molstar
Version:
A comprehensive macromolecular library.
78 lines (77 loc) • 3.01 kB
JavaScript
"use strict";
/**
* Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.EntityBuilder = void 0;
const types_1 = require("../../../mol-model/structure/model/types");
const db_1 = require("../../../mol-data/db");
const schema_1 = require("../basic/schema");
class EntityBuilder {
constructor() {
this.count = 0;
this.ids = [];
this.types = [];
this.descriptions = [];
this.compoundsMap = new Map();
this.namesMap = new Map();
this.heteroMap = new Map();
this.chainMap = new Map();
}
set(type, description) {
this.count += 1;
this.ids.push(`${this.count}`);
this.types.push(type);
this.descriptions.push([description]);
}
getEntityId(compId, moleculeType, chainId, options) {
if (moleculeType === types_1.MoleculeType.Water) {
if (this.waterId === undefined) {
this.set('water', (options === null || options === void 0 ? void 0 : options.customName) || 'Water');
this.waterId = `${this.count}`;
}
return this.waterId;
}
else if ((0, types_1.isPolymer)(moleculeType)) {
if (this.compoundsMap.has(chainId)) {
return this.compoundsMap.get(chainId);
}
else {
if (!this.chainMap.has(chainId)) {
this.set('polymer', (options === null || options === void 0 ? void 0 : options.customName) || `Polymer ${this.chainMap.size + 1}`);
this.chainMap.set(chainId, `${this.count}`);
}
return this.chainMap.get(chainId);
}
}
else {
if (!this.heteroMap.has(compId)) {
this.set('non-polymer', (options === null || options === void 0 ? void 0 : options.customName) || this.namesMap.get(compId) || compId);
this.heteroMap.set(compId, `${this.count}`);
}
return this.heteroMap.get(compId);
}
}
getEntityTable() {
return db_1.Table.ofPartialColumns(schema_1.BasicSchema.entity, {
id: db_1.Column.ofStringArray(this.ids),
type: db_1.Column.ofStringAliasArray(this.types),
pdbx_description: db_1.Column.ofStringListArray(this.descriptions),
}, this.count);
}
setCompounds(compounds) {
for (let i = 0, il = compounds.length; i < il; ++i) {
const { chains, description } = compounds[i];
this.set('polymer', description);
for (let j = 0, jl = chains.length; j < jl; ++j) {
this.compoundsMap.set(chains[j], `${this.count}`);
}
}
}
setNames(names) {
names.forEach(n => this.namesMap.set(n[0], n[1]));
}
}
exports.EntityBuilder = EntityBuilder;