molstar 3.0.0 → 3.0.1

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

@@ -1,390 +0,0 @@
-/**
- * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.354, IHM 1.17, MA 1.3.3.
- *
- * @author molstar/ciftools package
- */
-import { Database, Column } from '../../../../mol-data/db';
-import Schema = Column.Schema;
-export declare const CCD_Schema: {
-    /**
-     * Data items in the CHEM_COMP category give details about each
-     * of the chemical components from which the relevant chemical
-     * structures can be constructed, such as name, mass or charge.
-     *
-     * The related categories CHEM_COMP_ATOM, CHEM_COMP_BOND,
-     * CHEM_COMP_ANGLE etc. describe the detailed geometry of these
-     * chemical components.
-     */
-    chem_comp: {
-        /**
-         * The formula for the chemical component. Formulae are written
-         * according to the following rules:
-         *
-         * (1) Only recognized 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 cluster of
-         * (element symbol + count), but in general parentheses are
-         * not used.
-         *
-         * (4) The order of elements depends on whether carbon is
-         * present or not. 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;
-        /**
-         * Formula mass in daltons of the chemical component.
-         */
-        formula_weight: Schema.Float;
-        /**
-         * The value of _chem_comp.id must uniquely identify each item in
-         * the CHEM_COMP list.
-         *
-         * For protein polymer entities, this is the three-letter code for
-         * the amino acid.
-         *
-         * For nucleic acid polymer entities, this is the one-letter code
-         * for the base.
-         */
-        id: Schema.Str;
-        /**
-         * The identifier for the parent component of the nonstandard
-         * component. May be be a comma separated list if this component
-         * is derived from multiple components.
-         *
-         * Items in this indirectly point to _chem_comp.id in
-         * the CHEM_COMP category.
-         */
-        mon_nstd_parent_comp_id: Schema.List<string>;
-        /**
-         * The full name of the component.
-         */
-        name: Schema.Str;
-        /**
-         * For standard polymer components, the one-letter code for
-         * the component.   For non-standard polymer components, the
-         * one-letter code for parent component if this exists;
-         * otherwise, the one-letter code should be given as 'X'.
-         *
-         * Components that derived from multiple parents components
-         * are described by a sequence of one-letter-codes.
-         */
-        one_letter_code: Schema.Str;
-        /**
-         * For standard polymer components, the common three-letter code for
-         * the component.   Non-standard polymer components and non-polymer
-         * components are also assigned three-letter-codes.
-         *
-         * For ambiguous polymer components three-letter code should
-         * be given as 'UNK'.  Ambiguous ions are assigned the code 'UNX'.
-         * Ambiguous non-polymer components are assigned the code 'UNL'.
-         */
-        three_letter_code: Schema.Str;
-        /**
-         * For standard polymer components, the type of the monomer.
-         * Note that monomers that will form polymers are of three types:
-         * linking monomers, monomers with some type of N-terminal (or 5')
-         * cap and monomers with some type of C-terminal (or 3') cap.
-         */
-        type: Schema.Aliased<"other" | "D-peptide linking" | "L-peptide linking" | "D-peptide NH3 amino terminus" | "L-peptide NH3 amino terminus" | "D-peptide COOH carboxy terminus" | "L-peptide COOH carboxy terminus" | "DNA linking" | "RNA linking" | "L-RNA linking" | "L-DNA linking" | "DNA OH 5 prime terminus" | "RNA OH 5 prime terminus" | "DNA OH 3 prime terminus" | "RNA OH 3 prime terminus" | "D-saccharide, beta linking" | "D-saccharide, alpha linking" | "L-saccharide, beta linking" | "L-saccharide, alpha linking" | "L-saccharide" | "D-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "L-gamma-peptide, C-delta linking" | "D-gamma-peptide, C-delta linking" | "L-beta-peptide, C-gamma linking" | "D-beta-peptide, C-gamma linking">;
-        /**
-         * Synonym list for the component.
-         */
-        pdbx_synonyms: Schema.List<string>;
-        /**
-         * A preliminary classification used by PDB.
-         */
-        pdbx_type: Schema.Str;
-        /**
-         * A preliminary classification used by PDB to indicate
-         * that the chemistry of this component while described
-         * as clearly as possible is still ambiguous.  Software
-         * tools may not be able to process this component
-         * definition.
-         */
-        pdbx_ambiguous_flag: Schema.Str;
-        /**
-         * Identifies the _chem_comp.id of the component that
-         * has replaced this component.
-         */
-        pdbx_replaced_by: Schema.Str;
-        /**
-         * Identifies the _chem_comp.id's of the components
-         * which have been replaced by this component.
-         * Multiple id codes should be separated by commas.
-         */
-        pdbx_replaces: Schema.Str;
-        /**
-         * The net integer charge assigned to this component. This is the
-         * formal charge assignment normally found in chemical diagrams.
-         */
-        pdbx_formal_charge: Schema.Int;
-        /**
-         * This data item provides additional details about the model coordinates
-         * in the component definition.
-         */
-        pdbx_model_coordinates_details: Schema.Str;
-        /**
-         * This data item identifies the PDB database code from which the heavy
-         * atom model coordinates were obtained.
-         */
-        pdbx_model_coordinates_db_code: Schema.Str;
-        /**
-         * This data item identifies the source of the ideal coordinates in the
-         * component definition.
-         */
-        pdbx_ideal_coordinates_details: Schema.Str;
-        /**
-         * This data item identifies if ideal coordinates are missing in this definition.
-         */
-        pdbx_ideal_coordinates_missing_flag: Schema.Aliased<"N" | "Y">;
-        /**
-         * This data item identifies if model coordinates are missing in this definition.
-         */
-        pdbx_model_coordinates_missing_flag: Schema.Aliased<"N" | "Y">;
-        /**
-         * Date component was added to database.
-         */
-        pdbx_initial_date: Schema.Str;
-        /**
-         * Date component was last modified.
-         */
-        pdbx_modified_date: Schema.Str;
-        /**
-         * This data item holds the current release status for the component.
-         */
-        pdbx_release_status: Schema.Aliased<"REL" | "HOLD" | "HPUB" | "OBS" | "DEL" | "REF_ONLY">;
-        /**
-         * This data item identifies the deposition site that processed
-         * this chemical component defintion.
-         */
-        pdbx_processing_site: Schema.Aliased<"RCSB" | "EBI" | "PDBE" | "PDBJ" | "PDBC">;
-    };
-    /**
-     * Data items in the CHEM_COMP_ATOM category record details about
-     * the atoms in a chemical component. Specifying the atomic
-     * coordinates for the components in this category is an
-     * alternative to specifying the structure of the component
-     * via bonds, angles, planes etc. in the appropriate
-     * CHEM_COMP subcategories.
-     */
-    chem_comp_atom: {
-        /**
-         * An alternative identifier for the atom. This data item would be
-         * used in cases where alternative nomenclatures exist for labelling
-         * atoms in a group.
-         */
-        alt_atom_id: Schema.Str;
-        /**
-         * The value of _chem_comp_atom.atom_id must uniquely identify
-         * each atom in each monomer in the CHEM_COMP_ATOM list.
-         *
-         * The atom identifiers need not be unique over all atoms in the
-         * data block; they need only be unique for each atom in a
-         * component.
-         *
-         * Note that this item need not be a number; it can be any unique
-         * identifier.
-         */
-        atom_id: Schema.Str;
-        /**
-         * The net integer charge assigned to this atom. This is the
-         * formal charge assignment normally found in chemical diagrams.
-         */
-        charge: Schema.Int;
-        /**
-         * The x component of the coordinates for this atom in this
-         * component specified as orthogonal angstroms. The choice of
-         * reference axis frame for the coordinates is arbitrary.
-         *
-         * The set of coordinates input for the entity here is intended to
-         * correspond to the atomic model used to generate restraints for
-         * structure refinement, not to atom sites in the ATOM_SITE
-         * list.
-         */
-        model_Cartn_x: Schema.Coordinate;
-        /**
-         * The y component of the coordinates for this atom in this
-         * component specified as orthogonal angstroms. The choice of
-         * reference axis frame for the coordinates is arbitrary.
-         *
-         * The set of coordinates input for the entity here is intended to
-         * correspond to the atomic model used to generate restraints for
-         * structure refinement, not to atom sites in the ATOM_SITE
-         * list.
-         */
-        model_Cartn_y: Schema.Coordinate;
-        /**
-         * The z component of the coordinates for this atom in this
-         * component specified as orthogonal angstroms. The choice of
-         * reference axis frame for the coordinates is arbitrary.
-         *
-         * The set of coordinates input for the entity here is intended to
-         * correspond to the atomic model used to generate restraints for
-         * structure refinement, not to atom sites in the ATOM_SITE
-         * list.
-         */
-        model_Cartn_z: Schema.Coordinate;
-        /**
-         * This data item is a pointer to _chem_comp.id in the CHEM_COMP
-         * category.
-         */
-        comp_id: Schema.Str;
-        /**
-         * The code used to identify the atom species representing
-         * this atom type. Normally this code is the element
-         * symbol.
-         */
-        type_symbol: Schema.Str;
-        /**
-         * Atom name alignment offset in PDB atom field.
-         */
-        pdbx_align: Schema.Int;
-        /**
-         * Ordinal index for the component atom list.
-         */
-        pdbx_ordinal: Schema.Int;
-        /**
-         * An alternative x component of the coordinates for this atom in this
-         * component specified as orthogonal angstroms.
-         */
-        pdbx_model_Cartn_x_ideal: Schema.Coordinate;
-        /**
-         * An alternative y component of the coordinates for this atom in this
-         * component specified as orthogonal angstroms.
-         */
-        pdbx_model_Cartn_y_ideal: Schema.Coordinate;
-        /**
-         * An alternative z component of the coordinates for this atom in this
-         * component specified as orthogonal angstroms.
-         */
-        pdbx_model_Cartn_z_ideal: Schema.Coordinate;
-        /**
-         * The chiral configuration of the atom that is a chiral center.
-         */
-        pdbx_stereo_config: Schema.Aliased<"N" | "R" | "S">;
-        /**
-         * A flag indicating an aromatic atom.
-         */
-        pdbx_aromatic_flag: Schema.Aliased<"N" | "Y">;
-        /**
-         * A flag indicating a leaving atom.
-         */
-        pdbx_leaving_atom_flag: Schema.Aliased<"N" | "Y">;
-    };
-    /**
-     * Data items in the CHEM_COMP_BOND category record details about
-     * the bonds between atoms in a chemical component. Target values
-     * may be specified as bond orders, as a distance between the two
-     * atoms, or both.
-     */
-    chem_comp_bond: {
-        /**
-         * The ID of the first of the two atoms that define the bond.
-         *
-         * This data item is a pointer to _chem_comp_atom.atom_id in the
-         * CHEM_COMP_ATOM category.
-         */
-        atom_id_1: Schema.Str;
-        /**
-         * The ID of the second of the two atoms that define the bond.
-         *
-         * This data item is a pointer to _chem_comp_atom.atom_id in the
-         * CHEM_COMP_ATOM category.
-         */
-        atom_id_2: Schema.Str;
-        /**
-         * This data item is a pointer to _chem_comp.id in the CHEM_COMP
-         * category.
-         */
-        comp_id: Schema.Str;
-        /**
-         * The value that should be taken as the target for the chemical
-         * bond associated with the specified atoms, expressed as a bond
-         * order.
-         */
-        value_order: Schema.Aliased<"sing" | "doub" | "trip" | "quad" | "arom" | "poly" | "delo" | "pi">;
-        /**
-         * Ordinal index for the component bond list.
-         */
-        pdbx_ordinal: Schema.Int;
-        /**
-         * Stereochemical configuration across a double bond.
-         */
-        pdbx_stereo_config: Schema.Aliased<"N" | "E" | "Z">;
-        /**
-         * A flag indicating an aromatic bond.
-         */
-        pdbx_aromatic_flag: Schema.Aliased<"N" | "Y">;
-    };
-    /**
-     * Data items in the CHEM_COMP_DESCRIPTOR category provide
-     * string descriptors of component chemical structure.
-     */
-    pdbx_chem_comp_descriptor: {
-        /**
-         * This data item is a pointer to _chem_comp.id in the CHEM_COMP
-         * category.
-         */
-        comp_id: Schema.Str;
-        /**
-         * This data item contains the descriptor value for this
-         * component.
-         */
-        descriptor: Schema.Str;
-        /**
-         * This data item contains the descriptor type.
-         */
-        type: Schema.Aliased<"SMILES_CANNONICAL" | "SMILES_CANONICAL" | "SMILES" | "InChI" | "InChI_MAIN" | "InChI_MAIN_FORMULA" | "InChI_MAIN_CONNECT" | "InChI_MAIN_HATOM" | "InChI_CHARGE" | "InChI_STEREO" | "InChI_ISOTOPE" | "InChI_FIXEDH" | "InChI_RECONNECT" | "InChIKey">;
-        /**
-         * This data item contains the name of the program
-         * or library used to compute the descriptor.
-         */
-        program: Schema.Str;
-        /**
-         * This data item contains the version of the program
-         * or library used to compute the descriptor.
-         */
-        program_version: Schema.Str;
-    };
-    /**
-     * Data items in the CHEM_COMP_IDENTIFIER category provide
-     * identifiers for chemical components.
-     */
-    pdbx_chem_comp_identifier: {
-        /**
-         * This data item is a pointer to _chem_comp.id in the CHEM_COMP
-         * category.
-         */
-        comp_id: Schema.Str;
-        /**
-         * This data item contains the identifier value for this
-         * component.
-         */
-        identifier: Schema.Str;
-        /**
-         * This data item contains the identifier type.
-         */
-        type: Schema.Aliased<"COMMON NAME" | "SYSTEMATIC NAME" | "CAS REGISTRY NUMBER" | "PUBCHEM Identifier" | "MDL Identifier" | "SYNONYM" | "CONDENSED IUPAC CARB SYMBOL" | "IUPAC CARB SYMBOL" | "SNFG CARB SYMBOL" | "CONDENSED IUPAC CARBOHYDRATE SYMBOL" | "IUPAC CARBOHYDRATE SYMBOL" | "SNFG CARBOHYDRATE SYMBOL">;
-        /**
-         * This data item contains the name of the program
-         * or library used to compute the identifier.
-         */
-        program: Schema.Str;
-        /**
-         * This data item contains the version of the program
-         * or library used to compute the identifier.
-         */
-        program_version: Schema.Str;
-    };
-};
-export declare type CCD_Schema = typeof CCD_Schema;
-export interface CCD_Database extends Database<CCD_Schema> {
-}