molstar
Version:
A comprehensive macromolecular library.
119 lines (118 loc) • 5.62 kB
JavaScript
/**
* Copyright (c) 2019-2020 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 { Model } from '../../../../mol-model/structure';
import { MmcifFormat } from '../../../../mol-model-formats/structure/mmcif';
import { PluginConfig } from '../../../config';
export function getStreamingMethod(s, defaultKind = 'x-ray') {
if (!s)
return defaultKind;
const model = s.models[0];
if (!MmcifFormat.is(model.sourceData))
return defaultKind;
// Prefer EMDB entries over structure-factors (SF) e.g. for 'ELECTRON CRYSTALLOGRAPHY' entries
// like 6AXZ or 6KJ3 for which EMDB entries are available but map calculation from SF is hard.
if (Model.hasEmMap(model))
return 'em';
if (Model.hasXrayMap(model))
return 'x-ray';
// Fallbacks based on experimental method
if (Model.isFromEm(model))
return 'em';
if (Model.isFromXray(model))
return 'x-ray';
return defaultKind;
}
/** Returns EMD ID when available, otherwise falls back to PDB ID */
export function getEmIds(model) {
const ids = [];
if (!MmcifFormat.is(model.sourceData))
return [model.entryId];
const { db_id, db_name, content_type } = model.sourceData.data.db.pdbx_database_related;
if (!db_name.isDefined)
return [model.entryId];
for (let i = 0, il = db_name.rowCount; i < il; ++i) {
if (db_name.value(i).toUpperCase() === 'EMDB' && content_type.value(i) === 'associated EM volume') {
ids.push(db_id.value(i));
}
}
return ids;
}
export function getXrayIds(model) {
return [model.entryId];
}
export function getIds(method, s) {
if (!s || !s.models.length)
return [];
const model = s.models[0];
switch (method) {
case 'em': return getEmIds(model);
case 'x-ray': return getXrayIds(model);
}
}
export async function getContourLevel(provider, plugin, taskCtx, emdbId) {
switch (provider) {
case 'emdb': return getContourLevelEmdb(plugin, taskCtx, emdbId);
case 'pdbe': return getContourLevelPdbe(plugin, taskCtx, emdbId);
}
}
export async function getContourLevelEmdb(plugin, taskCtx, emdbId) {
const emdbHeaderServer = plugin.config.get(PluginConfig.VolumeStreaming.EmdbHeaderServer);
const header = await plugin.fetch({ url: `${emdbHeaderServer}/${emdbId.toUpperCase()}/header/${emdbId.toLowerCase()}.xml`, type: 'xml' }).runInContext(taskCtx);
const map = header.getElementsByTagName('map')[0];
const contours = map.getElementsByTagName('contour');
let primaryContour = contours[0];
for (let i = 1; i < contours.length; i++) {
if (contours[i].getAttribute('primary') === 'true') {
primaryContour = contours[i];
break;
}
}
const contourLevel = parseFloat(primaryContour.getElementsByTagName('level')[0].textContent);
return contourLevel;
}
export async function getContourLevelPdbe(plugin, taskCtx, emdbId) {
var _a, _b, _c, _d;
// TODO: parametrize URL in plugin settings?
emdbId = emdbId.toUpperCase();
const header = await plugin.fetch({ url: `https://www.ebi.ac.uk/emdb/api/entry/map/${emdbId}`, type: 'json' }).runInContext(taskCtx);
const contours = (_b = (_a = header === null || header === void 0 ? void 0 : header.map) === null || _a === void 0 ? void 0 : _a.contour_list) === null || _b === void 0 ? void 0 : _b.contour;
if (!contours || contours.length === 0) {
// try fallback to the old API
return getContourLevelPdbeLegacy(plugin, taskCtx, emdbId);
}
return (_d = (_c = contours.find((c) => c.primary)) === null || _c === void 0 ? void 0 : _c.level) !== null && _d !== void 0 ? _d : contours[0].level;
}
async function getContourLevelPdbeLegacy(plugin, taskCtx, emdbId) {
var _a, _b, _c;
// TODO: parametrize URL in plugin settings?
emdbId = emdbId.toUpperCase();
const header = await plugin.fetch({ url: `https://www.ebi.ac.uk/pdbe/api/emdb/entry/map/${emdbId}`, type: 'json' }).runInContext(taskCtx);
const emdbEntry = header === null || header === void 0 ? void 0 : header[emdbId];
let contourLevel = void 0;
if (((_c = (_b = (_a = emdbEntry === null || emdbEntry === void 0 ? void 0 : emdbEntry[0]) === null || _a === void 0 ? void 0 : _a.map) === null || _b === void 0 ? void 0 : _b.contour_level) === null || _c === void 0 ? void 0 : _c.value) !== void 0) {
contourLevel = +emdbEntry[0].map.contour_level.value;
}
return contourLevel;
}
export async function getEmdbIds(plugin, taskCtx, pdbId) {
var _a;
// TODO: parametrize to a differnt URL? in plugin settings perhaps
const summary = await plugin.fetch({ url: `https://www.ebi.ac.uk/pdbe/api/pdb/entry/summary/${pdbId}`, type: 'json' }).runInContext(taskCtx);
const summaryEntry = summary === null || summary === void 0 ? void 0 : summary[pdbId];
const emdbIds = [];
if ((_a = summaryEntry === null || summaryEntry === void 0 ? void 0 : summaryEntry[0]) === null || _a === void 0 ? void 0 : _a.related_structures) {
const emdb = summaryEntry[0].related_structures.filter((s) => s.resource === 'EMDB' && s.relationship === 'associated EM volume');
if (!emdb.length) {
throw new Error(`No related EMDB entry found for '${pdbId}'.`);
}
emdbIds.push(...emdb.map((e) => e.accession));
}
else {
throw new Error(`No related EMDB entry found for '${pdbId}'.`);
}
return emdbIds;
}