p2s_mapper 1.4.0 → 2.1.0

package/esm/pairwiseAlignment.d.ts

@@ -1,6 +1,6 @@
 import type { PairwiseAlignment } from './mappings.ts';
 import type { AlignmentAlgorithm } from './types.ts';
-interface AlignmentResult {
+export interface AlignmentResult {
     alignedSeq1: string;
     alignedSeq2: string;
     score: number;
@@ -27,9 +27,10 @@ export declare function needlemanWunsch(seq1: string, seq2: string, gapOpen?: nu
 export declare function smithWaterman(seq1: string, seq2: string, gapOpen?: number, gapExtend?: number): AlignmentResult;
 /** The score of a sequence aligned to itself with no gaps. */
 export declare function selfScore(seq: string): number;
-export declare function scoredAlignment(seq1: string, seq2: string, algorithm: AlignmentAlgorithm): {
+export declare function scoredAlignment(transcript: string, structure: string, algorithm: AlignmentAlgorithm): {
     alignment: PairwiseAlignment;
     score: number;
 };
-export declare function runLocalAlignment(seq1: string, seq2: string, algorithm: AlignmentAlgorithm): PairwiseAlignment;
-export {};
+export declare function alignSequences(transcript: string, structure: string, algorithm: AlignmentAlgorithm): PairwiseAlignment;
+/** @deprecated renamed to `alignSequences`, which runs either algorithm */
+export declare const runLocalAlignment: typeof alignSequences;

package/esm/pairwiseAlignment.js

@@ -307,10 +307,10 @@ export function selfScore(seq) {
     }
     return score;
 }
-export function scoredAlignment(seq1, seq2, algorithm) {
+export function scoredAlignment(transcript, structure, algorithm) {
     const { alignedSeq1, alignedSeq2, score } = algorithm === 'smith_waterman'
-        ? smithWaterman(seq1, seq2)
-        : needlemanWunsch(seq1, seq2);
+        ? smithWaterman(transcript, structure)
+        : needlemanWunsch(transcript, structure);
     return {
         alignment: {
             consensus: buildConsensus(alignedSeq1, alignedSeq2),
@@ -322,7 +322,9 @@ export function scoredAlignment(seq1, seq2, algorithm) {
         score,
     };
 }
-export function runLocalAlignment(seq1, seq2, algorithm) {
-    return scoredAlignment(seq1, seq2, algorithm).alignment;
+export function alignSequences(transcript, structure, algorithm) {
+    return scoredAlignment(transcript, structure, algorithm).alignment;
 }
+/** @deprecated renamed to `alignSequences`, which runs either algorithm */
+export const runLocalAlignment = alignSequences;
 //# sourceMappingURL=pairwiseAlignment.js.map

package/esm/pairwiseAlignment.js.map

@@ -1 +1 @@
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package/esm/pdbEntry.d.ts

@@ -0,0 +1,32 @@
+import type { FetchOptions } from './fetchUtils.ts';
+import type { UniProtStructureMapping } from './pdbUniProtMapping.ts';
+export declare const RCSB_DATA_GRAPHQL_URL = "https://data.rcsb.org/graphql";
+export interface PdbEntry {
+    /** every UniProt accession the entry's entities align to */
+    mappings: UniProtStructureMapping[];
+    /** one sequence per protein entity, in entity order; nucleic acids left
+     * out, since A, C, G, T and U are amino-acid letters too */
+    proteinSequences: string[];
+}
+export declare function pdbEntryQuery(pdbId: string): string;
+/**
+ * A GraphQL request. The server answers 200 whatever happened, so a failure
+ * is read from the body's `errors`, and counts as a 400: the server
+ * understood the query and declined it, so asking again gets the same answer.
+ */
+export declare function graphqlFetch(url: string, query: string, variables: Record<string, unknown> | undefined, opts?: FetchOptions): Promise<unknown>;
+/**
+ * The entry, retried twice: one failed request would otherwise leave a fusion
+ * construct mapped onto its partner for the whole session. An id RCSB has no
+ * entry for is a 404, which is not retried, since that answer cannot change.
+ */
+export declare function fetchPdbEntry(pdbId: string, opts?: FetchOptions): Promise<PdbEntry>;
+/** The entry's UniProt alignment alone. */
+export declare function fetchUniProtStructureMappings(pdbId: string, opts?: FetchOptions): Promise<UniProtStructureMapping[]>;
+/**
+ * Parses the `data` of `pdbEntryQuery`. Undefined when RCSB has no such
+ * entry; an entry nothing aligns to UniProt (DNA alone, say) parses to no
+ * mappings. An unparseable alignment is skipped rather than failing the
+ * entry, so a chimera with one malformed region still maps its other chains.
+ */
+export declare function parsePdbEntry(data: unknown): PdbEntry | undefined;

package/esm/pdbEntry.js

@@ -0,0 +1,174 @@
+// What RCSB knows about one PDB entry that a mapping needs, in one GraphQL
+// call: each polymer entity's sequence, its author chains, and its alignment
+// to UniProt. The alignment is what SIFTS publishes per chain, numbered the
+// same way (`entity_beg_seq_id` is label_seq_id, 1-based into the SEQRES),
+// and agreed with PDBe's SIFTS on every residue of 23 entries checked
+// (2026-10-11, 1TUP, 2RH1, 4HHB, 7K00 among them), in a tenth of the time.
+import { HttpError, isDefinitiveFailure, jsonfetch, timeout, } from "./fetchUtils.js";
+export const RCSB_DATA_GRAPHQL_URL = 'https://data.rcsb.org/graphql';
+export function pdbEntryQuery(pdbId) {
+    return `{ entry(entry_id: "${pdbId.toUpperCase()}") { polymer_entities {
+  rcsb_id
+  entity_poly { type pdbx_seq_one_letter_code_can }
+  rcsb_polymer_entity_container_identifiers { auth_asym_ids }
+  rcsb_polymer_entity_align {
+    reference_database_name reference_database_accession
+    aligned_regions { entity_beg_seq_id ref_beg_seq_id length }
+  }
+  uniprots { rcsb_id rcsb_uniprot_entry_name }
+} } }`;
+}
+const RETRY_DELAYS_MS = [1000, 3000];
+// bounded, since a view reports itself loading until the entry answers
+const TIMEOUT_MS = 20_000;
+/**
+ * A GraphQL request. The server answers 200 whatever happened, so a failure
+ * is read from the body's `errors`, and counts as a 400: the server
+ * understood the query and declined it, so asking again gets the same answer.
+ */
+export async function graphqlFetch(url, query, variables, opts) {
+    const json = await jsonfetch(url, {
+        ...opts,
+        method: 'POST',
+        headers: { 'Content-Type': 'application/json' },
+        body: JSON.stringify({ query, variables }),
+    });
+    const errors = isRecord(json) ? json.errors : undefined;
+    if (Array.isArray(errors) && errors.length > 0) {
+        const first = errors[0];
+        const message = isRecord(first) && typeof first.message === 'string'
+            ? first.message
+            : 'unknown error';
+        throw new HttpError(`${new URL(url).host}: ${message}`, 400);
+    }
+    return isRecord(json) ? json.data : undefined;
+}
+/**
+ * The entry, retried twice: one failed request would otherwise leave a fusion
+ * construct mapped onto its partner for the whole session. An id RCSB has no
+ * entry for is a 404, which is not retried, since that answer cannot change.
+ */
+export async function fetchPdbEntry(pdbId, opts) {
+    const { signal: caller, ...rest } = opts ?? {};
+    const signal = caller ?? undefined;
+    const deadline = () => signal
+        ? AbortSignal.any([signal, AbortSignal.timeout(TIMEOUT_MS)])
+        : AbortSignal.timeout(TIMEOUT_MS);
+    for (let attempt = 0;; attempt++) {
+        try {
+            const entry = parsePdbEntry(await graphqlFetch(RCSB_DATA_GRAPHQL_URL, pdbEntryQuery(pdbId), undefined, { ...rest, signal: deadline() }));
+            if (!entry) {
+                throw new HttpError(`RCSB has no entry ${pdbId.toUpperCase()}`, 404);
+            }
+            return entry;
+        }
+        catch (e) {
+            const delay = RETRY_DELAYS_MS[attempt];
+            // the caller's own abort is not a failure to retry either
+            if (delay === undefined || isDefinitiveFailure(e) || signal?.aborted) {
+                throw e;
+            }
+            await timeout(delay, signal);
+        }
+    }
+}
+/** The entry's UniProt alignment alone. */
+export async function fetchUniProtStructureMappings(pdbId, opts) {
+    return (await fetchPdbEntry(pdbId, opts)).mappings;
+}
+function isRecord(value) {
+    return typeof value === 'object' && value !== null && !Array.isArray(value);
+}
+function finiteNumber(value) {
+    return typeof value === 'number' && Number.isFinite(value) ? value : undefined;
+}
+function strings(value) {
+    return Array.isArray(value)
+        ? value.filter((v) => typeof v === 'string')
+        : [];
+}
+/**
+ * Parses the `data` of `pdbEntryQuery`. Undefined when RCSB has no such
+ * entry; an entry nothing aligns to UniProt (DNA alone, say) parses to no
+ * mappings. An unparseable alignment is skipped rather than failing the
+ * entry, so a chimera with one malformed region still maps its other chains.
+ */
+export function parsePdbEntry(data) {
+    const entry = isRecord(data) ? data.entry : undefined;
+    if (!isRecord(entry)) {
+        return undefined;
+    }
+    const entities = Array.isArray(entry.polymer_entities)
+        ? entry.polymer_entities.filter(isRecord)
+        : [];
+    const byAccession = new Map();
+    const proteinSequences = [];
+    for (const entity of entities.toSorted((a, b) => entityNumber(a.rcsb_id) - entityNumber(b.rcsb_id))) {
+        const entityId = String(entityNumber(entity.rcsb_id));
+        const poly = isRecord(entity.entity_poly) ? entity.entity_poly : undefined;
+        const sequence = poly?.pdbx_seq_one_letter_code_can;
+        if (typeof poly?.type === 'string' &&
+            poly.type.startsWith('polypeptide') &&
+            typeof sequence === 'string' &&
+            sequence.length > 0) {
+            proteinSequences.push(sequence);
+        }
+        const ids = entity.rcsb_polymer_entity_container_identifiers;
+        const chains = strings(isRecord(ids) ? ids.auth_asym_ids : undefined);
+        const names = new Map((Array.isArray(entity.uniprots) ? entity.uniprots : [])
+            .filter(isRecord)
+            .map(u => [u.rcsb_id, strings(u.rcsb_uniprot_entry_name)[0]]));
+        for (const align of Array.isArray(entity.rcsb_polymer_entity_align)
+            ? entity.rcsb_polymer_entity_align.filter(isRecord)
+            : []) {
+            const accession = align.reference_database_accession;
+            if (align.reference_database_name !== 'UniProt' ||
+                typeof accession !== 'string') {
+                continue;
+            }
+            const segments = (Array.isArray(align.aligned_regions) ? align.aligned_regions : []).flatMap(region => parseSegments(region, entityId, chains));
+            if (segments.length === 0) {
+                continue;
+            }
+            const mapping = byAccession.get(accession) ?? {
+                accession,
+                name: names.get(accession),
+                segments: [],
+            };
+            mapping.segments.push(...segments);
+            byAccession.set(accession, mapping);
+        }
+    }
+    return { mappings: [...byAccession.values()], proteinSequences };
+}
+function entityNumber(rcsbId) {
+    return typeof rcsbId === 'string' ? Number(rcsbId.split('_')[1]) : NaN;
+}
+/** One segment per chain carrying the entity, so a PDB-format file, whose
+ * entities Mol* numbers per chain, still matches by chain. */
+function parseSegments(region, entityId, chains) {
+    if (!isRecord(region)) {
+        return [];
+    }
+    const entityBeg = finiteNumber(region.entity_beg_seq_id);
+    const refBeg = finiteNumber(region.ref_beg_seq_id);
+    const length = finiteNumber(region.length);
+    if (entityBeg === undefined ||
+        refBeg === undefined ||
+        length === undefined ||
+        length < 1) {
+        return [];
+    }
+    const segment = {
+        entityId,
+        unpStart: refBeg,
+        unpEnd: refBeg + length - 1,
+        // SEQRES/label_seq_id is 1-based, structure positions are 0-based
+        structStart: entityBeg - 1,
+        structEnd: entityBeg + length - 2,
+    };
+    return chains.length === 0
+        ? [segment]
+        : chains.map(chainId => ({ ...segment, chainId }));
+}
+//# sourceMappingURL=pdbEntry.js.map

package/esm/pdbEntry.js.map

@@ -0,0 +1 @@
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package/esm/pdbUniProtMapping.d.ts

@@ -1,19 +1,14 @@
-import type { FetchOptions } from './fetchUtils.ts';
 /** One contiguous UniProt <-> structure correspondence for a single entity.
  * `unp*` are 1-based UniProt positions; `struct*` are 0-based inclusive
- * structure-sequence positions, this plugin's native coordinate. */
+ * structure-sequence positions, this package's native coordinate. */
 export interface UniProtStructureSegment {
     entityId: string;
-    /** author chain id, when the response names it */
+    /** author chain id, when the source names it */
     chainId?: string;
     unpStart: number;
     unpEnd: number;
     structStart: number;
     structEnd: number;
-    /** the endpoints' author residue numbers, the numbering a paper cites and a
-     * Mol* hover shows; absent when the response omits them */
-    authorStart?: number;
-    authorEnd?: number;
 }
 export interface UniProtStructureMapping {
     accession: string;
@@ -27,46 +22,26 @@ export interface UniProtStructureMapping {
  * the feature instead of drawing it somewhere misleading.
  */
 export type MapUniProtPosition = (uniprotPos: number) => number | undefined;
-export declare function pdbeSiftsUrl(pdbId: string): string;
-/**
- * SIFTS for an entry, retried twice: one failed request would otherwise leave a
- * fusion construct mapped onto its partner for the whole session.
- *
- * A 4xx is not retried. PDBe answers 404 for an entry it has no UniProt
- * mapping for at all — a DNA-only or obsolete entry — and that answer cannot
- * change, so the retries only postponed it: measured 2026-09-16, `1hhb` and
- * `1bna` each took three requests and ~4.8s to say so, which a caller shows as
- * four and a half seconds of "resolving" for a structure that will never
- * resolve.
- */
-export declare function fetchUniProtStructureMappings(pdbId: string, opts?: FetchOptions): Promise<UniProtStructureMapping[]>;
-/**
- * Parses a PDBe `mappings/uniprot/{pdbId}` response into one entry per UniProt
- * accession. Unparseable segments are skipped rather than failing the whole
- * response — a chimera with one malformed segment still maps its other chains.
- * The response is keyed by pdb id, so the single entry is taken whatever its key.
- */
-export declare function parseUniProtStructureMappings(json: unknown): UniProtStructureMapping[];
-/** The entity a SIFTS segment is matched against: its mmCIF id and the author
+/** The entity a segment is matched against: its mmCIF id and the author
  * chains carrying it. */
 export interface SegmentEntity {
     entityId: string;
     chains: readonly string[];
 }
 /**
- * Picks the UniProt entry that describes a given entity, with its segments
- * narrowed to that entity. Only the entity the plugin has mapped to the
- * transcript is relevant — a heteromer maps each of its chains to a different
- * accession, and using the wrong one would silently annotate the wrong protein.
- * When several accessions cover the same entity (a chimeric construct) the one
- * contributing the most residues wins.
+ * Picks the UniProt entry for a given entity, with its segments narrowed to
+ * that entity. Pass the entity mapped to the transcript: a heteromer's chains
+ * align to different accessions, and the wrong one would annotate the wrong
+ * protein. When several accessions cover one entity (a chimeric construct), the
+ * one covering the most residues wins.
  */
 export declare function chooseUniProtMappingForEntity(mappings: UniProtStructureMapping[], entity: SegmentEntity | undefined): UniProtStructureMapping | undefined;
 /**
- * Mapped structure positions that SIFTS assigns to a protein other than the
- * transcript's, on a chain that fuses two. Local alignment bridges a fusion
- * boundary, and on every GPCR fusion construct checked it scattered receptor
- * residues onto the partner, 33 of them onto T4 lysozyme in 2RH1.
+ * Mapped structure positions the entry's UniProt alignment assigns to a
+ * protein other than the transcript's, on a chain that fuses two. Local
+ * alignment bridges a fusion boundary, and on every GPCR fusion construct
+ * checked it scattered receptor residues onto the partner, 33 of them onto T4
+ * lysozyme in 2RH1.
  *
  * `mapped` is each mapped structure position and whether its pair is
  * identical. The transcript's own accession is the one whose covered positions
@@ -75,7 +50,7 @@ export declare function chooseUniProtMappingForEntity(mappings: UniProtStructure
  * fused to CDK2 covers 11 positions against 224 chance hits on the kinase, and
  * counting unmapped the peptide. Unless that accession reaches half identity
  * the transcript is taken to be neither protein, and nothing is unmapped.
- * Residues SIFTS assigns to no accession, such as tags, stay mapped.
+ * Residues assigned to no accession, such as tags, stay mapped.
  */
 export declare function fusionPartnerPositions(mappings: UniProtStructureMapping[], entity: SegmentEntity | undefined, mapped: ReadonlyMap<number, boolean>): Set<number>;
 /** 1-based UniProt position -> 0-based structure position, for an AlphaFold