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ccd.ts 15.25 KiB
/**
* Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.303, IHM 0.139, CARB draft.
*
* @author mol-star package (src/apps/schema-generator/generate)
*/
import { Database, Column } from 'mol-data/db'
import Schema = Column.Schema
const str = Schema.str;
const float = Schema.float;
const List = Schema.List;
const Aliased = Schema.Aliased;
const int = Schema.int;
const coord = Schema.coord;
export 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: str,
/**
* Formula mass in daltons of the chemical component.
*/
formula_weight: 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: 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: List(',', x => x),
/**
* The full name of the component.
*/
name: 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: 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: 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: Aliased<'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 1,4 and 1,4 linking' | 'L-saccharide 1,4 and 1,4 linking' | 'D-saccharide 1,4 and 1,6 linking' | 'L-saccharide 1,4 and 1,6 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' | 'other'>(str),
/**
* Synonym list for the component.
*/
pdbx_synonyms: List(';', x => x),
/**
* A preliminary classification used by PDB.
*/
pdbx_type: 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: str,
/**
* Identifies the _chem_comp.id of the component that
* has replaced this component.
*/
pdbx_replaced_by: 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: str,
/**
* The net integer charge assigned to this component. This is the
* formal charge assignment normally found in chemical diagrams.
*/
pdbx_formal_charge: int,
/**
* This data item provides additional details about the model coordinates * in the component definition.
*/
pdbx_model_coordinates_details: str,
/**
* This data item identifies the PDB database code from which the heavy
* atom model coordinates were obtained.
*/
pdbx_model_coordinates_db_code: str,
/**
* This data item identifies the source of the ideal coordinates in the
* component definition.
*/
pdbx_ideal_coordinates_details: str,
/**
* This data item identifies if ideal coordinates are missing in this definition.
*/
pdbx_ideal_coordinates_missing_flag: Aliased<'Y' | 'N'>(str),
/**
* This data item identifies if model coordinates are missing in this definition.
*/
pdbx_model_coordinates_missing_flag: Aliased<'Y' | 'N'>(str),
/**
* Date component was added to database.
*/
pdbx_initial_date: str,
/**
* Date component was last modified.
*/
pdbx_modified_date: str,
/**
* This data item identifies the deposition site that processed
* this chemical component defintion.
*/
pdbx_processing_site: Aliased<'PDBE' | 'EBI' | 'PDBJ' | 'RCSB'>(str),
},
/**
* 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: 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: str,
/**
* The net integer charge assigned to this atom. This is the
* formal charge assignment normally found in chemical diagrams.
*/
charge: 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: coord,
/**
* 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: coord,
/**
* 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: coord,
/**
* This data item is a pointer to _chem_comp.id in the CHEM_COMP
* category.
*/
comp_id: str,
/**
* The code used to identify the atom species representing
* this atom type. Normally this code is the element
* symbol.
*/
type_symbol: str,
/**
* Atom name alignment offset in PDB atom field.
*/
pdbx_align: int,
/**
* Ordinal index for the component atom list.
*/
pdbx_ordinal: int,
/**
* An alternative x component of the coordinates for this atom in this
* component specified as orthogonal angstroms.
*/
pdbx_model_Cartn_x_ideal: coord,
/**
* An alternative y component of the coordinates for this atom in this
* component specified as orthogonal angstroms.
*/
pdbx_model_Cartn_y_ideal: coord,
/**
* An alternative z component of the coordinates for this atom in this
* component specified as orthogonal angstroms.
*/
pdbx_model_Cartn_z_ideal: coord,
/**
* The chiral configuration of the atom that is a chiral center.
*/
pdbx_stereo_config: Aliased<'R' | 'S' | 'N'>(str),
/**
* A flag indicating an aromatic atom. */
pdbx_aromatic_flag: Aliased<'Y' | 'N'>(str),
/**
* A flag indicating a leaving atom.
*/
pdbx_leaving_atom_flag: Aliased<'Y' | 'N'>(str),
},
/**
* 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: 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: str,
/**
* This data item is a pointer to _chem_comp.id in the CHEM_COMP
* category.
*/
comp_id: 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: Aliased<'sing' | 'doub' | 'trip' | 'quad' | 'arom' | 'poly' | 'delo' | 'pi'>(str),
/**
* Ordinal index for the component bond list.
*/
pdbx_ordinal: int,
/**
* Stereochemical configuration across a double bond.
*/
pdbx_stereo_config: Aliased<'E' | 'Z' | 'N'>(str),
/**
* A flag indicating an aromatic bond.
*/
pdbx_aromatic_flag: Aliased<'Y' | 'N'>(str),
},
/**
* 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: str,
/**
* This data item contains the descriptor value for this
* component.
*/
descriptor: str,
/**
* This data item contains the descriptor type.
*/ type: Aliased<'SMILES_CANNONICAL' | 'SMILES_CANONICAL' | 'SMILES' | 'SMILES' | 'InChI' | 'InChI_MAIN' | 'InChI_MAIN_FORMULA' | 'InChI_MAIN_CONNECT' | 'InChI_MAIN_HATOM' | 'InChI_CHARGE' | 'InChI_STEREO' | 'InChI_ISOTOPE' | 'InChI_FIXEDH' | 'InChI_RECONNECT' | 'InChIKey'>(str),
/**
* This data item contains the name of the program
* or library used to compute the descriptor.
*/
program: str,
/**
* This data item contains the version of the program
* or library used to compute the descriptor.
*/
program_version: 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: str,
/**
* This data item contains the identifier value for this
* component.
*/
identifier: str,
/**
* This data item contains the identifier type.
*/
type: Aliased<'COMMON NAME' | 'SYSTEMATIC NAME' | 'CAS REGISTRY NUMBER' | 'PUBCHEM Identifier' | 'MDL Identifier' | 'SYNONYM' | 'CONDENSED IUPAC CARB SYMBOL' | 'IUPAC CARB SYMBOL' | 'SNFG CARB SYMBOL'>(str),
/**
* This data item contains the name of the program
* or library used to compute the identifier.
*/
program: str,
/**
* This data item contains the version of the program
* or library used to compute the identifier.
*/
program_version: str,
},
}
export type CCD_Schema = typeof CCD_Schema;
export interface CCD_Database extends Database<CCD_Schema> {}