molstar
Version:
A comprehensive macromolecular library.
105 lines (104 loc) • 4.01 kB
JavaScript
/**
* Copyright (c) 2019-2026 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { MoleculeType, isPolymer } from '../../../mol-model/structure/model/types.js';
import { Column, Table } from '../../../mol-data/db.js';
import { BasicSchema } from '../basic/schema.js';
export class EntityBuilder {
constructor() {
this.count = 0;
this.ids = [];
this.types = [];
this.descriptions = [];
this.compoundsMap = new Map();
this.seqresMap = new Map();
this.namesMap = new Map();
this.heteroMap = new Map();
this.chainMap = new Map();
this.sequenceMap = new Map();
this.polymerCount = 0;
}
set(type, description) {
this.count += 1;
this.ids.push(`${this.count}`);
this.types.push(type);
this.descriptions.push([description]);
}
addPolymer(map, key, options) {
if (!map.has(key)) {
this.polymerCount += 1;
this.set('polymer', (options === null || options === void 0 ? void 0 : options.customName) || `Polymer ${this.polymerCount}`);
map.set(key, `${this.count}`);
}
return map.get(key);
}
addNonPolymer(map, key, moleculeType, options) {
if (!map.has(key)) {
const type = moleculeType === MoleculeType.Saccharide ? 'branched' : 'non-polymer';
this.set(type, (options === null || options === void 0 ? void 0 : options.customName) || this.namesMap.get(key) || key);
map.set(key, `${this.count}`);
}
return map.get(key);
}
getEntityId(compId, moleculeType, chainId, options) {
if (moleculeType === MoleculeType.Water) {
if (this.waterId === undefined) {
this.set('water', (options === null || options === void 0 ? void 0 : options.customName) || 'Water');
this.waterId = `${this.count}`;
}
return this.waterId;
}
else if (isPolymer(moleculeType)) {
if (this.compoundsMap.has(chainId)) {
return this.compoundsMap.get(chainId);
}
else {
if (this.seqresMap.has(chainId)) {
const { key, residues } = this.seqresMap.get(chainId);
if (residues.has(compId)) {
return this.addPolymer(this.sequenceMap, key, options);
}
}
return this.addPolymer(this.chainMap, chainId, options);
}
}
else {
if (this.seqresMap.has(chainId)) {
const { key, residues } = this.seqresMap.get(chainId);
if (residues.has(compId)) {
return this.addNonPolymer(this.sequenceMap, key, moleculeType, options);
}
}
return this.addNonPolymer(this.heteroMap, compId, moleculeType, options);
}
}
getEntityTable() {
return Table.ofPartialColumns(BasicSchema.entity, {
id: Column.ofStringArray(this.ids),
type: Column.ofStringAliasArray(this.types),
pdbx_description: Column.ofStringListArray(this.descriptions),
}, this.count);
}
setCompounds(compounds) {
for (let i = 0, il = compounds.length; i < il; ++i) {
const { chains, description } = compounds[i];
this.set('polymer', description);
for (let j = 0, jl = chains.length; j < jl; ++j) {
this.compoundsMap.set(chains[j], `${this.count}`);
}
}
}
setNames(names) {
names.forEach(n => this.namesMap.set(n[0], n[1]));
}
setSeqres(seqresMap) {
for (const [chainId, residues] of seqresMap) {
this.seqresMap.set(chainId, {
key: residues.join('-'),
residues: new Set(residues)
});
}
}
}