p2s_mapper 1.4.0 → 2.1.0

package/esm/pdbUniProtMapping.js

@@ -1,4 +1,4 @@
-// SIFTS UniProt <-> PDB residue mapping.
+// UniProt <-> PDB residue mapping.
 //
 // UniProt feature coordinates are positions in the UniProt canonical sequence.
 // For an AlphaFold model that *is* the structure's own sequence, so a feature at
@@ -6,134 +6,19 @@
 // entry it is not: the deposited construct is usually a fragment, often with
 // tags or engineered residues, so the two numberings differ by a per-segment
 // offset (1TUP's p53 chain starts at UniProt 94; 6VXX's spike SEQRES 33 is
-// UniProt 14). SIFTS is the authoritative alignment between the two, published
-// per entity/chain by PDBe.
+// UniProt 14). The entry's own UniProt alignment, which `fetchPdbEntry` reads
+// from RCSB, is the authority on that correspondence.
 //
-// `residue_number` in the PDBe response is the 1-based index into the entity's
-// SEQRES, i.e. label_seq_id, which is exactly this plugin's structure-sequence
-// position + 1 (see applyLociInteractivity.ts for the other place that boundary
-// is crossed).
-import { isDefinitiveFailure, jsonfetch, timeout } from "./fetchUtils.js";
-export function pdbeSiftsUrl(pdbId) {
-    return `https://www.ebi.ac.uk/pdbe/api/mappings/uniprot/${pdbId.toLowerCase()}`;
-}
-const SIFTS_RETRY_DELAYS_MS = [1000, 3000];
-// bounded, since a view reports itself loading until SIFTS answers
-const SIFTS_TIMEOUT_MS = 20_000;
-/**
- * SIFTS for an entry, retried twice: one failed request would otherwise leave a
- * fusion construct mapped onto its partner for the whole session.
- *
- * A 4xx is not retried. PDBe answers 404 for an entry it has no UniProt
- * mapping for at all — a DNA-only or obsolete entry — and that answer cannot
- * change, so the retries only postponed it: measured 2026-09-16, `1hhb` and
- * `1bna` each took three requests and ~4.8s to say so, which a caller shows as
- * four and a half seconds of "resolving" for a structure that will never
- * resolve.
- */
-export async function fetchUniProtStructureMappings(pdbId, opts) {
-    const { signal: caller, ...rest } = opts ?? {};
-    const signal = caller ?? undefined;
-    const deadline = () => signal
-        ? AbortSignal.any([signal, AbortSignal.timeout(SIFTS_TIMEOUT_MS)])
-        : AbortSignal.timeout(SIFTS_TIMEOUT_MS);
-    for (let attempt = 0;; attempt++) {
-        try {
-            return parseUniProtStructureMappings(await jsonfetch(pdbeSiftsUrl(pdbId), { ...rest, signal: deadline() }));
-        }
-        catch (e) {
-            const delay = SIFTS_RETRY_DELAYS_MS[attempt];
-            // the caller's own abort is not a failure to retry either
-            if (delay === undefined || isDefinitiveFailure(e) || signal?.aborted) {
-                throw e;
-            }
-            await timeout(delay, signal);
-        }
-    }
-}
-function isRecord(value) {
-    return typeof value === 'object' && value !== null && !Array.isArray(value);
-}
-function finiteNumber(value) {
-    return typeof value === 'number' && Number.isFinite(value) ? value : undefined;
-}
-function residueNumber(endpoint) {
-    return isRecord(endpoint) ? finiteNumber(endpoint.residue_number) : undefined;
-}
-function authorResidueNumber(endpoint) {
-    return isRecord(endpoint)
-        ? finiteNumber(endpoint.author_residue_number)
-        : undefined;
-}
-function parseSegment(mapping) {
-    if (!isRecord(mapping)) {
-        return undefined;
-    }
-    const entityId = finiteNumber(mapping.entity_id);
-    const unpStart = finiteNumber(mapping.unp_start);
-    const unpEnd = finiteNumber(mapping.unp_end);
-    const structStart = residueNumber(mapping.start);
-    const structEnd = residueNumber(mapping.end);
-    const authorStart = authorResidueNumber(mapping.start);
-    const authorEnd = authorResidueNumber(mapping.end);
-    return entityId === undefined ||
-        unpStart === undefined ||
-        unpEnd === undefined ||
-        structStart === undefined ||
-        structEnd === undefined
-        ? undefined
-        : {
-            entityId: String(entityId),
-            ...(typeof mapping.chain_id === 'string'
-                ? { chainId: mapping.chain_id }
-                : {}),
-            unpStart,
-            unpEnd,
-            // SEQRES/label_seq_id is 1-based, structure positions are 0-based
-            structStart: structStart - 1,
-            structEnd: structEnd - 1,
-            ...(authorStart === undefined ? {} : { authorStart }),
-            ...(authorEnd === undefined ? {} : { authorEnd }),
-        };
-}
-/**
- * Parses a PDBe `mappings/uniprot/{pdbId}` response into one entry per UniProt
- * accession. Unparseable segments are skipped rather than failing the whole
- * response — a chimera with one malformed segment still maps its other chains.
- * The response is keyed by pdb id, so the single entry is taken whatever its key.
- */
-export function parseUniProtStructureMappings(json) {
-    const entry = isRecord(json) ? Object.values(json)[0] : undefined;
-    const uniprot = isRecord(entry) ? entry.UniProt : undefined;
-    if (!isRecord(uniprot)) {
-        return [];
-    }
-    const result = [];
-    for (const [accession, value] of Object.entries(uniprot)) {
-        const mappings = isRecord(value) ? value.mappings : undefined;
-        const segments = Array.isArray(mappings)
-            ? mappings.map(parseSegment).filter(s => s !== undefined)
-            : [];
-        if (segments.length > 0) {
-            result.push({
-                accession,
-                name: isRecord(value) && typeof value.name === 'string'
-                    ? value.name
-                    : undefined,
-                segments,
-            });
-        }
-    }
-    return result;
-}
+// Structure positions here index the entity's SEQRES from 0, i.e.
+// label_seq_id - 1, which is this package's structure-sequence position.
 function coveredResidues(segments) {
     return segments.reduce((a, s) => a + (s.structEnd - s.structStart + 1), 0);
 }
 /**
- * The segments of one accession that describe this entity. SIFTS numbers
- * entities as the mmCIF does, and a PDB-format file loaded through Mol* numbers
- * them per chain (1H26.pdb's chain C is entity 2, which in SIFTS is cyclin A),
- * so a segment naming its chain is matched by chain.
+ * The segments of one accession that describe this entity. The mapping
+ * numbers entities as the mmCIF does, and a PDB-format file loaded through
+ * Mol* numbers them per chain (1H26.pdb's chain C is entity 2, which in the
+ * mmCIF is cyclin A), so a segment naming its chain is matched by chain.
  */
 function segmentsForEntity(mapping, entity) {
     return dedupeSegments(mapping.segments.filter(s => s.chainId === undefined
@@ -141,12 +26,11 @@ function segmentsForEntity(mapping, entity) {
         : entity.chains.includes(s.chainId)));
 }
 /**
- * Picks the UniProt entry that describes a given entity, with its segments
- * narrowed to that entity. Only the entity the plugin has mapped to the
- * transcript is relevant — a heteromer maps each of its chains to a different
- * accession, and using the wrong one would silently annotate the wrong protein.
- * When several accessions cover the same entity (a chimeric construct) the one
- * contributing the most residues wins.
+ * Picks the UniProt entry for a given entity, with its segments narrowed to
+ * that entity. Pass the entity mapped to the transcript: a heteromer's chains
+ * align to different accessions, and the wrong one would annotate the wrong
+ * protein. When several accessions cover one entity (a chimeric construct), the
+ * one covering the most residues wins.
  */
 export function chooseUniProtMappingForEntity(mappings, entity) {
     if (entity === undefined) {
@@ -165,10 +49,11 @@ export function chooseUniProtMappingForEntity(mappings, entity) {
 const OWN_PSEUDOCOUNT = 5;
 const MIN_OWN_IDENTITY = 0.5;
 /**
- * Mapped structure positions that SIFTS assigns to a protein other than the
- * transcript's, on a chain that fuses two. Local alignment bridges a fusion
- * boundary, and on every GPCR fusion construct checked it scattered receptor
- * residues onto the partner, 33 of them onto T4 lysozyme in 2RH1.
+ * Mapped structure positions the entry's UniProt alignment assigns to a
+ * protein other than the transcript's, on a chain that fuses two. Local
+ * alignment bridges a fusion boundary, and on every GPCR fusion construct
+ * checked it scattered receptor residues onto the partner, 33 of them onto T4
+ * lysozyme in 2RH1.
  *
  * `mapped` is each mapped structure position and whether its pair is
  * identical. The transcript's own accession is the one whose covered positions
@@ -177,7 +62,7 @@ const MIN_OWN_IDENTITY = 0.5;
  * fused to CDK2 covers 11 positions against 224 chance hits on the kinase, and
  * counting unmapped the peptide. Unless that accession reaches half identity
  * the transcript is taken to be neither protein, and nothing is unmapped.
- * Residues SIFTS assigns to no accession, such as tags, stay mapped.
+ * Residues assigned to no accession, such as tags, stay mapped.
  */
 export function fusionPartnerPositions(mappings, entity, mapped) {
     const partners = new Set();
@@ -214,8 +99,8 @@ export function fusionPartnerPositions(mappings, entity, mapped) {
     }
     return partners;
 }
-// SIFTS lists one mapping per *chain*, so the several chains of a homodimer
-// repeat the same entity-level correspondence. They collapse to one segment.
+// The mapping lists one segment per *chain*, so the several chains of a
+// homodimer repeat the same entity-level correspondence. They collapse to one.
 function dedupeSegments(segments) {
     const seen = new Set();
     return segments.filter(s => {

package/esm/pdbUniProtMapping.js.map

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

@@ -1,19 +1,14 @@
 /**
  * Which molstar trajectory parser a structure needs.
  *
- * Getting this wrong is not a graceful failure in either direction: parsing a
- * PDB file as mmCIF throws ("Unexpected token. Expected data_, loop_, or data
- * name"), and — worse — parsing an mmCIF as PDB *succeeds* and yields a model
- * with zero polymer entities and thousands of misread atoms, so the view loads
- * with no sequence, no alignment and no genome mapping, and nothing reports an
- * error.
+ * A wrong choice fails either way. Parsing a PDB file as mmCIF throws
+ * ("Unexpected token. Expected data_, loop_, or data name"). Parsing an mmCIF
+ * as PDB succeeds and yields a model with zero polymer entities and thousands of
+ * misread atoms, so the structure loads with no sequence, no alignment and no
+ * genome mapping, and with no error.
  *
- * So detection lives here and is applied as the default at every entry point,
- * rather than at one of them.
- *
- * The two names are the subset of molstar's `BuiltInTrajectoryFormat` a
- * structure loaded from a file or a url can be, spelled out rather than
- * imported so nothing here depends on molstar.
+ * The two names are the subset of molstar's `BuiltInTrajectoryFormat` that a
+ * structure file or URL can be, written out so nothing here imports molstar.
  */
 export type StructureFormat = 'pdb' | 'mmcif';
 /** Trailing extension of a filename or URL, lowercased, ignoring any query or
@@ -21,18 +16,16 @@ export type StructureFormat = 'pdb' | 'mmcif';
 export declare function structureFileExtension(nameOrUrl: string): string;
 /**
  * Format for a filename or URL. Unknown extensions fall back to mmCIF, which is
- * what every URL this plugin generates itself serves (AlphaFold and RCSB both
- * hand out `.cif`).
+ * what AlphaFold and RCSB serve (`.cif`).
  */
 export declare function structureFormatFromName(nameOrUrl: string): StructureFormat;
 /** Whether a URL points at a binary-encoded structure, which molstar must be
  * told to download as bytes rather than text. */
 export declare function isBinaryStructureUrl(url: string): boolean;
 /**
- * Format for structure text that arrived without a filename — an inline `data`
- * snapshot, a pasted file, or the PDB the plugin synthesizes from Foldseek Cα
- * coordinates. Sniffs the content, which is strictly more reliable than a name
- * and is the only signal available here.
+ * Format for structure text with no filename, such as inline data, a pasted
+ * file, or a PDB built by `caCoordsToPdb`. The content is more reliable than a
+ * name, and here it is the only signal.
  *
  * mmCIF is line-oriented and its first meaningful line is a `data_` block
  * header (comments and blank lines may precede it); PDB has none.

package/esm/structureFormat.js

@@ -14,8 +14,7 @@ export function structureFileExtension(nameOrUrl) {
 }
 /**
  * Format for a filename or URL. Unknown extensions fall back to mmCIF, which is
- * what every URL this plugin generates itself serves (AlphaFold and RCSB both
- * hand out `.cif`).
+ * what AlphaFold and RCSB serve (`.cif`).
  */
 export function structureFormatFromName(nameOrUrl) {
     return PDB_EXTENSIONS.has(structureFileExtension(nameOrUrl)) ? 'pdb' : 'mmcif';
@@ -26,10 +25,9 @@ export function isBinaryStructureUrl(url) {
     return structureFileExtension(url) === 'bcif';
 }
 /**
- * Format for structure text that arrived without a filename — an inline `data`
- * snapshot, a pasted file, or the PDB the plugin synthesizes from Foldseek Cα
- * coordinates. Sniffs the content, which is strictly more reliable than a name
- * and is the only signal available here.
+ * Format for structure text with no filename, such as inline data, a pasted
+ * file, or a PDB built by `caCoordsToPdb`. The content is more reliable than a
+ * name, and here it is the only signal.
  *
  * mmCIF is line-oriented and its first meaningful line is a `data_` block
  * header (comments and blank lines may precede it); PDB has none.

package/esm/structureFormat.js.map

@@ -1 +1 @@
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+{"version":3,"file":"structureFormat.js","sourceRoot":"","sources":["../src/structureFormat.ts"],"names":[],"mappings":"AAcA,gFAAgF;AAChF,wEAAwE;AACxE,MAAM,cAAc,GAAG,IAAI,GAAG,CAAC,CAAC,KAAK,EAAE,KAAK,EAAE,MAAM,EAAE,MAAM,EAAE,MAAM,CAAC,CAAC,CAAA;AAEtE;mEACmE;AACnE,MAAM,UAAU,sBAAsB,CAAC,SAAiB;IACtD,MAAM,IAAI,GAAG,SAAS,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,IAAI,EAAE,CAAA;IAC7C,MAAM,IAAI,GAAG,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,GAAG,EAAE,IAAI,EAAE,CAAA;IACxC,MAAM,KAAK,GAAG,IAAI,CAAC,WAAW,EAAE,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;IAC3C,IAAI,KAAK,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,KAAK,IAAI,EAAE,CAAC;QAC1B,KAAK,CAAC,GAAG,EAAE,CAAA;IACb,CAAC;IACD,OAAO,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC,CAAC,CAAC,EAAE,CAAA;AACrD,CAAC;AAED;;;GAGG;AACH,MAAM,UAAU,uBAAuB,CAAC,SAAiB;IACvD,OAAO,cAAc,CAAC,GAAG,CAAC,sBAAsB,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,OAAO,CAAA;AAChF,CAAC;AAED;iDACiD;AACjD,MAAM,UAAU,oBAAoB,CAAC,GAAW;IAC9C,OAAO,sBAAsB,CAAC,GAAG,CAAC,KAAK,MAAM,CAAA;AAC/C,CAAC;AAED;;;;;;;GAOG;AACH,MAAM,UAAU,0BAA0B,CAAC,IAAY;IACrD,2EAA2E;IAC3E,wBAAwB;IACxB,KAAK,MAAM,IAAI,IAAI,IAAI,CAAC,KAAK,CAAC,CAAC,EAAE,IAAI,CAAC,CAAC,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC;QACnD,MAAM,OAAO,GAAG,IAAI,CAAC,IAAI,EAAE,CAAA;QAC3B,IAAI,OAAO,KAAK,EAAE,IAAI,CAAC,OAAO,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE,CAAC;YAC/C,OAAO,OAAO,CAAC,WAAW,EAAE,CAAC,UAAU,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,KAAK,CAAA;QACpE,CAAC;IACH,CAAC;IACD,OAAO,KAAK,CAAA;AACd,CAAC"}

package/esm/structureSources.d.ts

@@ -1,6 +1,8 @@
 import type { FetchOptions } from './fetchUtils.ts';
+export declare const RCSB_SEQUENCE_COORDINATES_URL = "https://sequence-coordinates.rcsb.org/graphql";
 export interface ExperimentalStructure {
     pdbId: string;
+    /** RCSB's name for it: 'X-ray', 'EM', 'NMR', ... */
     method: string;
     /** Å; absent for NMR and some EM entries */
     resolution?: number;
@@ -9,20 +11,42 @@ export interface ExperimentalStructure {
     end: number;
     /** fraction of the UniProt sequence the entry covers, 0..1 */
     coverage: number;
+    /** author chain ids of the protein */
+    chains: string[];
 }
-export declare function beaconsSummaryUrl(uniprotId: string): string;
+/** One polymer entity aligned to the accession. */
+export interface EntityAlignment {
+    /** RCSB's id, "1TUP_3" */
+    entityId: string;
+    pdbId: string;
+    start: number;
+    end: number;
+    coverage: number;
+}
+export interface EntityDetails {
+    method: string;
+    resolution?: number;
+    chains: string[];
+}
+export declare function entityAlignmentsQuery(uniprotId: string): string;
+export declare const ENTITY_DETAILS_QUERY = "query($ids: [String!]!) { polymer_entities(entity_ids: $ids) {\n  rcsb_id\n  rcsb_polymer_entity_container_identifiers { auth_asym_ids }\n  entry { rcsb_entry_info { experimental_method resolution_combined } }\n} }";
+/**
+ * PDB entities only: the same list carries RCSB's computed models
+ * (`AF_AFP04637F1_1`), which a residue mapping does not exist for. The range
+ * spans every aligned region, as 3D-Beacons reported it.
+ */
+export declare function parseEntityAlignments(data: unknown): EntityAlignment[];
+export declare function parseEntityDetails(data: unknown): Map<string, EntityDetails>;
+/**
+ * One row per entry, best coverage first and sharpest within a tie. An entry
+ * with several entities of the protein (a construct crystallised beside a
+ * different fragment of itself) takes the best-covering entity's range and
+ * every entity's chains.
+ */
+export declare function experimentalStructures(alignments: EntityAlignment[], details: ReadonlyMap<string, EntityDetails>): ExperimentalStructure[];
 /**
- * PDBe entries only, best-covering first and sharpest within a tie.
- *
- * Predicted entries (AlphaFold, SWISS-MODEL, AlphaFill) are left out because a
- * prediction comes from AlphaFold's own API, which answers per model. And
- * 3D-Beacons files SASBDB's small-angle-scattering fits under "experimentally
- * determined" too, with numeric ids and near-full coverage — dystrophin's best
- * "structure" by coverage was SASBDB 436 — which are not entries a residue
- * mapping exists for. Hence the `provider === 'PDBe'` gate rather than the
- * category alone.
+ * Every PDB entry aligned to the accession. An accession with none, or one
+ * RCSB does not know, is `[]`; an isoform accession is asked as its entry,
+ * which is what the alignment is numbered on.
  */
-export declare function parseExperimentalStructures(json: unknown): ExperimentalStructure[];
-/** Best-effort: an unreachable API reads as "no entries", which costs a
- * structure suggestion and nothing else. */
 export declare function fetchExperimentalStructures(uniprotId: string, opts?: FetchOptions): Promise<ExperimentalStructure[]>;

package/esm/structureSources.js

@@ -1,82 +1,166 @@
-// The experimental structures 3D-Beacons knows for a UniProt entry: every PDBe
-// entry mapped to the accession, with the UniProt range it covers and its
-// resolution, in one CORS-enabled call. That is what lets a page offer a
-// crystal structure beside a prediction without a PDB search of its own; take
-// the entry id from here and ask `fetchUniProtStructureMappings` for its
+// The experimental structures RCSB aligns to a UniProt entry: every PDB entity
+// carrying the accession, with the UniProt range it covers, then each entry's
+// method, resolution and chains. Two CORS-enabled calls, which is what lets a
+// page offer a crystal structure beside a prediction without a PDB search of
+// its own; take the entry id from here and ask `fetchPdbEntry` for its
 // residue mapping.
-import { rawfetch } from "./fetchUtils.js";
-// Unfiltered: the `?provider=pdbe` form answered BRAF, HBB and BRCA2 with a 404
-// about one time in three (2026-10-09), and the parser keeps PDBe's entries
-// anyway.
-export function beaconsSummaryUrl(uniprotId) {
-    return `https://www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/api/uniprot/summary/${encodeURIComponent(uniprotId)}.json`;
+import { RCSB_DATA_GRAPHQL_URL, graphqlFetch } from "./pdbEntry.js";
+import { isPdbId } from "./structureUrls.js";
+export const RCSB_SEQUENCE_COORDINATES_URL = 'https://sequence-coordinates.rcsb.org/graphql';
+export function entityAlignmentsQuery(uniprotId) {
+    return `{ alignments(from: UNIPROT, to: PDB_ENTITY, queryId: "${uniprotId}") {
+  target_alignments {
+    target_id
+    coverage { query_coverage }
+    aligned_regions { query_begin query_end }
+  }
+} }`;
 }
+export const ENTITY_DETAILS_QUERY = `query($ids: [String!]!) { polymer_entities(entity_ids: $ids) {
+  rcsb_id
+  rcsb_polymer_entity_container_identifiers { auth_asym_ids }
+  entry { rcsb_entry_info { experimental_method resolution_combined } }
+} }`;
+// RCSB's cap on ids per batch request
+const DETAILS_BATCH = 1000;
 function isRecord(value) {
     return typeof value === 'object' && value !== null && !Array.isArray(value);
 }
 function finiteNumber(value) {
     return typeof value === 'number' && Number.isFinite(value) ? value : undefined;
 }
+function strings(value) {
+    return Array.isArray(value)
+        ? value.filter((v) => typeof v === 'string')
+        : [];
+}
 /**
- * PDBe entries only, best-covering first and sharpest within a tie.
- *
- * Predicted entries (AlphaFold, SWISS-MODEL, AlphaFill) are left out because a
- * prediction comes from AlphaFold's own API, which answers per model. And
- * 3D-Beacons files SASBDB's small-angle-scattering fits under "experimentally
- * determined" too, with numeric ids and near-full coverage — dystrophin's best
- * "structure" by coverage was SASBDB 436 — which are not entries a residue
- * mapping exists for. Hence the `provider === 'PDBe'` gate rather than the
- * category alone.
+ * PDB entities only: the same list carries RCSB's computed models
+ * (`AF_AFP04637F1_1`), which a residue mapping does not exist for. The range
+ * spans every aligned region, as 3D-Beacons reported it.
  */
-export function parseExperimentalStructures(json) {
-    const structures = isRecord(json) ? json.structures : undefined;
-    if (!Array.isArray(structures)) {
+export function parseEntityAlignments(data) {
+    const alignments = isRecord(data) ? data.alignments : undefined;
+    const targets = isRecord(alignments)
+        ? alignments.target_alignments
+        : undefined;
+    if (!Array.isArray(targets)) {
         return [];
     }
-    return structures
-        .flatMap(entry => {
-        const s = isRecord(entry) ? entry.summary : undefined;
-        if (!isRecord(s)) {
+    return targets.flatMap(target => {
+        if (!isRecord(target) || typeof target.target_id !== 'string') {
             return [];
         }
-        const start = finiteNumber(s.uniprot_start);
-        const end = finiteNumber(s.uniprot_end);
-        const coverage = finiteNumber(s.coverage);
-        return typeof s.model_identifier === 'string' &&
-            s.provider === 'PDBe' &&
-            s.model_category === 'EXPERIMENTALLY DETERMINED' &&
-            start !== undefined &&
-            end !== undefined &&
-            coverage !== undefined
+        const [pdbId] = target.target_id.split('_');
+        const coverage = isRecord(target.coverage)
+            ? finiteNumber(target.coverage.query_coverage)
+            : undefined;
+        const regions = Array.isArray(target.aligned_regions)
+            ? target.aligned_regions.filter(isRecord)
+            : [];
+        const begins = regions.map(r => finiteNumber(r.query_begin));
+        const ends = regions.map(r => finiteNumber(r.query_end));
+        return pdbId !== undefined &&
+            isPdbId(pdbId) &&
+            coverage !== undefined &&
+            begins.length > 0 &&
+            begins.every(b => b !== undefined) &&
+            ends.every(e => e !== undefined)
             ? [
                 {
-                    pdbId: s.model_identifier.toLowerCase(),
-                    method: typeof s.experimental_method === 'string'
-                        ? s.experimental_method
-                        : 'experimental',
-                    resolution: finiteNumber(s.resolution),
-                    start,
-                    end,
+                    entityId: target.target_id,
+                    pdbId: pdbId.toLowerCase(),
+                    start: Math.min(...begins),
+                    end: Math.max(...ends),
                     coverage,
                 },
             ]
             : [];
-    })
-        .sort((a, b) => b.coverage - a.coverage ||
+    });
+}
+export function parseEntityDetails(data) {
+    const entities = isRecord(data) ? data.polymer_entities : undefined;
+    const details = new Map();
+    for (const entity of Array.isArray(entities) ? entities : []) {
+        if (!isRecord(entity) || typeof entity.rcsb_id !== 'string') {
+            continue;
+        }
+        const ids = entity.rcsb_polymer_entity_container_identifiers;
+        const info = isRecord(entity.entry)
+            ? entity.entry.rcsb_entry_info
+            : undefined;
+        const resolutions = isRecord(info) ? info.resolution_combined : undefined;
+        const resolution = Array.isArray(resolutions)
+            ? finiteNumber(resolutions[0])
+            : undefined;
+        details.set(entity.rcsb_id, {
+            method: isRecord(info) && typeof info.experimental_method === 'string'
+                ? info.experimental_method
+                : 'experimental',
+            ...(resolution === undefined ? {} : { resolution }),
+            chains: strings(isRecord(ids) ? ids.auth_asym_ids : undefined),
+        });
+    }
+    return details;
+}
+/**
+ * One row per entry, best coverage first and sharpest within a tie. An entry
+ * with several entities of the protein (a construct crystallised beside a
+ * different fragment of itself) takes the best-covering entity's range and
+ * every entity's chains.
+ */
+export function experimentalStructures(alignments, details) {
+    const byEntry = new Map();
+    for (const a of alignments) {
+        const d = details.get(a.entityId);
+        if (!d) {
+            continue;
+        }
+        const existing = byEntry.get(a.pdbId);
+        if (!existing) {
+            byEntry.set(a.pdbId, {
+                pdbId: a.pdbId,
+                method: d.method,
+                ...(d.resolution === undefined ? {} : { resolution: d.resolution }),
+                start: a.start,
+                end: a.end,
+                coverage: a.coverage,
+                chains: [...d.chains],
+            });
+            continue;
+        }
+        for (const chain of d.chains) {
+            if (!existing.chains.includes(chain)) {
+                existing.chains.push(chain);
+            }
+        }
+        if (a.coverage > existing.coverage) {
+            Object.assign(existing, {
+                start: a.start,
+                end: a.end,
+                coverage: a.coverage,
+            });
+        }
+    }
+    return [...byEntry.values()].sort((a, b) => b.coverage - a.coverage ||
         (a.resolution ?? Infinity) - (b.resolution ?? Infinity));
 }
-/** Best-effort: an unreachable API reads as "no entries", which costs a
- * structure suggestion and nothing else. */
+const ISOFORM_SUFFIX = /-\d+$/;
+/**
+ * Every PDB entry aligned to the accession. An accession with none, or one
+ * RCSB does not know, is `[]`; an isoform accession is asked as its entry,
+ * which is what the alignment is numbered on.
+ */
 export async function fetchExperimentalStructures(uniprotId, opts) {
-    for (let attempt = 0; attempt < 2; attempt++) {
-        const res = await rawfetch(beaconsSummaryUrl(uniprotId), opts).catch(() => undefined);
-        if (res?.ok) {
-            return parseExperimentalStructures(await res.json());
-        }
-        if (res?.status === 404 || opts?.signal?.aborted) {
-            return [];
+    const alignments = parseEntityAlignments(await graphqlFetch(RCSB_SEQUENCE_COORDINATES_URL, entityAlignmentsQuery(uniprotId.replace(ISOFORM_SUFFIX, '')), undefined, opts));
+    const ids = alignments.map(a => a.entityId);
+    const details = new Map();
+    for (let i = 0; i < ids.length; i += DETAILS_BATCH) {
+        const batch = parseEntityDetails(await graphqlFetch(RCSB_DATA_GRAPHQL_URL, ENTITY_DETAILS_QUERY, { ids: ids.slice(i, i + DETAILS_BATCH) }, opts));
+        for (const [id, d] of batch) {
+            details.set(id, d);
         }
     }
-    return [];
+    return experimentalStructures(alignments, details);
 }
 //# sourceMappingURL=structureSources.js.map

package/esm/structureSources.js.map

@@ -1 +1 @@
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