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util.ts 4.36 KiB
/**
* Copyright (c) 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 { Structure, Model } from '../../../../mol-model/structure';
import { VolumeServerInfo } from './model';
import { PluginContext } from '../../../../mol-plugin/context';
import { RuntimeContext } from '../../../../mol-task';
import { getXMLNodeByName, XMLDocument } from '../../../../mol-util/xml-parser';
export function getStreamingMethod(s?: Structure, defaultKind: VolumeServerInfo.Kind = 'x-ray'): VolumeServerInfo.Kind {
if (!s) return defaultKind;
const model = s.models[0];
if (model.sourceData.kind !== 'mmCIF') return defaultKind;
const data = model.sourceData.data.exptl.method;
for (let i = 0; i < data.rowCount; i++) {
const v = data.value(i).toUpperCase();
if (v.indexOf('MICROSCOPY') >= 0) return 'em';
}
return 'x-ray';
}
/** Returns EMD ID when available, otherwise falls back to PDB ID */
export function getEmIds(model: Model): string[] {
const ids: string[] = []
if (model.sourceData.kind !== 'mmCIF') return [ model.entryId ]
const { db_id, db_name, content_type } = model.sourceData.data.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: Model): string[] {
return [ model.entryId ]
}
export function getIds(method: VolumeServerInfo.Kind, s?: Structure): string[] {
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: 'wwpdb' | 'pdbe', plugin: PluginContext, taskCtx: RuntimeContext, emdbId: string) {
switch (provider) {
case 'wwpdb': return getContourLevelWwpdb(plugin, taskCtx, emdbId)
case 'pdbe': return getContourLevelPdbe(plugin, taskCtx, emdbId)
}
}
export async function getContourLevelWwpdb(plugin: PluginContext, taskCtx: RuntimeContext, emdbId: string) {
// TODO: parametrize to a differnt URL? in plugin settings perhaps
const header = await plugin.fetch<XMLDocument>({ url: `https://ftp.wwpdb.org/pub/emdb/structures/${emdbId.toUpperCase()}/header/${emdbId.toLowerCase()}.xml`, type: 'xml' }).runInContext(taskCtx);
const map = getXMLNodeByName('map', header!.root!.children!)!
const contourLevel = parseFloat(getXMLNodeByName('contourLevel', map.children!)!.content!)
return contourLevel;
}
export async function getContourLevelPdbe(plugin: PluginContext, taskCtx: RuntimeContext, emdbId: string) {
emdbId = emdbId.toUpperCase()
// TODO: parametrize to a differnt URL? in plugin settings perhaps
const header = await plugin.fetch({ url: `https://www.ebi.ac.uk/pdbe/api/emdb/entry/map/${emdbId}`, type: 'json' }).runInContext(taskCtx);
const emdbEntry = header && header[emdbId];
let contourLevel: number | undefined = void 0;
if (emdbEntry && emdbEntry[0] && emdbEntry[0].map && emdbEntry[0].map.contour_level && emdbEntry[0].map.contour_level.value !== void 0) {
contourLevel = +emdbEntry[0].map.contour_level.value;
}
return contourLevel;
}
export async function getEmdbIds(plugin: PluginContext, taskCtx: RuntimeContext, pdbId: string) {
// TODO: parametrize to a differnt URL? in plugin settings perhaps
const summary = await plugin.fetch({ url: `https://www.ebi.ac.uk/pdbe/api/pdb/entry/summary/${pdbId}`, type: 'json' }).runInContext(taskCtx);
const summaryEntry = summary && summary[pdbId];
let emdbIds: string[] = [];
if (summaryEntry && summaryEntry[0] && summaryEntry[0].related_structures) {
const emdb = summaryEntry[0].related_structures.filter((s: any) => s.resource === 'EMDB' && s.relationship === 'associated EM volume');
if (!emdb.length) {
throw new Error(`No related EMDB entry found for '${pdbId}'.`);
}
emdbIds.push(...emdb.map((e: { accession: string }) => e.accession));
} else {
throw new Error(`No related EMDB entry found for '${pdbId}'.`);
}
return emdbIds
}