TmMolStar/src/extensions/volumes-and-segmentations/external-api.ts

/**
 * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
 *
 * @author Adam Midlik <midlik@gmail.com>
 */

import { splitEntryId } from './helpers';


/** Try to get author-defined contour value for isosurface from EMDB API. Return relative value 1.0, if not applicable or fails.  */
export async function tryGetIsovalue(entryId: string): Promise<{ kind: 'absolute' | 'relative', value: number } | undefined> {
    const split = splitEntryId(entryId);
    if (split.source === 'emdb') {
        try {
            const response = await fetch(`https://www.ebi.ac.uk/emdb/api/entry/map/${split.entryNumber}`);
            const json = await response.json();
            const contours: any[] = json?.map?.contour_list?.contour;
            if (contours && contours.length > 0) {
                const theContour = contours.find(c => c.primary) || contours[0];
                if (theContour.level === undefined) throw new Error('EMDB API response missing contour level.');
                return { kind: 'absolute', value: theContour.level };
            }
        } catch {
            // do nothing
        }
    }
    return undefined;
}

export async function getPdbIdsForEmdbEntry(entryId: string): Promise<string[]> {
    const split = splitEntryId(entryId);
    const result = [];
    if (split.source === 'emdb') {
        entryId = entryId.toUpperCase();
        const apiUrl = `https://www.ebi.ac.uk/pdbe/api/emdb/entry/fitted/${entryId}`;
        try {
            const response = await fetch(apiUrl);
            if (response.ok) {
                const json = await response.json();
                const jsonEntry = json[entryId] ?? [];
                for (const record of jsonEntry) {
                    const pdbs = record?.fitted_emdb_id_list?.pdb_id ?? [];
                    result.push(...pdbs);
                }
            }
        } catch (ex) {
            // do nothing
        }
    }
    return result;
}