p2s_mapper 1.3.0 → 2.0.0

package/README.md

@@ -1,28 +1,19 @@
 # p2s_mapper
 
-Map a transcript's translation onto a protein structure.
-
-- **Align** the transcript to the structure's sequence (Smith-Waterman or
-  Needleman-Wunsch, BLOSUM62)
-- **Convert coordinates** both ways between transcript, alignment, structure,
-  Mol\* and UniProt numbering
-- **Choose the chain** that best matches the gene's protein
-- **Use SIFTS** to place UniProt annotations and drop fusion-partner residues
-- **Find structures** through AlphaFold, 3D-Beacons, PDBe and UniProt
-
-## Works with g2p_mapper
-
-p2s_mapper covers **protein ↔ structure**. The other half, **genome ↔ protein**,
-is [g2p_mapper](https://github.com/GMOD/g2p_mapper): it turns a transcript's CDS
-into per-codon genome positions, on either strand and across exon boundaries. It
-is p2s_mapper's only runtime dependency, and chaining the two takes you from a
-genome coordinate to a residue in 3D and back.
-
-Extracted from
-[jbrowse-plugin-protein3d](https://github.com/GMOD/jbrowse-plugin-protein3d),
-where we made the measurements behind the scoring rules. The package has no
-React, JBrowse or Mol\* dependency: a loaded Mol\* model reaches it through
-narrow structural interfaces.
+Find which residue of a 3D protein structure each amino acid of a transcript
+lands on, and back.
+
+Give it a transcript's translation and a structure, an AlphaFold model or a PDB
+entry. p2s_mapper picks the chain that is the gene's protein, aligns the two,
+and builds the lookups between transcript positions, structure positions and the
+residue ids a viewer such as Mol\* uses. It also finds structures for a gene,
+judges whether a match is real, and uses a PDB entry's UniProt alignment to
+place UniProt annotations and drop the residues of a fusion partner.
+
+Pair it with [g2p_mapper](https://github.com/GMOD/g2p_mapper), which maps genome
+positions to protein positions, to go from a genome coordinate to a residue in
+3D. The package has no React, JBrowse or Mol\* dependency; it came out of
+[jbrowse-plugin-protein3d](https://github.com/GMOD/jbrowse-plugin-protein3d).
 
 ## Install
 
@@ -30,28 +21,219 @@ narrow structural interfaces.
 npm install p2s_mapper
 ```
 
+## Usage
+
+### Map a transcript onto a structure
+
+Pass the transcript's translation and the structure's chain sequences.
+`chooseMappedEntity` picks the chain, `isLowSimilarity` checks the match is not
+chance, and `makeCoordinateMapper` converts positions both ways.
+
+```ts
+import {
+  alignmentQuality,
+  chooseMappedEntity,
+  describeAlignmentQuality,
+  isLowSimilarity,
+  makeCoordinateMapper,
+  structurePos,
+  transcriptPos,
+} from 'p2s_mapper'
+
+// p53's N-terminus, and a structure holding a DNA strand and a tagged fragment
+const transcript = 'MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDP*'
+const chains = [
+  { seq: 'TTTCCTAGACTTGCCCAATTA', nucleicAcid: true },
+  { seq: 'GSHMSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQW' },
+]
+
+const picked = chooseMappedEntity(transcript, chains, 'smith_waterman')
+if (picked) {
+  picked.index // 1: the protein chain
+
+  const quality = alignmentQuality(picked.alignment)
+  isLowSimilarity(quality) // false
+  describeAlignmentQuality(quality)
+  // '98% identity over 40 of 43 structure residues'
+
+  const mapper = makeCoordinateMapper(picked.alignment)
+  mapper.transcriptToStructure(transcriptPos(16)) // 6
+  mapper.structureToTranscript(structurePos(6)) // 16
+  mapper.structureToTranscript(structurePos(0)) // undefined: the GSH tag
+}
+```
+
+Every position is 0-based. The two kinds are separate branded types, so passing
+a structure position where a transcript position belongs is a compile error.
+
+### From a genome position to a residue, and back
+
+g2p_mapper turns the transcript's CDS into genome ↔ protein tables; p2s_mapper
+carries a protein position on to the structure and to the `label_seq_id` Mol\*
+addresses residues by.
+
+```ts
+import { genomeToTranscriptSeqMapping } from 'g2p_mapper'
+import {
+  chooseMappedEntity,
+  codonGenomeSpan,
+  makeCoordinateMapper,
+  makeLabelSeqIdIndex,
+  residueNumber,
+  structurePos,
+  toLabelSeqIds,
+  transcriptPos,
+} from 'p2s_mapper'
+import type { Entity } from 'p2s_mapper'
+
+const transcript = 'MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDP*'
+const { g2p, p2gCodon } = genomeToTranscriptSeqMapping({
+  refName: 'chr17',
+  start: 1000,
+  end: 2117,
+  strand: 1,
+  subfeatures: [
+    { refName: 'chr17', start: 1000, end: 1060, type: 'CDS', phase: 0 },
+    { refName: 'chr17', start: 2000, end: 2117, type: 'CDS' },
+  ],
+})
+
+// normally from extractEntities(model); here the author numbering starts at 12
+const entity: Entity = {
+  entityId: '1',
+  seq: 'GSHMSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQW',
+  seqIds: Array.from({ length: 43 }, (_, i) => i + 1),
+  authSeqIds: Array.from({ length: 43 }, (_, i) => i + 12),
+  chains: ['A'],
+}
+const picked = chooseMappedEntity(transcript, [entity], 'smith_waterman')!
+const mapper = makeCoordinateMapper(picked.alignment)
+
+// genome -> structure
+const proteinPos = g2p[2000] // 20
+if (proteinPos !== undefined) {
+  const pos = mapper.transcriptToStructure(transcriptPos(proteinPos)) // 10
+  if (pos !== undefined) {
+    toLabelSeqIds(entity, [pos]) // [11]: what to highlight in Mol*
+    residueNumber(entity, pos) // 22: what to show the user
+  }
+}
+
+// a Mol* hover on label_seq_id 15 -> genome
+const hovered = makeLabelSeqIdIndex(entity).get(15) // 14
+if (hovered !== undefined) {
+  const t = mapper.structureToTranscript(structurePos(hovered)) // 24
+  if (t !== undefined) {
+    codonGenomeSpan(p2gCodon, t) // [2012, 2015]
+  }
+}
+```
+
+### With a structure loaded in Mol\*
+
+`extractEntities` reads each chain's sequence, ids and numbering from a loaded
+Mol\* model, through a narrow structural type rather than a Mol\* import.
+
+```ts
+import {
+  chooseMappedEntity,
+  extractEntities,
+  rangeToLabelSeqIds,
+} from 'p2s_mapper'
+import type { StructureModel } from 'p2s_mapper'
+
+// e.g. what plugin.builders.structure.createModel resolves to
+declare const model: StructureModel
+declare const transcript: string
+
+const entities = extractEntities(model) ?? []
+const picked = chooseMappedEntity(transcript, entities, 'smith_waterman')
+const entity = picked ? entities[picked.index] : undefined
+
+// the label_seq_ids of structure positions 10-19, for a Mol* selection
+rangeToLabelSeqIds(entity, { start: 10, end: 20 })
+```
+
+### Find a structure for a gene
+
+```ts
+import {
+  fetchAlphaFoldModels,
+  fetchExperimentalStructures,
+  getPdbStructureUrl,
+  pickAlphaFoldModel,
+  searchUniProtEntries,
+} from 'p2s_mapper'
+
+declare const translation: string
+
+const { entries } = await searchUniProtEntries({
+  recognizedIds: ['GeneID:7157', 'ENST00000269305'],
+  geneName: 'TP53',
+  organismId: 9606,
+})
+const accession = entries[0]?.accession // 'P04637'
+
+if (accession) {
+  // predicted: the model folded from this exact translation, else the canonical one
+  const models = await fetchAlphaFoldModels(accession)
+  const predicted = pickAlphaFoldModel(models, { tx1: { seq: translation } })
+
+  // experimental: PDB entries, best coverage first
+  const [best] = await fetchExperimentalStructures(accession)
+  const url = predicted?.url ?? (best && getPdbStructureUrl(best.pdbId))
+}
+```
+
+Every network function takes `{ fetch?, signal? }` last, defaulting to
+`globalThis.fetch`, so a host can pass its own fetch and abort a stale request.
+
+### Place UniProt annotations on a PDB entry
+
+A PDB construct is usually a fragment, numbered differently from UniProt. The
+entry's UniProt alignment, read from RCSB, says how the two line up.
+
+```ts
+import {
+  chooseUniProtMappingForEntity,
+  fetchUniProtStructureMappings,
+  makeUniProtPositionMap,
+} from 'p2s_mapper'
+
+const mappings = await fetchUniProtStructureMappings('1tup')
+const mapping = chooseUniProtMappingForEntity(mappings, {
+  entityId: '3',
+  chains: ['A', 'B', 'C'],
+})
+const toStructure = makeUniProtPositionMap(mapping?.segments ?? [])
+toStructure(248) // 154: UniProt residue 248 is structure position 154
+```
+
 ## How it fits together
 
 ![From a gene on the genome to a residue in 3D, and back](docs/img/pipeline.svg)
 
 ## Docs
 
-- [faq.md](docs/faq.md) — can I trust the mapping? What the package checks, and
-  what it leaves to you
-- [pipeline.md](docs/pipeline.md) — the flow above, step by step, and why chain
+- [api.md](docs/api.md): every export, with its signature, types and an example
+- [pipeline.md](docs/pipeline.md): the flow above, step by step, and why chain
   choice divides by the shorter sequence
-- [coordinates.md](docs/coordinates.md) — the four numberings of a residue and
+- [coordinates.md](docs/coordinates.md): the four numberings of a residue and
   the one route between each
-- [api.md](docs/api.md) — every export, grouped by job
+- [faq.md](docs/faq.md): can I trust the mapping? What the package checks, and
+  what it leaves to you
 
 ## Things to know first
 
-- Every coordinate in the API is **0-based**, branded by space so the compiler
-  rejects mixing them. See [coordinates.md](docs/coordinates.md).
+- Every coordinate is **0-based** and branded by space, so the compiler rejects
+  mixing them. UniProt positions and author residue numbers are 1-based. See
+  [coordinates.md](docs/coordinates.md).
 - A `PairwiseAlignment` has **row 0 = transcript, row 1 = structure**. Use the
   accessors, not indexes.
-- Network functions take `{ fetch?, signal? }` and default to
-  `globalThis.fetch`.
+- The best-matching chain always wins, even a poor match. Check it with
+  `isLowSimilarity` before trusting the mapping.
+- Cross into Mol\* only through `Entity.seqIds`: `label_seq_id` is not always
+  position + 1.
 
 ## License
 

package/dist/alphaFoldModels.d.ts

@@ -2,8 +2,12 @@ import type { FetchOptions } from './fetchUtils.ts';
 export interface AlphaFoldModel {
     /** UniProt accession, with an isoform suffix on an isoform model */
     accession: string;
+    /** AlphaFold DB's id for the model, e.g. AF-P04637-F1 */
+    entity?: string;
     url: string;
     confidenceUrl?: string;
+    /** mean per-residue confidence (pLDDT), 0-100 */
+    meanPlddt?: number;
     sequence: string;
 }
 export declare function parseAlphaFoldModels(json: unknown): AlphaFoldModel[];

package/dist/alphaFoldModels.js

@@ -16,8 +16,12 @@ function parseAlphaFoldModels(json) {
         ? [
             {
                 accession: e.uniprotAccession,
+                entity: typeof e.modelEntityId === 'string' ? e.modelEntityId : undefined,
                 url: e.cifUrl,
                 confidenceUrl: typeof e.plddtDocUrl === 'string' ? e.plddtDocUrl : undefined,
+                meanPlddt: typeof e.globalMetricValue === 'number'
+                    ? e.globalMetricValue
+                    : undefined,
                 sequence: e.sequence,
             },
         ]

package/dist/alphaFoldModels.js.map

@@ -1 +1 @@
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+{"version":3,"file":"alphaFoldModels.js","sourceRoot":"","sources":["../src/alphaFoldModels.ts"],"names":[],"mappings":";;AA8BA,oDAuBC;AAUD,oDAaC;AAUD,gDAgBC;AAtGD,mDAAqD;AAGrD,2DAAoD;AAuBpD,SAAS,iBAAiB,CAAC,KAAc;IACvC,OAAO,OAAO,KAAK,KAAK,QAAQ,IAAI,KAAK,KAAK,IAAI,CAAA;AACpD,CAAC;AAED,SAAgB,oBAAoB,CAAC,IAAa;IAChD,OAAO,CAAC,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE,CACnD,iBAAiB,CAAC,CAAC,CAAC;QACpB,OAAO,CAAC,CAAC,gBAAgB,KAAK,QAAQ;QACtC,OAAO,CAAC,CAAC,MAAM,KAAK,QAAQ;QAC5B,OAAO,CAAC,CAAC,QAAQ,KAAK,QAAQ;QAC5B,CAAC,CAAC;YACE;gBACE,SAAS,EAAE,CAAC,CAAC,gBAAgB;gBAC7B,MAAM,EACJ,OAAO,CAAC,CAAC,aAAa,KAAK,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAC,aAAa,CAAC,CAAC,CAAC,SAAS;gBACnE,GAAG,EAAE,CAAC,CAAC,MAAM;gBACb,aAAa,EACX,OAAO,CAAC,CAAC,WAAW,KAAK,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC,SAAS;gBAC/D,SAAS,EACP,OAAO,CAAC,CAAC,iBAAiB,KAAK,QAAQ;oBACrC,CAAC,CAAC,CAAC,CAAC,iBAAiB;oBACrB,CAAC,CAAC,SAAS;gBACf,QAAQ,EAAE,CAAC,CAAC,QAAQ;aACrB;SACF;QACH,CAAC,CAAC,EAAE,CACP,CAAA;AACH,CAAC;AAED;;;;;;;GAOG;AACI,KAAK,UAAU,oBAAoB,CACxC,SAAiB,EACjB,IAAmB;IAEnB,MAAM,GAAG,GAAG,8CAA8C,kBAAkB,CAAC,SAAS,CAAC,EAAE,CAAA;IACzF,MAAM,GAAG,GAAG,MAAM,IAAA,wBAAQ,EAAC,GAAG,EAAE,IAAI,CAAC,CAAA;IACrC,IAAI,GAAG,CAAC,MAAM,KAAK,GAAG,IAAI,GAAG,CAAC,MAAM,KAAK,GAAG,EAAE,CAAC;QAC7C,OAAO,EAAE,CAAA;IACX,CAAC;IACD,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC;QACZ,MAAM,MAAM,IAAA,yBAAS,EAAC,GAAG,EAAE,GAAG,CAAC,CAAA;IACjC,CAAC;IACD,OAAO,oBAAoB,CAAC,MAAM,GAAG,CAAC,IAAI,EAAE,CAAC,CAAA;AAC/C,CAAC;AAED;;;;;;;GAOG;AACH,SAAgB,kBAAkB,CAChC,MAAwB,EACxB,gBAA6D;IAE7D,MAAM,YAAY,GAAG,IAAI,GAAG,CAC1B,MAAM,CAAC,MAAM,CAAC,gBAAgB,IAAI,EAAE,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,IAAA,kCAAc,EAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CACtE,CAAA;IACD,MAAM,cAAc,GAAG,CAAC,GAAG,MAAM,CAAC,CAAC,IAAI,CACrC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CACP,MAAM,CAAC,CAAC,CAAC,SAAS,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,GAAG,MAAM,CAAC,CAAC,CAAC,SAAS,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CACxE,CAAA;IACD,OAAO,CACL,cAAc,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,YAAY,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC;QACtD,cAAc,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC;QACpD,CAAC,GAAG,MAAM,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,QAAQ,CAAC,MAAM,GAAG,CAAC,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CACrE,CAAA;AACH,CAAC"}

package/dist/coordinates.d.ts

@@ -11,12 +11,15 @@ import type { PairwiseAlignment } from './mappings.ts';
  * sequence; TranscriptPos the ungapped transcript sequence; 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;
@@ -63,4 +66,3 @@ export declare function transcriptRangeToStructureRange(mapper: CoordinateMapper
     start: number;
     end: number;
 } | undefined;
-export {};

package/dist/coordinates.js.map

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

@@ -1,4 +1,4 @@
-type DbType = 'ensembl' | 'refseq' | 'ccds' | 'hgnc';
+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/dist/dbIds.js

@@ -18,6 +18,10 @@ const DB_ID_PATTERNS = [
     { db: 'refseq', pattern: /^[NXYA]P_\d+/i, label: 'RefSeq protein' },
     { db: 'ccds', pattern: /^CCDS\d+/i, label: 'CCDS' },
     { db: 'hgnc', pattern: /^HGNC:\d+/i, label: 'HGNC' },
+    // NCBI's GFFs carry `Dbxref=GeneID:7157`, and UniProt keeps the GeneID
+    // cross-reference for every organism NCBI annotates, where a symbol search
+    // needs a taxon and misses a TrEMBL-only gene.
+    { db: 'geneid', pattern: /^GeneID:\d+$/i, label: 'NCBI Gene' },
 ];
 function matchDbIdPattern(id) {
     return DB_ID_PATTERNS.find(p => p.pattern.test(id));
@@ -37,7 +41,7 @@ function getDbIdLabel(id) {
 function buildUniProtXrefQuery(id) {
     const match = matchDbIdPattern(id);
     return match
-        ? `xref:${match.db}-${match.db === 'hgnc' ? id.replace('HGNC:', '') : id}`
+        ? `xref:${match.db}-${match.db === 'hgnc' || match.db === 'geneid' ? id.replace(/^[^:]+:/, '') : id}`
         : undefined;
 }
 function stripTrailingVersion(s) {

package/dist/dbIds.js.map

@@ -1 +1 @@
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+{"version":3,"file":"dbIds.js","sourceRoot":"","sources":["../src/dbIds.ts"],"names":[],"mappings":";;AA0BA,4CAEC;AAGD,wDAEC;AAID,oCAGC;AAID,sDAKC;AAED,oDAEC;AA9CD,MAAM,cAAc,GAAqD;IACvE,EAAE,EAAE,EAAE,SAAS,EAAE,OAAO,EAAE,iBAAiB,EAAE,KAAK,EAAE,cAAc,EAAE;IACpE,EAAE,EAAE,EAAE,SAAS,EAAE,OAAO,EAAE,iBAAiB,EAAE,KAAK,EAAE,oBAAoB,EAAE;IAC1E,EAAE,EAAE,EAAE,SAAS,EAAE,OAAO,EAAE,iBAAiB,EAAE,KAAK,EAAE,iBAAiB,EAAE;IACvE,EAAE,EAAE,EAAE,QAAQ,EAAE,OAAO,EAAE,aAAa,EAAE,KAAK,EAAE,aAAa,EAAE;IAC9D,EAAE,EAAE,EAAE,QAAQ,EAAE,OAAO,EAAE,aAAa,EAAE,KAAK,EAAE,cAAc,EAAE;IAC/D,4EAA4E;IAC5E,2EAA2E;IAC3E,qEAAqE;IACrE,4EAA4E;IAC5E,EAAE,EAAE,EAAE,QAAQ,EAAE,OAAO,EAAE,eAAe,EAAE,KAAK,EAAE,gBAAgB,EAAE;IACnE,EAAE,EAAE,EAAE,MAAM,EAAE,OAAO,EAAE,WAAW,EAAE,KAAK,EAAE,MAAM,EAAE;IACnD,EAAE,EAAE,EAAE,MAAM,EAAE,OAAO,EAAE,YAAY,EAAE,KAAK,EAAE,MAAM,EAAE;IACpD,uEAAuE;IACvE,2EAA2E;IAC3E,+CAA+C;IAC/C,EAAE,EAAE,EAAE,QAAQ,EAAE,OAAO,EAAE,eAAe,EAAE,KAAK,EAAE,WAAW,EAAE;CAC/D,CAAA;AAED,SAAgB,gBAAgB,CAAC,EAAU;IACzC,OAAO,cAAc,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC,CAAA;AACrD,CAAC;AAED,8DAA8D;AAC9D,SAAgB,sBAAsB,CAAC,EAAU;IAC/C,OAAO,gBAAgB,CAAC,EAAE,CAAC,KAAK,SAAS,CAAA;AAC3C,CAAC;AAED;8CAC8C;AAC9C,SAAgB,YAAY,CAAC,EAAU;IACrC,MAAM,KAAK,GAAG,gBAAgB,CAAC,EAAE,CAAC,CAAA;IAClC,OAAO,KAAK,CAAC,CAAC,CAAC,GAAG,EAAE,KAAK,KAAK,CAAC,KAAK,GAAG,CAAC,CAAC,CAAC,EAAE,CAAA;AAC9C,CAAC;AAED;4EAC4E;AAC5E,SAAgB,qBAAqB,CAAC,EAAU;IAC9C,MAAM,KAAK,GAAG,gBAAgB,CAAC,EAAE,CAAC,CAAA;IAClC,OAAO,KAAK;QACV,CAAC,CAAC,QAAQ,KAAK,CAAC,EAAE,IAAI,KAAK,CAAC,EAAE,KAAK,MAAM,IAAI,KAAK,CAAC,EAAE,KAAK,QAAQ,CAAC,CAAC,CAAC,EAAE,CAAC,OAAO,CAAC,SAAS,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,EAAE,EAAE;QACrG,CAAC,CAAC,SAAS,CAAA;AACf,CAAC;AAED,SAAgB,oBAAoB,CAAC,CAAU;IAC7C,OAAO,CAAC,EAAE,OAAO,CAAC,WAAW,EAAE,EAAE,CAAC,CAAA;AACpC,CAAC"}

package/dist/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/dist/extractStructureSequences.d.ts

@@ -20,30 +20,30 @@
  * So carry the real ids and convert through them.
  */
 export interface Entity {
+    /** mmCIF entity id, molstar's own bookkeeping */
     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 carrying this entity, e.g. ['A', 'B'] for a homodimer:
+     * what a user recognises from the PDB entry page */
     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. Its letters spell
+     * amino acids too (A, C, G, T, U), so it is kept out of the alignment
+     * rather than left to score low. */
     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. Display only;
+     * address Mol* through `seqIds`. 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?: {
@@ -139,4 +139,3 @@ 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/dist/fetchUtils.js

@@ -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);

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

@@ -14,8 +14,11 @@ export interface RankedIsoform {
     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/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;
@@ -32,4 +32,3 @@ export declare function scoredAlignment(seq1: string, seq2: string, algorithm: A
     score: number;
 };
 export declare function runLocalAlignment(seq1: string, seq2: string, algorithm: AlignmentAlgorithm): PairwiseAlignment;
-export {};

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;