column.Schema.Str;
-    charge: import("../../../../mol-data/db/column").Column.Schema.Int;
-    pdbx_stereo_config: import("../../../../mol-data/db/column").Column.Schema.Aliased<"N" | "R" | "S">;
-};

package/lib/commonjs/mol-io/reader/cif/schema/ccd-extras.js

@@ -1,18 +0,0 @@
-"use strict";
-/**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.ccd_chemCompAtom_schema = void 0;
-var ccd_1 = require("./ccd");
-// a reduced chem_comp_atom schema that provides charge and stereo_config information
-exports.ccd_chemCompAtom_schema = {
-    comp_id: ccd_1.CCD_Schema.chem_comp_atom.comp_id,
-    atom_id: ccd_1.CCD_Schema.chem_comp_atom.atom_id,
-    charge: ccd_1.CCD_Schema.chem_comp_atom.charge,
-    pdbx_stereo_config: ccd_1.CCD_Schema.chem_comp_atom.pdbx_stereo_config
-};
-//# sourceMappingURL=ccd-extras.js.map