molstar
Version:
A comprehensive macromolecular library.
55 lines (54 loc) • 2.87 kB
JavaScript
;
/**
* Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Adam Midlik <midlik@gmail.com>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.VolsegModelData = void 0;
const data_1 = require("../../mol-plugin-state/transforms/data");
const misc_1 = require("../../mol-plugin-state/transforms/misc");
const model_1 = require("../../mol-plugin-state/transforms/model");
const state_1 = require("../../mol-plugin/behavior/static/state");
class VolsegModelData {
constructor(rootData) {
this.entryData = rootData;
}
async loadPdb(pdbId, parent) {
const url = `https://www.ebi.ac.uk/pdbe/entry-files/download/${pdbId}.bcif`;
const dataNode = await this.entryData.plugin.build().to(parent).apply(data_1.Download, { url: url, isBinary: true }, { tags: ['fitted-model-data', `pdbid-${pdbId}`] }).commit();
const cifNode = await this.entryData.plugin.build().to(dataNode).apply(data_1.ParseCif).commit();
const trajectoryNode = await this.entryData.plugin.build().to(cifNode).apply(model_1.TrajectoryFromMmCif).commit();
await this.entryData.plugin.builders.structure.hierarchy.applyPreset(trajectoryNode, 'default', { representationPreset: 'polymer-cartoon' });
return dataNode;
}
async showPdbs(pdbIds) {
var _a, _b, _c;
const segmentsToShow = new Set(pdbIds);
const visuals = this.entryData.findNodesByTags('fitted-model-data');
for (const visual of visuals) {
const theTag = (_b = (_a = visual.obj) === null || _a === void 0 ? void 0 : _a.tags) === null || _b === void 0 ? void 0 : _b.find(tag => tag.startsWith('pdbid-'));
if (!theTag)
continue;
const id = theTag.split('-')[1];
const visibility = segmentsToShow.has(id);
(0, state_1.setSubtreeVisibility)(this.entryData.plugin.state.data, visual.transform.ref, !visibility); // true means hide, ¯\_(ツ)_/¯
segmentsToShow.delete(id);
}
const segmentsToCreate = Array.from(segmentsToShow);
if (segmentsToCreate.length === 0)
return;
let group = (_c = this.entryData.findNodesByTags('fitted-models-group')[0]) === null || _c === void 0 ? void 0 : _c.transform.ref;
if (!group) {
const newGroupNode = await this.entryData.newUpdate().apply(misc_1.CreateGroup, { label: 'Fitted Models' }, { tags: ['fitted-models-group'], state: { isCollapsed: true } }).commit();
group = newGroupNode.ref;
}
const awaiting = [];
for (const pdbId of segmentsToCreate) {
awaiting.push(this.loadPdb(pdbId, group));
}
for (const promise of awaiting)
await promise;
}
}
exports.VolsegModelData = VolsegModelData;