/** * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info. * * Code-generated 'CCD' 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 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; /** * 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; /** * 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<"y" | "n">; /** * This data item identifies if model coordinates are missing in this definition. */ pdbx_model_coordinates_missing_flag: Schema.Aliased<"y" | "n">; /** * 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" | "PDBE" | "PDBJ" | "PDBC" | "EBI">; }; /** * 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<"r" | "s" | "n">; /** * A flag indicating an aromatic atom. */ pdbx_aromatic_flag: Schema.Aliased<"y" | "n">; /** * A flag indicating a leaving atom. */ pdbx_leaving_atom_flag: Schema.Aliased<"y" | "n">; }; /** * 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<"z" | "n" | "e">; /** * A flag indicating an aromatic bond. */ pdbx_aromatic_flag: Schema.Aliased<"y" | "n">; }; /** * 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 type CCD_Schema = typeof CCD_Schema; export interface CCD_Database extends Database { }