molstar
Version:
A comprehensive macromolecular library.
240 lines (239 loc) • 9.6 kB
TypeScript
/**
* Copyright (c) 2017-2019 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>
*/
import { Column, Table } from '../../../../../mol-data/db';
import { Segmentation } from '../../../../../mol-data/int';
import { ElementSymbol, MoleculeType, PolymerType } from '../../types';
import { ChainIndex, EntityIndex, ResidueIndex, ElementIndex } from '../../indexing';
import { SortedRanges } from '../../../../../mol-data/int/sorted-ranges';
export declare const AtomsSchema: {
/**
* The chemical element of this atom site.
* For mmCIF files, this points to atom_type.symbol in the ATOM_TYPE category.
*/
type_symbol: Column.Schema.Aliased<ElementSymbol>;
/**
* A component of the identifier for this atom site.
* This is a standardized name for the atom within its residue.
* For mmCIF files, this points to chem_comp_atom.atom_id in the CHEM_COMP_ATOM category.
*/
label_atom_id: Column.Schema.Str;
/**
* An alternative identifier for label_atom_id that may be provided by an author
* in order to match the identification used in the publication that describes the structure.
*/
auth_atom_id: Column.Schema.Str;
/**
* A component of the identifier for this atom site.
* Identifies an alternative conformation for this atom site.
*/
label_alt_id: Column.Schema.Str;
/**
* A component of the identifier for this atom site.
* For mmCIF files, this points to chem_comp.id in the CHEM_COMP category.
*/
label_comp_id: Column.Schema.Str;
/**
* An alternative identifier for atom_site.label_comp_id that may be provided by an author
* in order to match the identification used in the publication that describes the structure.
*/
auth_comp_id: Column.Schema.Str;
/**
* The net integer charge assigned to this atom.
* This is the formal charge assignment normally found in chemical diagrams.
*/
pdbx_formal_charge: Column.Schema.Int;
};
export declare type AtomsSchema = typeof AtomsSchema;
export declare type Atoms = Table<AtomsSchema>;
export declare const ResiduesSchema: {
/**
* The group of atoms to which the atom site belongs. This data item is provided for
* compatibility with the original Protein Data Bank format, and only for that purpose.
*/
group_PDB: Column.Schema.Aliased<"ATOM" | "HETATM">;
/**
* For mmCIF files, this points to entity_poly_seq.num in the ENTITY_POLY_SEQ category.
*/
label_seq_id: Column.Schema.Int;
/**
* An alternative identifier for atom_site.label_seq_id that may be provided by an author
* in order to match the identification used in the publication that describes the structure.
*/
auth_seq_id: Column.Schema.Int;
/**
* PDB insertion code.
*/
pdbx_PDB_ins_code: Column.Schema.Str;
};
export declare type ResiduesSchema = typeof ResiduesSchema;
export declare type Residues = Table<ResiduesSchema>;
export declare const ChainsSchema: {
/**
* A component of the identifier for this atom site.
* For mmCIF files, this points to struct_asym.id in the STRUCT_ASYM category.
*/
label_asym_id: Column.Schema.Str;
/**
* An alternative identifier for atomsite.label_asym_id that may be provided by an author
* in order to match the identification used in the publication that describes the structure.
*/
auth_asym_id: Column.Schema.Str;
/**
* For mmCIF files, this points to _entity.id in the ENTITY category.
*/
label_entity_id: Column.Schema.Str;
};
export declare type ChainsSchema = typeof ChainsSchema;
export declare type Chains = Table<ChainsSchema>;
export interface AtomicData {
atoms: Atoms;
/**
* The index of this atom in the input data.
* Required because of sorting of atoms.
*/
atomSourceIndex: Column<number>;
residues: Residues;
chains: Chains;
}
export interface AtomicDerivedData {
readonly atom: {
readonly atomicNumber: ArrayLike<number>;
};
readonly residue: {
readonly traceElementIndex: ArrayLike<ElementIndex | -1>;
readonly directionFromElementIndex: ArrayLike<ElementIndex | -1>;
readonly directionToElementIndex: ArrayLike<ElementIndex | -1>;
readonly moleculeType: ArrayLike<MoleculeType>;
readonly polymerType: ArrayLike<PolymerType>;
};
}
export interface AtomicSegments {
/** Maps residueIndex to a range of atoms [segments[rI], segments[rI + 1]) */
residueAtomSegments: Segmentation<ElementIndex, ResidueIndex>;
/**
* Maps chainIndex to a range of atoms [segments[cI], segments[cI + 1]),
*
* residues of i-th chain are accessed like this:
* const rI = residueAtomSegments.index, offsets = chainAtomSegments.offsets;
* const start = rI[offsets[i]], const end = rI[offsets[i + 1] - 1] + 1;
* for (let j = start; j < end; i++) { }
*/
chainAtomSegments: Segmentation<ElementIndex, ChainIndex>;
}
export interface AtomicIndex {
/** @returns index or -1 if not present. */
getEntityFromChain(cI: ChainIndex): EntityIndex;
/** @returns index or -1 if not present. */
findEntity(label_asym_id: string): EntityIndex;
/**
* Find chain using label_ mmCIF properties
* @returns index or -1 if not present.
*/
findChainLabel(key: AtomicIndex.ChainLabelKey): ChainIndex;
/**
* Find chain using auth_ mmCIF properties
* @returns index or -1 if not present.
*/
findChainAuth(key: AtomicIndex.ChainAuthKey): ChainIndex;
/**
* Index of the 1st occurence of this residue.
* auth_seq_id is used because label_seq_id is undefined for "ligands" in mmCIF.
* @param key.pdbx_PDB_ins_code Empty string for undefined
* @returns index or -1 if not present.
*/
findResidue(key: AtomicIndex.ResidueKey): ResidueIndex;
findResidue(label_entity_id: string, label_asym_id: string, auth_seq_id: number, pdbx_PDB_ins_code?: string): ResidueIndex;
/**
* Index of the 1st occurence of this residue.
* @param key.pdbx_PDB_ins_code Empty string for undefined
* @returns index or -1 if not present.
*/
findResidueAuth(key: AtomicIndex.ResidueAuthKey): ResidueIndex;
/**
* Find the residue index where the spefied residue should be inserted to maintain the ordering (entity_id, asym_id, seq_id, ins_code).
* Useful for determining ranges for sequence-level annotations.
* @param key.pdbx_PDB_ins_code Use empty string for undefined
*/
findResidueInsertion(key: AtomicIndex.ResidueLabelKey): ResidueIndex;
/**
* Find element index of an atom.
* @param key
* @returns index or -1 if the atom is not present.
*/
findAtom(key: AtomicIndex.AtomKey): ElementIndex;
/**
* Find element index of an atom.
* @param key
* @returns index or -1 if the atom is not present.
*/
findAtomAuth(key: AtomicIndex.AtomAuthKey): ElementIndex;
/**
* Find element index of an atom on a given residue.
* @returns index or -1 if the atom is not present.
*/
findAtomOnResidue(residueIndex: ResidueIndex, label_atom_id: string, label_alt_id?: string): ElementIndex;
/**
* Find element index of any given atom on a given residue.
* @returns first found index or -1 if none of the given atoms are present.
*/
findAtomsOnResidue(residueIndex: ResidueIndex, label_atom_ids: Set<string>): ElementIndex;
}
export declare namespace AtomicIndex {
interface ChainLabelKey {
label_entity_id: string;
label_asym_id: string;
}
interface ChainAuthKey {
auth_asym_id: string;
auth_seq_id: number;
}
interface ResidueKey {
label_entity_id: string;
label_asym_id: string;
auth_seq_id: number;
pdbx_PDB_ins_code?: string;
}
function EmptyResidueKey(): ResidueKey;
interface ResidueAuthKey {
auth_asym_id: string;
auth_comp_id: string;
auth_seq_id: number;
pdbx_PDB_ins_code?: string;
}
interface ResidueLabelKey {
label_entity_id: string;
label_asym_id: string;
label_seq_id: number;
pdbx_PDB_ins_code?: string;
}
interface AtomKey extends ResidueKey {
label_atom_id: string;
label_alt_id?: string;
}
interface AtomAuthKey extends ResidueAuthKey {
auth_atom_id: string;
label_alt_id?: string;
}
}
export interface AtomicRanges {
polymerRanges: SortedRanges<ElementIndex>;
gapRanges: SortedRanges<ElementIndex>;
cyclicPolymerMap: Map<ResidueIndex, ResidueIndex>;
}
declare type _Hierarchy = AtomicData & AtomicSegments;
export interface AtomicHierarchy extends _Hierarchy {
index: AtomicIndex;
derived: AtomicDerivedData;
}
export declare namespace AtomicHierarchy {
/** Start residue inclusive */
function chainStartResidueIndex(segs: AtomicSegments, cI: ChainIndex): ResidueIndex;
/** End residue exclusive */
function chainEndResidueIndexExcl(segs: AtomicSegments, cI: ChainIndex): ResidueIndex;
function chainResidueCount(segs: AtomicSegments, cI: ChainIndex): number;
}
export {};