p2s_mapper 1.4.0 → 2.1.0

package/esm/structureUrls.d.ts

@@ -9,21 +9,18 @@ export declare function uniprotEntryUrl(uniprotId: string): string;
  */
 export declare function getAlphaFoldStructureUrl(uniprotId: string, version?: string): string;
 export declare function getPdbStructureUrl(pdbId: string): string;
+export declare function isPdbId(value: string): boolean;
+export declare function rcsbEntryUrl(pdbId: string): string;
 /**
- * Resolve the `{ pdbId }` shorthand to a concrete structure URL, so a
- * hand-authored snapshot or a short launch URL doesn't have to know RCSB's
- * filename format. An explicit `url` (or inline `data`) always wins.
- * Idempotent: re-resolving an already-resolved spec returns the same url.
+ * Resolve the `{ pdbId }` shorthand to a structure URL, so a hand-written config
+ * or a short launch URL needs no RCSB filename. An explicit `url` (or inline
+ * `data`) always wins, and resolving an already-resolved spec returns the same
+ * url.
  *
- * `uniprotId` deliberately resolves to no url here, and still outranks a
- * `pdbId`. An accession's files are whatever AlphaFold DB currently holds — an
- * isoform model, several fragments, a new model version — so the structure
- * keeps the accession and the structure loader asks the prediction API which
- * file to open.
- *
- * Shared by the Structure model's snapshot preprocessor and the
- * LaunchView-ProteinView extension point, which would otherwise each carry
- * their own copy of the same precedence rule.
+ * `uniprotId` resolves to no url and still outranks a `pdbId`. AlphaFold DB's
+ * files for an accession change (an isoform model, several fragments, a new
+ * model version), so the caller keeps the accession and asks
+ * `fetchAlphaFoldModels` which file to open.
  */
 export declare function resolveStructureUrl({ url, data, uniprotId, pdbId, }: {
     url?: string;
@@ -43,9 +40,9 @@ export declare function getUniprotIdFromAlphaFoldTarget(target: string): string
 export declare function getStructureUrlFromTarget(target: string, db: string): string | undefined;
 export declare function getConfidenceUrlFromTarget(target: string): string | undefined;
 /**
- * What a structure is called in the UI: its PDB id, its AlphaFold accession,
- * else the file's name. Shared by the view title, the alignment panel heading
- * and the hover readout, so one structure reads the same everywhere.
+ * The name to show for a structure: its PDB id, its AlphaFold accession, else
+ * the file's name. Use it wherever a structure is named, so each place shows
+ * the same name.
  */
 export declare function structureDisplayLabel({ url, data, uniprotId, }: {
     url?: string;

package/esm/structureUrls.js

@@ -1,11 +1,7 @@
-// Pure structure-URL builders and target parsers. Kept dependency-free so both
-// the launch flow and the ProteinView model (e.g. resolving a `uniprotId`/`pdbId`
-// shorthand at hydration) can import them without pulling in heavy launch code.
+// Structure URL builders and target parsers, with no dependencies.
 const ALPHAFOLD_VERSION = 'v6';
-// UniProt endpoints. rest.* is the machine API (the GFF the feature tracks and
-// the alignment's annotation rows both read, the FASTA the temporary protein
-// assembly is built from); www.*/entry is the human-facing entry page the UI
-// links to. Centralized so a path change is one edit rather than a grep.
+// UniProt endpoints. rest.* is the machine API, serving the features as GFF
+// and the sequence as FASTA; www.*/entry is the entry page for people.
 export function uniprotGffUrl(uniprotId) {
     return `https://rest.uniprot.org/uniprotkb/${uniprotId}.gff`;
 }
@@ -27,21 +23,25 @@ export function getAlphaFoldStructureUrl(uniprotId, version = ALPHAFOLD_VERSION)
 export function getPdbStructureUrl(pdbId) {
     return `https://files.rcsb.org/download/${pdbId}.cif`;
 }
+// A PDB id is four characters, the first a digit: 1TUP, 6ZIO. Checked before
+// a typed one reaches a fetch, so three characters on the way to four are not
+// a 404 apiece.
+export function isPdbId(value) {
+    return /^[1-9][A-Za-z0-9]{3}$/.test(value);
+}
+export function rcsbEntryUrl(pdbId) {
+    return `https://www.rcsb.org/structure/${pdbId.toUpperCase()}`;
+}
 /**
- * Resolve the `{ pdbId }` shorthand to a concrete structure URL, so a
- * hand-authored snapshot or a short launch URL doesn't have to know RCSB's
- * filename format. An explicit `url` (or inline `data`) always wins.
- * Idempotent: re-resolving an already-resolved spec returns the same url.
- *
- * `uniprotId` deliberately resolves to no url here, and still outranks a
- * `pdbId`. An accession's files are whatever AlphaFold DB currently holds — an
- * isoform model, several fragments, a new model version — so the structure
- * keeps the accession and the structure loader asks the prediction API which
- * file to open.
+ * Resolve the `{ pdbId }` shorthand to a structure URL, so a hand-written config
+ * or a short launch URL needs no RCSB filename. An explicit `url` (or inline
+ * `data`) always wins, and resolving an already-resolved spec returns the same
+ * url.
  *
- * Shared by the Structure model's snapshot preprocessor and the
- * LaunchView-ProteinView extension point, which would otherwise each carry
- * their own copy of the same precedence rule.
+ * `uniprotId` resolves to no url and still outranks a `pdbId`. AlphaFold DB's
+ * files for an accession change (an isoform model, several fragments, a new
+ * model version), so the caller keeps the accession and asks
+ * `fetchAlphaFoldModels` which file to open.
  */
 export function resolveStructureUrl({ url, data, uniprotId, pdbId, }) {
     if (url !== undefined || data !== undefined) {
@@ -108,9 +108,9 @@ export function getConfidenceUrlFromTarget(target) {
     return undefined;
 }
 /**
- * What a structure is called in the UI: its PDB id, its AlphaFold accession,
- * else the file's name. Shared by the view title, the alignment panel heading
- * and the hover readout, so one structure reads the same everywhere.
+ * The name to show for a structure: its PDB id, its AlphaFold accession, else
+ * the file's name. Use it wherever a structure is named, so each place shows
+ * the same name.
  */
 export function structureDisplayLabel({ url, data, uniprotId, }) {
     if (url === undefined) {

package/esm/structureUrls.js.map

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package/esm/types.d.ts

@@ -5,10 +5,7 @@ export declare const ALIGNMENT_ALGORITHMS: {
 };
 export declare const DEFAULT_ALIGNMENT_ALGORITHM: AlignmentAlgorithm;
 export declare const ALIGNMENT_ALGORITHM_VALUES: AlignmentAlgorithm[];
-/**
- * Parses an untrusted algorithm name (a URL session-spec param) into the union.
- * The only place a coercion is needed: the model property is an enumeration, so
- * everything downstream of hydration is already typed.
- */
+/** Parses an untrusted algorithm name, such as a URL parameter, falling back
+ * to Smith-Waterman. */
 export declare function coerceAlignmentAlgorithm(value: string): AlignmentAlgorithm;
 export declare const ALIGNMENT_ALGORITHM_LABELS: Record<AlignmentAlgorithm, string>;

package/esm/types.js

@@ -7,11 +7,8 @@ export const ALIGNMENT_ALGORITHM_VALUES = [
     'needleman_wunsch',
     'smith_waterman',
 ];
-/**
- * Parses an untrusted algorithm name (a URL session-spec param) into the union.
- * The only place a coercion is needed: the model property is an enumeration, so
- * everything downstream of hydration is already typed.
- */
+/** Parses an untrusted algorithm name, such as a URL parameter, falling back
+ * to Smith-Waterman. */
 export function coerceAlignmentAlgorithm(value) {
     return (ALIGNMENT_ALGORITHM_VALUES.find(v => v === value) ??
         DEFAULT_ALIGNMENT_ALGORITHM);

package/esm/types.js.map

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package/esm/uniProtSearch.js

@@ -47,7 +47,6 @@ async function searchByXref(id, opts) {
         return { entries: await searchUniProt(query, 10, opts), error: undefined };
     }
     catch (e) {
-        console.error(`xref search failed for ${id}:`, e);
         return { entries: [], error: e };
     }
 }
@@ -59,18 +58,14 @@ async function searchByGeneName(geneName, organismId, opts) {
         // are 284812. The descendants are asked only on a miss, because for a
         // species with reviewed subspecies entries (human and Neanderthal) they
         // turn one answer into two.
-        // The taxon itself has answered, so the wider question failing leaves
-        // that answer standing rather than turning an empty result into an error.
+        // When the descendant search fails, the taxon's own empty result stands
+        // rather than becoming an error.
         const entries = exact.length === 0 && organismId
-            ? await searchUniProt(buildGeneNameQuery(geneName, organismId, 'taxonomy_id'), 5, opts).catch((e) => {
-                console.error(`descendant-taxon search failed for ${geneName}:`, e);
-                return exact;
-            })
+            ? await searchUniProt(buildGeneNameQuery(geneName, organismId, 'taxonomy_id'), 5, opts).catch(() => exact)
             : exact;
         return { entries, error: undefined };
     }
     catch (e) {
-        console.error(`gene name search failed for ${geneName}:`, e);
         return { entries: [], error: e };
     }
 }

package/esm/uniProtSearch.js.map

@@ -1 +1 @@
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+{"version":3,"file":"uniProtSearch.js","sourceRoot":"","sources":["../src/uniProtSearch.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,SAAS,EAAE,MAAM,iBAAiB,CAAA;AAC3C,OAAO,EACL,qBAAqB,EACrB,sBAAsB,EACtB,oBAAoB,GACrB,MAAM,YAAY,CAAA;AAsCnB,MAAM,cAAc,GAClB,6DAA6D,CAAA;AAE/D,SAAS,mBAAmB,CAC1B,MAAsC;IAEtC,OAAO;QACL,SAAS,EAAE,MAAM,CAAC,gBAAgB;QAClC,EAAE,EAAE,MAAM,CAAC,WAAW;QACtB,QAAQ,EAAE,MAAM,CAAC,KAAK,EAAE,CAAC,CAAC,CAAC,EAAE,QAAQ,EAAE,KAAK;QAC5C,YAAY,EACV,MAAM,CAAC,QAAQ,EAAE,UAAU,IAAI,MAAM,CAAC,QAAQ,EAAE,cAAc;QAChE,WAAW,EAAE,MAAM,CAAC,kBAAkB,EAAE,eAAe,EAAE,QAAQ,EAAE,KAAK;QACxE,UAAU,EAAE,MAAM,CAAC,SAAS,KAAK,iCAAiC;KACnE,CAAA;AACH,CAAC;AAED,KAAK,UAAU,aAAa,CAC1B,KAAa,EACb,IAAY,EACZ,IAAmB;IAEnB,MAAM,GAAG,GAAG,mDAAmD,kBAAkB,CAAC,KAAK,CAAC,WAAW,cAAc,SAAS,IAAI,EAAE,CAAA;IAChI,MAAM,IAAI,GAAG,MAAM,SAAS,CAAmB,GAAG,EAAE,IAAI,CAAC,CAAA;IACzD,OAAO,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,mBAAmB,CAAC,CAAA;AAC9C,CAAC;AAED;;;;;;;;;;;;GAYG;AACH,MAAM,UAAU,kBAAkB,CAChC,QAAgB,EAChB,UAAmB,EACnB,QAAuC,aAAa;IAEpD,OAAO;QACL,eAAe,QAAQ,CAAC,UAAU,CAAC,GAAG,EAAE,KAAK,CAAC,GAAG;QACjD,UAAU,CAAC,CAAC,CAAC,GAAG,KAAK,IAAI,UAAU,EAAE,CAAC,CAAC,CAAC,SAAS;QACjD,eAAe;KAChB;SACE,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,KAAK,SAAS,CAAC;SAC5B,IAAI,CAAC,OAAO,CAAC,CAAA;AAClB,CAAC;AAOD,KAAK,UAAU,YAAY,CACzB,EAAU,EACV,IAAmB;IAEnB,MAAM,KAAK,GAAG,qBAAqB,CAAC,EAAE,CAAC,CAAA;IACvC,IAAI,CAAC,KAAK,EAAE,CAAC;QACX,OAAO,EAAE,OAAO,EAAE,EAAE,EAAE,KAAK,EAAE,SAAS,EAAE,CAAA;IAC1C,CAAC;IACD,IAAI,CAAC;QACH,OAAO,EAAE,OAAO,EAAE,MAAM,aAAa,CAAC,KAAK,EAAE,EAAE,EAAE,IAAI,CAAC,EAAE,KAAK,EAAE,SAAS,EAAE,CAAA;IAC5E,CAAC;IAAC,OAAO,CAAC,EAAE,CAAC;QACX,OAAO,EAAE,OAAO,EAAE,EAAE,EAAE,KAAK,EAAE,CAAC,EAAE,CAAA;IAClC,CAAC;AACH,CAAC;AAED,KAAK,UAAU,gBAAgB,CAC7B,QAAgB,EAChB,UAA8B,EAC9B,IAAmB;IAEnB,IAAI,CAAC;QACH,MAAM,KAAK,GAAG,MAAM,aAAa,CAC/B,kBAAkB,CAAC,QAAQ,EAAE,UAAU,CAAC,EACxC,UAAU,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,EACnB,IAAI,CACL,CAAA;QACD,0EAA0E;QAC1E,0EAA0E;QAC1E,sEAAsE;QACtE,wEAAwE;QACxE,4BAA4B;QAC5B,wEAAwE;QACxE,iCAAiC;QACjC,MAAM,OAAO,GACX,KAAK,CAAC,MAAM,KAAK,CAAC,IAAI,UAAU;YAC9B,CAAC,CAAC,MAAM,aAAa,CACjB,kBAAkB,CAAC,QAAQ,EAAE,UAAU,EAAE,aAAa,CAAC,EACvD,CAAC,EACD,IAAI,CACL,CAAC,KAAK,CAAC,GAAG,EAAE,CAAC,KAAK,CAAC;YACtB,CAAC,CAAC,KAAK,CAAA;QACX,OAAO,EAAE,OAAO,EAAE,KAAK,EAAE,SAAS,EAAE,CAAA;IACtC,CAAC;IAAC,OAAO,CAAC,EAAE,CAAC;QACX,OAAO,EAAE,OAAO,EAAE,EAAE,EAAE,KAAK,EAAE,CAAC,EAAE,CAAA;IAClC,CAAC;AACH,CAAC;AAED,SAAS,kBAAkB,CAAC,OAAuB;IACjD,MAAM,IAAI,GAAG,IAAI,GAAG,EAAU,CAAA;IAC9B,MAAM,MAAM,GAAmB,EAAE,CAAA;IACjC,KAAK,MAAM,KAAK,IAAI,OAAO,EAAE,CAAC;QAC5B,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,SAAS,CAAC,EAAE,CAAC;YAC/B,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,SAAS,CAAC,CAAA;YACzB,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;QACpB,CAAC;IACH,CAAC;IACD,OAAO,MAAM,CAAA;AACf,CAAC;AAQD,MAAM,CAAC,KAAK,UAAU,oBAAoB,CACxC,EACE,aAAa,GAAG,EAAE,EAClB,MAAM,EACN,QAAQ,EACR,UAAU,GAOX,EACD,IAAmB;IAEnB,MAAM,WAAW,GAAG,IAAI,GAAG,CAAC,aAAa,CAAC,CAAA;IAC1C,MAAM,cAAc,GAAG,MAAM,CAAC,CAAC,CAAC,oBAAoB,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;IACxE,IAAI,cAAc,IAAI,sBAAsB,CAAC,cAAc,CAAC,EAAE,CAAC;QAC7D,WAAW,CAAC,GAAG,CAAC,cAAc,CAAC,CAAA;IACjC,CAAC;IAED,6EAA6E;IAC7E,2EAA2E;IAC3E,uEAAuE;IACvE,MAAM,CAAC,WAAW,EAAE,UAAU,CAAC,GAAG,MAAM,OAAO,CAAC,GAAG,CAAC;QAClD,OAAO,CAAC,GAAG,CAAC,CAAC,GAAG,WAAW,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,CAAC,YAAY,CAAC,EAAE,EAAE,IAAI,CAAC,CAAC,CAAC;QAC/D,QAAQ,CAAC,CAAC,CAAC,gBAAgB,CAAC,QAAQ,EAAE,UAAU,EAAE,IAAI,CAAC,CAAC,CAAC,CAAC,SAAS;KACpE,CAAC,CAAA;IAEF,IAAI,OAAO,GAAG,kBAAkB,CAAC,WAAW,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAA;IACrE,wEAAwE;IACxE,6EAA6E;IAC7E,yEAAyE;IACzE,MAAM,mBAAmB,GACvB,UAAU,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,SAAS,CAAA;IACzE,IAAI,mBAAmB,EAAE,CAAC;QACxB,OAAO,GAAG,kBAAkB,CAAC,CAAC,GAAG,OAAO,EAAE,GAAG,mBAAmB,CAAC,OAAO,CAAC,CAAC,CAAA;IAC5E,CAAC;IAED,MAAM,cAAc,GAAG,WAAW,CAAC,IAAI,GAAG,CAAC,mBAAmB,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IACvE,MAAM,WAAW,GACf,WAAW,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,KAAK,KAAK,SAAS,CAAC,CAAC,MAAM;QACrD,CAAC,mBAAmB,EAAE,KAAK,KAAK,SAAS,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IAEpD,4EAA4E;IAC5E,6EAA6E;IAC7E,IACE,OAAO,CAAC,MAAM,KAAK,CAAC;QACpB,cAAc,GAAG,CAAC;QAClB,cAAc,KAAK,WAAW,EAC9B,CAAC;QACD,MAAM,CACJ,mBAAmB,EAAE,KAAK;YAC1B,WAAW,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,KAAK,KAAK,SAAS,CAAC,EAAE,KAAK,CACpD,CAAA;IACH,CAAC;IAED,OAAO;QACL,OAAO,EAAE,OAAO,CAAC,QAAQ,CACvB,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,MAAM,CAAC,CAAC,CAAC,UAAU,CAAC,GAAG,MAAM,CAAC,CAAC,CAAC,UAAU,CAAC,CACtD;QACD,cAAc;QACd,WAAW;KACZ,CAAA;AACH,CAAC"}

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "p2s_mapper",
-  "description": "Map a transcript's translation onto a protein structure: alignment, coordinates, chain choice, SIFTS, and the AlphaFold and PDBe lookups that find the structure",
-  "version": "1.4.0",
+  "description": "Map a transcript's translation onto a protein structure: alignment, coordinates, chain choice, UniProt mapping, and the AlphaFold and RCSB lookups that find the structure",
+  "version": "2.1.0",
   "packageManager": "pnpm@11.15.1",
   "repository": {
     "type": "git",
@@ -25,6 +25,7 @@
     "clean": "rimraf dist esm",
     "format": "prettier --write .",
     "format:check": "prettier --check .",
+    "docs:api": "node scripts/api-doc.ts",
     "lint": "eslint --report-unused-disable-directives --max-warnings 0",
     "typecheck": "tsc --noEmit -p tsconfig.lint.json",
     "prebuild": "pnpm clean",

package/src/alignmentQuality.ts

@@ -7,21 +7,21 @@ import {
 import type { PairwiseAlignment } from './mappings.ts'
 
 export interface AlignmentQuality {
-  /** columns carrying a residue on both rows, i.e. mapped positions */
+  /** columns with a residue in both rows, i.e. mapped positions */
   aligned: number
   identical: number
   transcriptLength: number
   structureLength: number
   /** identical over aligned; 0 when nothing aligned */
   identity: number
-  /** identical over the shorter of the two sequences: the statistic that
-   * separates a real match from a chance local alignment, see below */
+  /** identical over the shorter of the two sequences, which separates a
+   * real match from a chance local alignment (see LOW_IDENTITY_OVER_SHORTER) */
   identityOverShorter: number
   /** aligned over the structure's length */
   structureCoverage: number
   /** first and last transcript residue the alignment covers, 1-based
-   * inclusive; 0 when nothing aligned. A structure is usually a fragment, and
-   * which part of the protein it holds is the reader's first question. */
+   * inclusive; 0 when nothing aligned. A structure is usually a fragment, so
+   * these show which part of the protein it contains. */
   transcriptStart: number
   transcriptEnd: number
 }

package/src/alphaFoldModels.ts

@@ -78,11 +78,11 @@ export async function fetchAlphaFoldModels(
 
 /**
  * The model to open for a gene's transcripts: one folded from exactly a
- * transcript's translation, canonical first, so the view maps it as an
- * identity; else the canonical model; else the longest isoform model.
+ * transcript's translation, canonical first, so every residue maps to itself;
+ * else the canonical model; else the longest isoform model.
  *
- * Takes any record of sequences, since the structure loader knows one
- * translation rather than a gene's isoforms.
+ * Takes any record of sequences, since a caller may know one translation rather
+ * than a gene's isoforms.
  */
 export function pickAlphaFoldModel(
   models: AlphaFoldModel[],

package/src/chooseMappedEntity.ts

@@ -24,13 +24,13 @@ export function interactionMatchesMappedEntity(
 }
 
 export interface EntitySelection extends ScoredAlignment {
-  /** index into the candidate array of the entity that is the transcript's */
+  /** index of the chosen entity in the candidate array */
   index: number
 }
 
 export interface ScoredAlignment {
-  /** alignment of the transcript against the entity (stop codons stripped on
-   * both sides, matching the rest of the mapping pipeline) */
+  /** alignment of the transcript against the entity, with stop codons
+   * stripped from both */
   alignment: PairwiseAlignment
   /** identical aligned residues */
   matches: number
@@ -56,8 +56,7 @@ export interface EntityCandidate {
  * usually is: on 1H26 the 11-residue p53 peptide matches 11 while CDK2 accrues
  * 58 scattered identities, and on 4ZZJ SIRT1 beats the 7-residue p53 peptide
  * 63 to 6. The Smith-Waterman score is no better there (56 vs 58). Dividing
- * by length asks the question the picker actually has, which chain *is* this
- * gene's product: the peptide scores 0.69 and 0.50, the partners 0.19 and
+ * by the shorter length identifies the chain that *is* this gene's product: the peptide scores 0.69 and 0.50, the partners 0.19 and
  * 0.17, and across a ribosome's 55 chains no decoy passes 0.29.
  *
  * Dividing by the *entity's* length alone penalised a fusion construct: a
@@ -136,18 +135,16 @@ export function alignTranscriptToEntity(
 }
 
 /**
- * Pick which polymer entity of a structure corresponds to the transcript.
+ * Pick the polymer entity of a structure that is the transcript's protein.
  *
- * The plugin historically hardcoded entity `[0]`, which silently mis-maps every
- * heteromeric / protein-DNA / processed-peptide structure where the protein of
- * interest is some other chain. Selecting by alignment makes the structure self-
- * describe which entity is the gene's protein: an exact sequence match wins
- * outright, otherwise the entity with the highest identity over the shorter
- * sequence (see `explainedFraction`). Nucleic-acid entities are never
- * candidates.
+ * Taking entity `[0]` mis-maps every heteromeric, protein-DNA or
+ * processed-peptide structure where the protein is another chain. An exact
+ * sequence match wins outright; otherwise the entity with the highest identity
+ * over the shorter sequence wins (see `explainedFraction`). Nucleic-acid
+ * entities are never candidates.
  *
- * Returns `undefined` only when there is nothing to map (no transcript or no
- * protein entities) — never a silent fallback to the wrong entity.
+ * Returns `undefined` only when there is nothing to map: no transcript, or no
+ * protein entity. It never falls back to another entity.
  */
 export function chooseMappedEntity(
   transcript: string,

package/src/coordinates.ts

@@ -8,21 +8,19 @@ import { invertMap } from './invertMap.ts'
 import type { PairwiseAlignment } from './mappings.ts'
 
 /**
- * Branded coordinate spaces. Every position in this plugin is a bare `number`,
- * but the *meaning* differs: a structure residue index is not interchangeable
- * with a transcript residue index or an alignment column, and mixing them is
- * the root cause of the off-by-one class of bugs. Branding makes the compiler
- * reject cross-space mixing; construct values with the helpers below at the
- * boundaries where raw numbers enter (molstar picks, hover events, features).
+ * Branded coordinate spaces. Every position is a plain `number` at runtime, but
+ * a structure residue index, a transcript residue index and an alignment column
+ * mean different things, and mixing them causes off-by-one bugs. The brands
+ * make the compiler reject mixing; wrap a raw number with the helpers below
+ * where it enters, such as a molstar pick, a hover event or a feature.
  *
- * Conventions: all are 0-based. StructurePos indexes the ungapped structure
- * sequence; TranscriptPos the ungapped transcript sequence; AlignmentCol a
- * column of the pairwise alignment (gaps included).
+ * All are 0-based. StructurePos indexes the ungapped structure sequence,
+ * TranscriptPos the ungapped transcript sequence, and AlignmentCol a column of
+ * the pairwise alignment, gaps included.
  */
-type Branded<B extends string> = number & { readonly __brand: B }
-export type StructurePos = Branded<'StructurePos'>
-export type TranscriptPos = Branded<'TranscriptPos'>
-export type AlignmentCol = Branded<'AlignmentCol'>
+export type StructurePos = number & { readonly __brand: 'StructurePos' }
+export type TranscriptPos = number & { readonly __brand: 'TranscriptPos' }
+export type AlignmentCol = number & { readonly __brand: 'AlignmentCol' }
 
 export const structurePos = (n: number) => n as StructurePos
 export const transcriptPos = (n: number) => n as TranscriptPos
@@ -45,10 +43,9 @@ export interface CoordinateMapper {
   transcriptToAlignment: (p: TranscriptPos) => AlignmentCol | undefined
   alignmentToTranscript: (c: AlignmentCol) => TranscriptPos | undefined
   /**
-   * Raw lookup tables, for consumers that iterate the whole map rather than
-   * convert a single position (e.g. per-residue track rendering, selection of
-   * all aligned residues). Plain numbers — prefer the typed methods above for
-   * point conversions.
+   * The lookup tables as plain numbers, for code that iterates a whole map,
+   * such as drawing a per-residue track or selecting every aligned residue.
+   * Use the typed methods above to convert one position.
    */
   readonly maps: CoordinateMaps
 }

package/src/dbIds.ts

@@ -3,7 +3,7 @@
 // keyword, the regex (Ensembl patterns cover human ENS, mouse ENSMUS, zebrafish
 // ENSDAR, etc.), and a human-readable label. Recognition, label rendering, and
 // xref-query building all derive from this list, so a new ID type is one entry.
-type DbType = 'ensembl' | 'refseq' | 'ccds' | 'hgnc' | 'geneid'
+export type DbType = 'ensembl' | 'refseq' | 'ccds' | 'hgnc' | 'geneid'
 
 const DB_ID_PATTERNS: { db: DbType; pattern: RegExp; label: string }[] = [
   { db: 'ensembl', pattern: /^ENS[A-Z]*G\d+/i, label: 'Ensembl gene' },

package/src/extractPerResidueConfidence.ts

@@ -2,7 +2,7 @@
 // store the per-residue pLDDT in the B-factor column (B_iso_or_equiv), so the
 // first atom of each residue yields pLDDT for a predicted model and the
 // crystallographic B-factor for an experimental one.
-interface ConfidenceModel {
+export interface ConfidenceModel {
   obj?: {
     data: {
       atomicConformation: {

package/src/extractStructureSequences.ts

@@ -1,51 +1,44 @@
 /** A polymer entity of a loaded structure: its mmCIF entity id, its one-letter
- * sequence, and the molstar `label_seq_id` of each of those residues.
+ * sequence, and the molstar `label_seq_id` of each residue.
  *
- * The entity id is what lets every downstream step talk about "the gene's
- * protein" by identity instead of by the fragile entity-[0] position.
+ * Structure positions are 0-based indices into `seq`, and molstar selects
+ * residues by `label_seq_id`. The two differ by 1 only when the entity's
+ * sequence covers every residue from 1, which holds for any mmCIF with an
+ * `entity_poly_seq` category (all of RCSB and AlphaFold) and for a PDB file
+ * with SEQRES records, from which molstar builds that category.
  *
- * `seqIds` is what lets it talk about a *residue* by identity. Structure
- * positions in this plugin are 0-based indices into `seq`; molstar addresses
- * residues by `label_seq_id`. Those are related by `+1` only when the entity's
- * sequence covers every residue from 1 — true for any mmCIF with an
- * `entity_poly_seq` category (all of RCSB and AlphaFold) and for PDB files
- * carrying SEQRES records, because molstar synthesizes the category from them.
- *
- * A PDB-format file with no SEQRES has no such category, so molstar falls back
- * to `StructureSequence.fromHierarchy` and takes `label_seq_id` straight from
- * the observed residues' author numbering: a chain whose coordinates start at
- * residue 94 yields seqIds 94.., and an unobserved loop leaves a hole. Deriving
- * the id arithmetically there is off by the whole offset, in both directions —
- * every hover reads the wrong residue and every highlight paints the wrong one.
- * So carry the real ids and convert through them.
+ * For a PDB file without SEQRES, molstar falls back to
+ * `StructureSequence.fromHierarchy` and takes `label_seq_id` from the observed
+ * residues' author numbering: a chain whose coordinates start at residue 94 has
+ * seqIds 94.., and an unobserved loop leaves a gap. Adding 1 there is off by the
+ * whole offset, in both directions, so convert through `seqIds`.
  */
 export interface Entity {
+  /** mmCIF entity id */
   entityId: string
+  /** one letter per residue, observed or not */
   seq: string
+  /** molstar `label_seq_id` per position of `seq` */
   seqIds: number[]
-  /** author chain ids carrying this entity, e.g. ['A', 'B'] for a homodimer;
-   * what a user recognises from the PDB entry page, where the entity id is
-   * molstar's own bookkeeping */
+  /** author chain ids of this entity, e.g. ['A', 'B'] for a homodimer, as
+   * the PDB entry page lists them */
   chains: string[]
-  /** DNA, RNA or a hybrid, by molstar's entity subtype. Its one-letter
-   * sequence spells amino acids too (A, C, G, T, U), so it has to be kept
-   * out of the transcript alignment rather than merely scoring low. */
+  /** DNA, RNA or a hybrid, by molstar's entity subtype. A, C, G, T and U
+   * are amino-acid letters too, so chooseMappedEntity skips these. */
   nucleicAcid?: boolean
-  /** `auth_seq_id` per position: the numbering the depositors chose, which
-   * for an RCSB entry is the one papers and UniProt cite (1TUP's position 154
-   * is R248) and what Mol*'s own hover label shows. Display only; every
-   * coordinate the plugin computes with stays a 0-based position, and molstar
-   * is addressed through `seqIds`. Absent when the model has no atomic
-   * hierarchy to read it from. See `residueNumber`. */
+  /** `auth_seq_id` per position: the depositors' numbering, which papers cite
+   * (1TUP's position 154 is R248) and Mol*'s hover shows. For display only;
+   * use `seqIds` to select residues in Mol*. Absent when the model has no
+   * atomic hierarchy. See `residueNumber`. */
   authSeqIds?: number[]
 }
 
-interface Column<T> {
+export interface Column<T> {
   rowCount: number
   value(row: number): T
 }
 
-interface StructureModel {
+export interface StructureModel {
   obj?: {
     data: {
       entities?: {
@@ -284,8 +277,8 @@ export function entityLabel(entity: Entity) {
   return `${chains} (${entity.seq.length} ${entity.nucleicAcid ? 'nt' : 'aa'})`
 }
 
-/** The protein chains' sequences, for the launch dialog's isoform matching,
- * which has no use for a DNA strand that happens to align. */
+/** The protein chains' sequences, for ranking isoforms against a structure.
+ * DNA chains are left out, because their letters align as amino acids. */
 export function extractStructureSequences(
   model: StructureModel,
 ): string[] | undefined {

package/src/fetchUtils.ts

@@ -36,9 +36,9 @@ export function isDefinitiveFailure(e: unknown) {
 }
 
 /**
- * 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 async function httpError(response: Response, url: string) {
   const detail = firstLine(await response.text().catch(() => ''))
@@ -75,10 +75,32 @@ export interface FetchOptions extends RequestInit {
   fetch?: typeof globalThis.fetch
 }
 
+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: RequestInit) {
+  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 }
+}
+
 export async function rawfetch(url: string, args?: FetchOptions) {
   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)
   }
@@ -105,10 +127,10 @@ export async function jsonfetch<T = unknown>(
 }
 
 /**
- * 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 function abortError(signal: AbortSignal) {
   return signal.reason instanceof Error

package/src/index.ts

@@ -16,14 +16,12 @@ export * from './extractStructureSequences.ts'
 export * from './extractPerResidueConfidence.ts'
 export * from './isoformRanking.ts'
 
-// SIFTS
+// UniProt mapping
 export * from './pdbUniProtMapping.ts'
-export * from './siftsNumbering.ts'
+export * from './pdbEntry.ts'
 
 // Structure sources
 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/src/isoformRanking.ts

@@ -17,16 +17,16 @@ 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 {
-  // protein matches the structure residues, longest first
+  /** translates to exactly the structure's sequence, longest first */
   matches: RankedIsoform[]
-  // has a protein sequence but doesn't match the structure, best-aligning first
+  /** translates to something else, best-aligning first */
   nonMatches: RankedIsoform[]
-  // ids of the isoforms no protein sequence could be computed for
+  /** ids of the isoforms with no translation */
   noData: string[]
 }