TmMolStar/src/mol-plugin/behavior/dynamic/volume-streaming/util.ts

/**
 * 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 { Structure, Model } from '../../../../mol-model/structure';
import { VolumeServerInfo } from './model';
import { PluginContext } from '../../../../mol-plugin/context';
import { RuntimeContext } from '../../../../mol-task';
import { MmcifFormat } from '../../../../mol-model-formats/structure/mmcif';
import { PluginConfig } from '../../../config';

export function getStreamingMethod(s?: Structure, defaultKind: VolumeServerInfo.Kind = 'x-ray'): VolumeServerInfo.Kind {
    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: Model): string[] {
    const ids: string[] = [];
    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: 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: 'emdb' | 'pdbe', plugin: PluginContext, taskCtx: RuntimeContext, emdbId: string) {
    switch (provider) {
        case 'emdb': return getContourLevelEmdb(plugin, taskCtx, emdbId);
        case 'pdbe': return getContourLevelPdbe(plugin, taskCtx, emdbId);
    }
}

export async function getContourLevelEmdb(plugin: PluginContext, taskCtx: RuntimeContext, emdbId: string) {
    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 contourLevel = parseFloat(map.getElementsByTagName('contourLevel')[0].textContent!);

    return contourLevel;
}

export async function getContourLevelPdbe(plugin: PluginContext, taskCtx: RuntimeContext, emdbId: string) {
    // 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 = header?.map?.contour_list?.contour;

    if (!contours || contours.length === 0) {
        // try fallback to the old API
        return getContourLevelPdbeLegacy(plugin, taskCtx, emdbId);
    }

    return contours.find((c: any) => c.primary)?.level ?? contours[0].level;
}

async function getContourLevelPdbeLegacy(plugin: PluginContext, taskCtx: RuntimeContext, emdbId: string) {
    // 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?.[emdbId];
    let contourLevel: number | undefined = void 0;
    if (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?.[pdbId];
    let emdbIds: string[] = [];
    if (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;
}