p2s_mapper 1.4.0 → 2.1.0

package/esm/alphaFoldModels.js

@@ -43,11 +43,11 @@ export async function fetchAlphaFoldModels(uniprotId, opts) {
 }
 /**
  * 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, isoformSequences) {
     const translations = new Set(Object.values(isoformSequences ?? {}).map(v => stripStopCodon(v.seq)));

package/esm/chooseMappedEntity.d.ts

@@ -9,12 +9,12 @@ import type { AlignmentAlgorithm } from './types.ts';
  */
 export declare function interactionMatchesMappedEntity(entityId: string, mappedEntityId: string | undefined): boolean;
 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;
@@ -39,17 +39,15 @@ export declare function explainedFraction(matches: number, transcriptLength: num
  */
 export declare function alignTranscriptToEntity(transcript: string, entitySeq: string, algorithm: AlignmentAlgorithm): ScoredAlignment | undefined;
 /**
- * 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 declare function chooseMappedEntity(transcript: string, entities: readonly (string | EntityCandidate)[], algorithm: AlignmentAlgorithm): EntitySelection | undefined;

package/esm/chooseMappedEntity.js

@@ -19,8 +19,7 @@ export function interactionMatchesMappedEntity(entityId, mappedEntityId) {
  * 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
@@ -85,18 +84,16 @@ export function alignTranscriptToEntity(transcript, entitySeq, algorithm) {
     };
 }
 /**
- * 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, entities, algorithm) {
     const t = stripStopCodon(transcript);

package/esm/chooseMappedEntity.js.map

@@ -1 +1 @@
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+{"version":3,"file":"chooseMappedEntity.js","sourceRoot":"","sources":["../src/chooseMappedEntity.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,iBAAiB,EACjB,eAAe,EACf,SAAS,GACV,MAAM,wBAAwB,CAAA;AAC/B,OAAO,EAAE,cAAc,EAAE,MAAM,qBAAqB,CAAA;AACpD,OAAO,EAAE,mBAAmB,EAAE,oBAAoB,EAAE,MAAM,eAAe,CAAA;AAKzE;;;;;;GAMG;AACH,MAAM,UAAU,8BAA8B,CAC5C,QAAgB,EAChB,cAAkC;IAElC,OAAO,cAAc,KAAK,SAAS,IAAI,QAAQ,KAAK,cAAc,CAAA;AACpE,CAAC;AA2BD;;;;;;;;;;;;;;;;;;;GAmBG;AACH,MAAM,qBAAqB,GAAG,CAAC,CAAA;AAE/B,MAAM,UAAU,iBAAiB,CAC/B,OAAe,EACf,gBAAwB,EACxB,YAAoB;IAEpB,OAAO,CACL,OAAO,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,gBAAgB,EAAE,YAAY,CAAC,GAAG,qBAAqB,CAAC,CAC7E,CAAA;AACH,CAAC;AAED,SAAS,YAAY,CAAC,EAAqB;IACzC,MAAM,CAAC,GAAG,oBAAoB,CAAC,EAAE,CAAC,CAAA;IAClC,MAAM,CAAC,GAAG,mBAAmB,CAAC,EAAE,CAAC,CAAA;IACjC,IAAI,OAAO,GAAG,CAAC,CAAA;IACf,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QAClC,MAAM,EAAE,GAAG,CAAC,CAAC,CAAC,CAAC,CAAA;QACf,MAAM,EAAE,GAAG,CAAC,CAAC,CAAC,CAAC,CAAA;QACf,IAAI,EAAE,KAAK,GAAG,IAAI,EAAE,KAAK,GAAG,IAAI,EAAE,EAAE,WAAW,EAAE,KAAK,EAAE,EAAE,WAAW,EAAE,EAAE,CAAC;YACxE,OAAO,EAAE,CAAA;QACX,CAAC;IACH,CAAC;IACD,OAAO,OAAO,CAAA;AAChB,CAAC;AAED;;;;;GAKG;AACH,MAAM,UAAU,uBAAuB,CACrC,UAAkB,EAClB,SAAiB,EACjB,SAA6B;IAE7B,MAAM,CAAC,GAAG,cAAc,CAAC,UAAU,CAAC,CAAA;IACpC,MAAM,CAAC,GAAG,cAAc,CAAC,SAAS,CAAC,CAAA;IACnC,IAAI,CAAC,CAAC,IAAI,CAAC,CAAC,IAAI,iBAAiB,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC,EAAE,CAAC;QACtD,OAAO,SAAS,CAAA;IAClB,CAAC;IACD,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC;QACZ,OAAO;YACL,SAAS,EAAE;gBACT,SAAS,EAAE,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,MAAM,CAAC;gBAC/B,IAAI,EAAE;oBACJ,EAAE,EAAE,EAAE,MAAM,EAAE,GAAG,EAAE,CAAC,EAAE;oBACtB,EAAE,EAAE,EAAE,MAAM,EAAE,GAAG,EAAE,CAAC,EAAE;iBACvB;aACF;YACD,OAAO,EAAE,CAAC,CAAC,MAAM;YACjB,SAAS,EAAE,iBAAiB,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;YAC1D,KAAK,EAAE,SAAS,CAAC,CAAC,CAAC;SACpB,CAAA;IACH,CAAC;IACD,MAAM,EAAE,SAAS,EAAE,KAAK,EAAE,GAAG,eAAe,CAAC,CAAC,EAAE,CAAC,EAAE,SAAS,CAAC,CAAA;IAC7D,MAAM,OAAO,GAAG,YAAY,CAAC,SAAS,CAAC,CAAA;IACvC,OAAO;QACL,SAAS;QACT,OAAO;QACP,SAAS,EAAE,iBAAiB,CAAC,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACzD,KAAK;KACN,CAAA;AACH,CAAC;AAED;;;;;;;;;;;GAWG;AACH,MAAM,UAAU,kBAAkB,CAChC,UAAkB,EAClB,QAA+C,EAC/C,SAA6B;IAE7B,MAAM,CAAC,GAAG,cAAc,CAAC,UAAU,CAAC,CAAA;IACpC,IAAI,CAAC,CAAC,EAAE,CAAC;QACP,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,MAAM,UAAU,GAAG,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAClC,OAAO,CAAC,KAAK,QAAQ;QACnB,CAAC,CAAC,EAAE,GAAG,EAAE,cAAc,CAAC,CAAC,CAAC,EAAE;QAC5B,CAAC,CAAC,EAAE,GAAG,CAAC,EAAE,GAAG,EAAE,cAAc,CAAC,CAAC,CAAC,GAAG,CAAC,EAAE,CACzC,CAAA;IACD,MAAM,UAAU,GAAG,UAAU,CAAC,SAAS,CACrC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,WAAW,IAAI,CAAC,CAAC,GAAG,CAAC,MAAM,GAAG,CAAC,IAAI,CAAC,CAAC,GAAG,KAAK,CAAC,CACvD,CAAA;IACD,IAAI,UAAU,KAAK,CAAC,CAAC,EAAE,CAAC;QACtB,MAAM,KAAK,GAAG,uBAAuB,CACnC,CAAC,EACD,UAAU,CAAC,UAAU,CAAE,CAAC,GAAG,EAC3B,SAAS,CACT,CAAA;QACF,OAAO,EAAE,KAAK,EAAE,UAAU,EAAE,GAAG,KAAK,EAAE,CAAA;IACxC,CAAC;IAED,4EAA4E;IAC5E,2EAA2E;IAC3E,kEAAkE;IAClE,MAAM,KAAK,GAAG,IAAI,GAAG,EAAuC,CAAA;IAC5D,IAAI,IAAiC,CAAA;IACrC,KAAK,IAAI,KAAK,GAAG,CAAC,EAAE,KAAK,GAAG,UAAU,CAAC,MAAM,EAAE,KAAK,EAAE,EAAE,CAAC;QACvD,MAAM,EAAE,GAAG,EAAE,WAAW,EAAE,GAAG,UAAU,CAAC,KAAK,CAAE,CAAA;QAC/C,IAAI,WAAW,EAAE,CAAC;YAChB,SAAQ;QACV,CAAC;QACD,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC;YACpB,KAAK,CAAC,GAAG,CAAC,GAAG,EAAE,uBAAuB,CAAC,CAAC,EAAE,GAAG,EAAE,SAAS,CAAC,CAAC,CAAA;QAC5D,CAAC;QACD,MAAM,MAAM,GAAG,KAAK,CAAC,GAAG,CAAC,GAAG,CAAC,CAAA;QAC7B,IAAI,MAAM,IAAI,CAAC,CAAC,IAAI,IAAI,MAAM,CAAC,SAAS,GAAG,IAAI,CAAC,SAAS,CAAC,EAAE,CAAC;YAC3D,IAAI,GAAG,EAAE,KAAK,EAAE,GAAG,MAAM,EAAE,CAAA;QAC7B,CAAC;IACH,CAAC;IACD,OAAO,IAAI,CAAA;AACb,CAAC"}

package/esm/coordinates.d.ts

@@ -1,22 +1,24 @@
 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 = number & {
+    readonly __brand: 'StructurePos';
+};
+export type TranscriptPos = number & {
+    readonly __brand: 'TranscriptPos';
+};
+export type AlignmentCol = number & {
+    readonly __brand: 'AlignmentCol';
 };
-export type StructurePos = Branded<'StructurePos'>;
-export type TranscriptPos = Branded<'TranscriptPos'>;
-export type AlignmentCol = Branded<'AlignmentCol'>;
 export declare const structurePos: (n: number) => StructurePos;
 export declare const transcriptPos: (n: number) => TranscriptPos;
 export declare const alignmentCol: (n: number) => AlignmentCol;
@@ -36,10 +38,9 @@ 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;
 }
@@ -63,4 +64,3 @@ export declare function transcriptRangeToStructureRange(mapper: CoordinateMapper
     start: number;
     end: number;
 } | undefined;
-export {};

package/esm/coordinates.js.map

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

@@ -1,4 +1,4 @@
-type DbType = 'ensembl' | 'refseq' | 'ccds' | 'hgnc' | 'geneid';
+export type DbType = 'ensembl' | 'refseq' | 'ccds' | 'hgnc' | 'geneid';
 export declare function matchDbIdPattern(id: string): {
     db: DbType;
     pattern: RegExp;
@@ -13,4 +13,3 @@ export declare function getDbIdLabel(id: string): string;
  * "xref:ensembl-ENST00000123". HGNC strips its redundant "HGNC:" prefix. */
 export declare function buildUniProtXrefQuery(id: string): string | undefined;
 export declare function stripTrailingVersion(s?: string): string | undefined;
-export {};

package/esm/extractPerResidueConfidence.d.ts

@@ -1,4 +1,4 @@
-interface ConfidenceModel {
+export interface ConfidenceModel {
     obj?: {
         data: {
             atomicConformation: {
@@ -46,4 +46,3 @@ export declare function extractPerResidueConfidence(model: ConfidenceModel): Ent
  * indicate the track wouldn't be meaningful as confidence.
  */
 export declare function looksLikePlddt(values: number[] | undefined): values is number[];
-export {};

package/esm/extractStructureSequences.d.ts

@@ -1,49 +1,42 @@
 /** 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?: {
@@ -123,8 +116,8 @@ export declare function oneLetterSequence(codes: ArrayLike<string>, canonical: s
 export declare function extractEntities(model: StructureModel): Entity[] | undefined;
 /** A user-facing name for an entity: its chains when known, else its id. */
 export declare function entityLabel(entity: Entity): string;
-/** 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 declare function extractStructureSequences(model: StructureModel): string[] | undefined;
 /**
  * The molstar `label_seq_id`s for a set of 0-based structure positions. Unknown
@@ -139,4 +132,3 @@ export declare function rangeToLabelSeqIds(entity: Entity | undefined, range: {
 } | undefined): number[];
 /** Reverse of `seqIds`: molstar's label_seq_id -> 0-based structure position. */
 export declare function makeLabelSeqIdIndex(entity: Entity | undefined): Map<number, number>;
-export {};

package/esm/extractStructureSequences.js

@@ -157,8 +157,8 @@ export function entityLabel(entity) {
         : `Entity ${entity.entityId}`;
     return `${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) {
     return extractEntities(model)
         ?.filter(e => !e.nucleicAcid)

package/esm/extractStructureSequences.js.map

@@ -1 +1 @@
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package/esm/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/esm/fetchUtils.js

@@ -31,9 +31,9 @@ export 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.
  */
 export async function httpError(response, url) {
     const detail = firstLine(await response.text().catch(() => ''));
@@ -51,10 +51,28 @@ export 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 };
+}
 export 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);
@@ -74,10 +92,10 @@ export 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.
  */
 export function abortError(signal) {
     return signal.reason instanceof Error

package/esm/fetchUtils.js.map

@@ -1 +1 @@
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package/esm/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/esm/index.js

@@ -13,13 +13,11 @@ export * from "./chooseMappedEntity.js";
 export * from "./extractStructureSequences.js";
 export * from "./extractPerResidueConfidence.js";
 export * from "./isoformRanking.js";
-// SIFTS
+// UniProt mapping
 export * from "./pdbUniProtMapping.js";
-export * from "./siftsNumbering.js";
+export * from "./pdbEntry.js";
 // Structure sources
 export * from "./alphaFoldModels.js";
-export * from "./pdbeBestStructures.js";
-export * from "./pdbeEntryMolecules.js";
 export * from "./structureSources.js";
 export * from "./uniProtSearch.js";
 export * from "./dbIds.js";

package/esm/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,YAAY;AACZ,cAAc,YAAY,CAAA;AAC1B,cAAc,eAAe,CAAA;AAC7B,cAAc,wBAAwB,CAAA;AACtC,cAAc,uBAAuB,CAAA;AACrC,cAAc,sBAAsB,CAAA;AAEpC,cAAc;AACd,cAAc,kBAAkB,CAAA;AAChC,cAAc,gBAAgB,CAAA;AAC9B,cAAc,qBAAqB,CAAA;AAEnC,eAAe;AACf,cAAc,yBAAyB,CAAA;AACvC,cAAc,gCAAgC,CAAA;AAC9C,cAAc,kCAAkC,CAAA;AAChD,cAAc,qBAAqB,CAAA;AAEnC,kBAAkB;AAClB,cAAc,wBAAwB,CAAA;AACtC,cAAc,eAAe,CAAA;AAE7B,oBAAoB;AACpB,cAAc,sBAAsB,CAAA;AACpC,cAAc,uBAAuB,CAAA;AACrC,cAAc,oBAAoB,CAAA;AAClC,cAAc,YAAY,CAAA;AAE1B,mBAAmB;AACnB,cAAc,oBAAoB,CAAA;AAClC,cAAc,sBAAsB,CAAA;AACpC,cAAc,oBAAoB,CAAA;AAClC,cAAc,iBAAiB,CAAA"}

package/esm/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/esm/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/esm/mappings.js

@@ -5,11 +5,10 @@ export const structureAlignedSeq = (pa) => pa.alns[1].seq;
  * `pairwiseAlignmentProblem` is what guarantees it. */
 export const alignmentLength = (pa) => transcriptAlignedSeq(pa).length;
 /**
- * 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 function pairwiseAlignmentProblem(pa) {
     const transcript = transcriptAlignedSeq(pa);

package/esm/mappings.js.map

@@ -1 +1 @@
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