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@@ -0,0 +1,105 @@
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+import { Mat4 } from 'molstar/lib/mol-math/linear-algebra';
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+
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+const ALIGNMENT_URL = 'https://alignment.rcsb.org/api/v1-beta/';
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+
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+// TODO probably move to selection.ts
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+export type Residue = { label_asym_id: string, struct_oper_id?: string, label_seq_id: number };
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+export type MotifSelection = { entry_id: string, residue_ids: Residue[] }
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+export type MotifAlignmentRequest = {
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+ query: {
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+ entry_id: string,
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+ residue_ids: Residue[]
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+ },
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+ hits: ({
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+ id: string,
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+ assembly_id: string,
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+ } & MotifSelection)[]
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+}
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+
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+export async function alignMotifs(query: MotifSelection, hit: MotifSelection): Promise<{ rmsd: number, matrix: Mat4 }> {
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+ const q = {
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+ mode: 'pairwise',
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+ method: {
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+ name: 'qcp',
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+ parameters: {
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+ atom_pairing_strategy: 'all'
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+ }
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+ },
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+ structures: [
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+ {
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+ entry_id: query.entry_id,
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+ residue_ids: convertToPecosIdentifiers(query.residue_ids)
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+ },
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+ {
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+ entry_id: hit.entry_id,
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+ residue_ids: convertToPecosIdentifiers(hit.residue_ids)
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+ }
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+ ]
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+ };
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+
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+ const formData = new FormData();
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+ formData.append('query', JSON.stringify(q));
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+
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+ const r = await fetch(ALIGNMENT_URL + 'structures/submit', { method: 'POST', body: formData });
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+
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+ if (r.status !== 200) {
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+ throw new Error('Failed to submit the job');
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+ }
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+
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+ const uuid = await r.text();
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+ const url = ALIGNMENT_URL + 'structures/results?uuid=' + uuid;
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+ // polls every 25ms for up to 10 seconds
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+ const result = await pollUntilDone(url, 25, 10 * 1000);
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+
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+ const { alignment_summary, rigid_blocks } = result.results[0];
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+ return { rmsd: alignment_summary.scores[0].value, matrix: rigid_blocks[0].transformations[0] };
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+}
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+
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+// convert strucmotif/arches residue identifiers to the pecos/sierra flavor
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+function convertToPecosIdentifiers(identifiers: Residue[]) {
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+ return identifiers.map(i => {
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+ const o = Object.create(null);
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+ Object.assign(o, {
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+ asym_id: i.label_asym_id,
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+ seq_id: i.label_seq_id
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+ });
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+ if (i.struct_oper_id) Object.assign(o, { struct_oper_id: i.struct_oper_id });
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+ return o;
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+ });
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+}
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+
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+// create a promise that resolves after a short delay
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+function delay(t: number) {
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+ return new Promise(function(resolve) {
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+ setTimeout(resolve, t);
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+ });
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+}
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+
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+/**
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+ * Poll until results are available.
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+ * @param url is the URL to request
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+ * @param interval is how often to poll
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+ * @param timeout is how long to poll waiting for a result (0 means try forever)
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+ */
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+async function pollUntilDone(url: string, interval: number, timeout: number) {
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+ const start = Date.now();
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+ async function run(): Promise<any> {
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+ const r = await fetch(url);
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+ const data = await r.json();
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+ if (data.info.status === 'COMPLETE') {
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+ // we know we're done here, return from here whatever you
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+ // want the final resolved value of the promise to be
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+ return data;
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+ } else if (data.info.status === 'ERROR') {
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+ throw new Error('Failed to complete the job. Error: ' + data.info.message);
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+ } else {
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+ if (timeout !== 0 && Date.now() - start > timeout) {
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+ throw new Error('timeout error on pollUntilDone');
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+ } else {
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+ // run again with a short delay
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+ return delay(interval).then(run);
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+ }
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+ }
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+ }
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+ return run();
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+}
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JonStargaryen