molstar
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A comprehensive macromolecular library.
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/**
* Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.401, IHM 1.27, MA 1.4.7.
*
* @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<"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<"s" | "r" | "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<CCD_Schema> {
}