p2s_mapper 1.4.0 → 2.1.0

package/dist/extractStructureSequences.js.map

@@ -1 +1 @@
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package/dist/fetchUtils.d.ts

@@ -12,9 +12,9 @@ export declare class HttpError extends Error {
  * not. */
 export declare function isDefinitiveFailure(e: unknown): boolean;
 /**
- * The error a failed response deserves: status and host, plus at most the first
- * line of the body. A whole body is an HTML error page or a megabyte of JSON,
- * and pasting it into the dialog buries the one line that says what went wrong.
+ * The error for a failed response: status and host, plus at most the first line
+ * of the body. A whole body is an HTML error page or a megabyte of JSON, which
+ * hides the line that says what went wrong.
  */
 export declare function httpError(response: Response, url: string): Promise<HttpError>;
 /**
@@ -38,10 +38,10 @@ export declare function rawfetch(url: string, args?: FetchOptions): Promise<Resp
 export declare function myfetch(url: string, args?: FetchOptions): Promise<Response>;
 export declare function jsonfetch<T = unknown>(url: string, args?: FetchOptions): Promise<T>;
 /**
- * An AbortSignal's reason as a real Error. `signal.reason` is `any` — usually a
- * DOMException, but a caller can abort with anything at all — and throwing a
- * non-Error loses the stack and breaks `instanceof Error` checks in the UI's
- * error rendering. Normalize at every throw site.
+ * An AbortSignal's reason as a real Error. `signal.reason` is `any`, usually a
+ * DOMException, but a caller can abort with any value, and throwing a non-Error
+ * loses the stack and breaks `instanceof Error` checks. Use it at every throw
+ * site.
  */
 export declare function abortError(signal: AbortSignal): Error;
 export declare function timeout(time: number, signal?: AbortSignal): Promise<void>;

package/dist/fetchUtils.js

@@ -43,9 +43,9 @@ function isDefinitiveFailure(e) {
     return e instanceof HttpError && e.status >= 400 && e.status < 500;
 }
 /**
- * The error a failed response deserves: status and host, plus at most the first
- * line of the body. A whole body is an HTML error page or a megabyte of JSON,
- * and pasting it into the dialog buries the one line that says what went wrong.
+ * The error for a failed response: status and host, plus at most the first line
+ * of the body. A whole body is an HTML error page or a megabyte of JSON, which
+ * hides the line that says what went wrong.
  */
 async function httpError(response, url) {
     const detail = firstLine(await response.text().catch(() => ''));
@@ -63,10 +63,28 @@ function networkError(url, cause) {
         ? new Error(`Could not reach ${hostOf(url)}. Check your network connection; the server may also be refusing cross-origin requests from this page.`, { cause })
         : cause;
 }
+const USER_AGENT = 'p2s_mapper (+https://github.com/GMOD/p2s_mapper)';
+/**
+ * AlphaFold's prediction API answers 403 to `node`, the user agent Node's fetch
+ * sends (measured 2026-10-11), so outside a browser every request names this
+ * package unless the caller named something else. A browser sends its own, and
+ * a script-set one would cost a CORS preflight on every call.
+ */
+function withUserAgent(init) {
+    if (typeof navigator !== 'undefined' &&
+        navigator.userAgent.startsWith('Mozilla')) {
+        return init;
+    }
+    const headers = new Headers(init.headers);
+    if (!headers.has('user-agent')) {
+        headers.set('user-agent', USER_AGENT);
+    }
+    return { ...init, headers };
+}
 async function rawfetch(url, args) {
     const { fetch: f = globalThis.fetch, ...init } = args ?? {};
     try {
-        return await f(url, init);
+        return await f(url, withUserAgent(init));
     }
     catch (e) {
         throw networkError(url, e);
@@ -86,10 +104,10 @@ async function jsonfetch(url, args) {
     return response.json();
 }
 /**
- * An AbortSignal's reason as a real Error. `signal.reason` is `any` — usually a
- * DOMException, but a caller can abort with anything at all — and throwing a
- * non-Error loses the stack and breaks `instanceof Error` checks in the UI's
- * error rendering. Normalize at every throw site.
+ * An AbortSignal's reason as a real Error. `signal.reason` is `any`, usually a
+ * DOMException, but a caller can abort with any value, and throwing a non-Error
+ * loses the stack and breaks `instanceof Error` checks. Use it at every throw
+ * site.
  */
 function abortError(signal) {
     return signal.reason instanceof Error

package/dist/fetchUtils.js.map

@@ -1 +1 @@
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package/dist/index.d.ts

@@ -11,10 +11,8 @@ export * from './extractStructureSequences.ts';
 export * from './extractPerResidueConfidence.ts';
 export * from './isoformRanking.ts';
 export * from './pdbUniProtMapping.ts';
-export * from './siftsNumbering.ts';
+export * from './pdbEntry.ts';
 export * from './alphaFoldModels.ts';
-export * from './pdbeBestStructures.ts';
-export * from './pdbeEntryMolecules.ts';
 export * from './structureSources.ts';
 export * from './uniProtSearch.ts';
 export * from './dbIds.ts';

package/dist/index.js

@@ -29,13 +29,11 @@ __exportStar(require("./chooseMappedEntity.js"), exports);
 __exportStar(require("./extractStructureSequences.js"), exports);
 __exportStar(require("./extractPerResidueConfidence.js"), exports);
 __exportStar(require("./isoformRanking.js"), exports);
-// SIFTS
+// UniProt mapping
 __exportStar(require("./pdbUniProtMapping.js"), exports);
-__exportStar(require("./siftsNumbering.js"), exports);
+__exportStar(require("./pdbEntry.js"), exports);
 // Structure sources
 __exportStar(require("./alphaFoldModels.js"), exports);
-__exportStar(require("./pdbeBestStructures.js"), exports);
-__exportStar(require("./pdbeEntryMolecules.js"), exports);
 __exportStar(require("./structureSources.js"), exports);
 __exportStar(require("./uniProtSearch.js"), exports);
 __exportStar(require("./dbIds.js"), exports);

package/dist/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;AAAA,YAAY;AACZ,6CAA0B;AAC1B,gDAA6B;AAC7B,yDAAsC;AACtC,wDAAqC;AACrC,uDAAoC;AAEpC,cAAc;AACd,mDAAgC;AAChC,iDAA8B;AAC9B,sDAAmC;AAEnC,eAAe;AACf,0DAAuC;AACvC,iEAA8C;AAC9C,mEAAgD;AAChD,sDAAmC;AAEnC,kBAAkB;AAClB,yDAAsC;AACtC,gDAA6B;AAE7B,oBAAoB;AACpB,uDAAoC;AACpC,wDAAqC;AACrC,qDAAkC;AAClC,6CAA0B;AAE1B,mBAAmB;AACnB,qDAAkC;AAClC,uDAAoC;AACpC,qDAAkC;AAClC,kDAA+B"}

package/dist/isoformRanking.d.ts

@@ -10,12 +10,15 @@ export interface RankedIsoform {
     /** identical residues against the structure, for an isoform that does not
      * match it exactly; undefined with no structure to compare to */
     identical?: number;
-    /** that alignment's score, which is what ranks non-matching isoforms */
+    /** that alignment's score, which ranks the non-matching isoforms */
     score?: number;
 }
 export interface ClassifiedIsoforms {
+    /** translates to exactly the structure's sequence, longest first */
     matches: RankedIsoform[];
+    /** translates to something else, best-aligning first */
     nonMatches: RankedIsoform[];
+    /** ids of the isoforms with no translation */
     noData: string[];
 }
 /**

package/dist/mappings.d.ts

@@ -3,13 +3,11 @@ export interface AlignmentRow {
     seq: string;
 }
 /**
- * A two-row alignment whose ROW ORDER IS A CONTRACT: row 0 is the transcript,
- * row 1 is the structure. Every producer honors it — runLocalAlignment is
- * always called as (transcript, structure), and the manual-import dialog tells
- * the user to paste them in that order — and every consumer depends on it, but
- * nothing in the type can enforce it, and swapping the two silently inverts
- * every coordinate map. Read the rows through the accessors below rather than
- * indexing, so a call site states which sequence it means.
+ * A two-row alignment: row 0 is the transcript and row 1 is the structure.
+ * alignSequences takes them in that order and every consumer depends on it,
+ * but the type cannot enforce it, and swapped rows invert every coordinate map
+ * without an error. Read the rows with the accessors below, so a call site
+ * names the sequence it means.
  */
 export interface PairwiseAlignment {
     consensus: string;
@@ -21,11 +19,10 @@ export declare const structureAlignedSeq: (pa: PairwiseAlignment) => string;
  * `pairwiseAlignmentProblem` is what guarantees it. */
 export declare const alignmentLength: (pa: PairwiseAlignment) => number;
 /**
- * Why a pairwise alignment can't be used, or undefined if it's usable. The two
- * rows must be the same non-zero length — every coordinate map walks them in
- * lockstep, so a ragged pair would map positions to nonsense. Callers that
- * accept alignments from outside (the manual-import dialog) check this and
- * report it; the internal map builders assert on it.
+ * Why a pairwise alignment can't be used, or undefined if it's usable. Both
+ * rows must have the same non-zero length, because every coordinate map walks
+ * them in step. Check an alignment from outside the package with this; the
+ * internal map builders throw on it.
  */
 export declare function pairwiseAlignmentProblem(pa: PairwiseAlignment): string | undefined;
 /**

package/dist/mappings.js

@@ -19,11 +19,10 @@ exports.structureAlignedSeq = structureAlignedSeq;
 const alignmentLength = (pa) => (0, exports.transcriptAlignedSeq)(pa).length;
 exports.alignmentLength = alignmentLength;
 /**
- * Why a pairwise alignment can't be used, or undefined if it's usable. The two
- * rows must be the same non-zero length — every coordinate map walks them in
- * lockstep, so a ragged pair would map positions to nonsense. Callers that
- * accept alignments from outside (the manual-import dialog) check this and
- * report it; the internal map builders assert on it.
+ * Why a pairwise alignment can't be used, or undefined if it's usable. Both
+ * rows must have the same non-zero length, because every coordinate map walks
+ * them in step. Check an alignment from outside the package with this; the
+ * internal map builders throw on it.
  */
 function pairwiseAlignmentProblem(pa) {
     const transcript = (0, exports.transcriptAlignedSeq)(pa);

package/dist/mappings.js.map

@@ -1 +1 @@
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package/dist/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/dist/pairwiseAlignment.js

@@ -1,12 +1,12 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.MAX_ALIGNMENT_CELLS = void 0;
+exports.runLocalAlignment = exports.MAX_ALIGNMENT_CELLS = void 0;
 exports.alignmentTooLarge = alignmentTooLarge;
 exports.needlemanWunsch = needlemanWunsch;
 exports.smithWaterman = smithWaterman;
 exports.selfScore = selfScore;
 exports.scoredAlignment = scoredAlignment;
-exports.runLocalAlignment = runLocalAlignment;
+exports.alignSequences = alignSequences;
 // BLOSUM62 scoring matrix — standard 20 amino acids + B, Z, X, *
 // prettier-ignore
 const AMINO_ACIDS = ['A', 'R', 'N', 'D', 'C', 'Q', 'E', 'G', 'H', 'I', 'L', 'K', 'M', 'F', 'P', 'S', 'T', 'W', 'Y', 'V', 'B', 'Z', 'X', '*'];
@@ -316,10 +316,10 @@ function selfScore(seq) {
     }
     return score;
 }
-function scoredAlignment(seq1, seq2, algorithm) {
+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),
@@ -331,7 +331,9 @@ function scoredAlignment(seq1, seq2, algorithm) {
         score,
     };
 }
-function runLocalAlignment(seq1, seq2, algorithm) {
-    return scoredAlignment(seq1, seq2, algorithm).alignment;
+function alignSequences(transcript, structure, algorithm) {
+    return scoredAlignment(transcript, structure, algorithm).alignment;
 }
+/** @deprecated renamed to `alignSequences`, which runs either algorithm */
+exports.runLocalAlignment = alignSequences;
 //# sourceMappingURL=pairwiseAlignment.js.map

package/dist/pairwiseAlignment.js.map

@@ -1 +1 @@
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package/dist/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;