p2s_mapper 1.4.0 → 2.0.0

package/dist/structureSources.js

@@ -1,87 +1,174 @@
 "use strict";
-// 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.
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.beaconsSummaryUrl = beaconsSummaryUrl;
-exports.parseExperimentalStructures = parseExperimentalStructures;
+exports.ENTITY_DETAILS_QUERY = exports.RCSB_SEQUENCE_COORDINATES_URL = void 0;
+exports.entityAlignmentsQuery = entityAlignmentsQuery;
+exports.parseEntityAlignments = parseEntityAlignments;
+exports.parseEntityDetails = parseEntityDetails;
+exports.experimentalStructures = experimentalStructures;
 exports.fetchExperimentalStructures = fetchExperimentalStructures;
-const fetchUtils_ts_1 = require("./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.
-function beaconsSummaryUrl(uniprotId) {
-    return `https://www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/api/uniprot/summary/${encodeURIComponent(uniprotId)}.json`;
+const pdbEntry_ts_1 = require("./pdbEntry.js");
+const structureUrls_ts_1 = require("./structureUrls.js");
+exports.RCSB_SEQUENCE_COORDINATES_URL = 'https://sequence-coordinates.rcsb.org/graphql';
+function entityAlignmentsQuery(uniprotId) {
+    return `{ alignments(from: UNIPROT, to: PDB_ENTITY, queryId: "${uniprotId}") {
+  target_alignments {
+    target_id
+    coverage { query_coverage }
+    aligned_regions { query_begin query_end }
+  }
+} }`;
 }
+exports.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.
  */
-function parseExperimentalStructures(json) {
-    const structures = isRecord(json) ? json.structures : undefined;
-    if (!Array.isArray(structures)) {
+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 &&
+            (0, structureUrls_ts_1.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 ||
+    });
+}
+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.
+ */
+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.
+ */
 async function fetchExperimentalStructures(uniprotId, opts) {
-    for (let attempt = 0; attempt < 2; attempt++) {
-        const res = await (0, fetchUtils_ts_1.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 (0, pdbEntry_ts_1.graphqlFetch)(exports.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 (0, pdbEntry_ts_1.graphqlFetch)(pdbEntry_ts_1.RCSB_DATA_GRAPHQL_URL, exports.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/dist/structureSources.js.map

@@ -1 +1 @@
-{"version":3,"file":"structureSources.js","sourceRoot":"","sources":["../src/structureSources.ts"],"names":[],"mappings":";AAAA,+EAA+E;AAC/E,0EAA0E;AAC1E,yEAAyE;AACzE,8EAA8E;AAC9E,yEAAyE;AACzE,mBAAmB;;AAqBnB,8CAEC;AAqBD,kEA0CC;AAID,kEAgBC;AAxGD,mDAA0C;AAgB1C,gFAAgF;AAChF,4EAA4E;AAC5E,UAAU;AACV,SAAgB,iBAAiB,CAAC,SAAiB;IACjD,OAAO,oEAAoE,kBAAkB,CAAC,SAAS,CAAC,OAAO,CAAA;AACjH,CAAC;AAED,SAAS,QAAQ,CAAC,KAAc;IAC9B,OAAO,OAAO,KAAK,KAAK,QAAQ,IAAI,KAAK,KAAK,IAAI,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;AAC7E,CAAC;AAED,SAAS,YAAY,CAAC,KAAc;IAClC,OAAO,OAAO,KAAK,KAAK,QAAQ,IAAI,MAAM,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,SAAS,CAAA;AAChF,CAAC;AAED;;;;;;;;;;GAUG;AACH,SAAgB,2BAA2B,CACzC,IAAa;IAEb,MAAM,UAAU,GAAG,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,UAAU,CAAC,CAAC,CAAC,SAAS,CAAA;IAC/D,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,UAAU,CAAC,EAAE,CAAC;QAC/B,OAAO,EAAE,CAAA;IACX,CAAC;IACD,OAAO,UAAU;SACd,OAAO,CAAC,KAAK,CAAC,EAAE;QACf,MAAM,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,SAAS,CAAA;QACrD,IAAI,CAAC,QAAQ,CAAC,CAAC,CAAC,EAAE,CAAC;YACjB,OAAO,EAAE,CAAA;QACX,CAAC;QACD,MAAM,KAAK,GAAG,YAAY,CAAC,CAAC,CAAC,aAAa,CAAC,CAAA;QAC3C,MAAM,GAAG,GAAG,YAAY,CAAC,CAAC,CAAC,WAAW,CAAC,CAAA;QACvC,MAAM,QAAQ,GAAG,YAAY,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAA;QACzC,OAAO,OAAO,CAAC,CAAC,gBAAgB,KAAK,QAAQ;YAC3C,CAAC,CAAC,QAAQ,KAAK,MAAM;YACrB,CAAC,CAAC,cAAc,KAAK,2BAA2B;YAChD,KAAK,KAAK,SAAS;YACnB,GAAG,KAAK,SAAS;YACjB,QAAQ,KAAK,SAAS;YACtB,CAAC,CAAC;gBACE;oBACE,KAAK,EAAE,CAAC,CAAC,gBAAgB,CAAC,WAAW,EAAE;oBACvC,MAAM,EACJ,OAAO,CAAC,CAAC,mBAAmB,KAAK,QAAQ;wBACvC,CAAC,CAAC,CAAC,CAAC,mBAAmB;wBACvB,CAAC,CAAC,cAAc;oBACpB,UAAU,EAAE,YAAY,CAAC,CAAC,CAAC,UAAU,CAAC;oBACtC,KAAK;oBACL,GAAG;oBACH,QAAQ;iBACT;aACF;YACH,CAAC,CAAC,EAAE,CAAA;IACR,CAAC,CAAC;SACD,IAAI,CACH,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CACP,CAAC,CAAC,QAAQ,GAAG,CAAC,CAAC,QAAQ;QACvB,CAAC,CAAC,CAAC,UAAU,IAAI,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,UAAU,IAAI,QAAQ,CAAC,CAC1D,CAAA;AACL,CAAC;AAED;4CAC4C;AACrC,KAAK,UAAU,2BAA2B,CAC/C,SAAiB,EACjB,IAAmB;IAEnB,KAAK,IAAI,OAAO,GAAG,CAAC,EAAE,OAAO,GAAG,CAAC,EAAE,OAAO,EAAE,EAAE,CAAC;QAC7C,MAAM,GAAG,GAAG,MAAM,IAAA,wBAAQ,EAAC,iBAAiB,CAAC,SAAS,CAAC,EAAE,IAAI,CAAC,CAAC,KAAK,CAClE,GAAG,EAAE,CAAC,SAAS,CAChB,CAAA;QACD,IAAI,GAAG,EAAE,EAAE,EAAE,CAAC;YACZ,OAAO,2BAA2B,CAAC,MAAM,GAAG,CAAC,IAAI,EAAE,CAAC,CAAA;QACtD,CAAC;QACD,IAAI,GAAG,EAAE,MAAM,KAAK,GAAG,IAAI,IAAI,EAAE,MAAM,EAAE,OAAO,EAAE,CAAC;YACjD,OAAO,EAAE,CAAA;QACX,CAAC;IACH,CAAC;IACD,OAAO,EAAE,CAAA;AACX,CAAC"}
+{"version":3,"file":"structureSources.js","sourceRoot":"","sources":["../src/structureSources.ts"],"names":[],"mappings":";AAAA,+EAA+E;AAC/E,8EAA8E;AAC9E,8EAA8E;AAC9E,6EAA6E;AAC7E,uEAAuE;AACvE,mBAAmB;;;AAyCnB,sDAQC;AA8BD,sDAsCC;AAED,gDAyBC;AAQD,wDAyCC;AASD,kEA4BC;AApOD,+CAAmE;AACnE,yDAA4C;AAI/B,QAAA,6BAA6B,GACxC,+CAA+C,CAAA;AAiCjD,SAAgB,qBAAqB,CAAC,SAAiB;IACrD,OAAO,yDAAyD,SAAS;;;;;;IAMvE,CAAA;AACJ,CAAC;AAEY,QAAA,oBAAoB,GAAG;;;;IAIhC,CAAA;AAEJ,sCAAsC;AACtC,MAAM,aAAa,GAAG,IAAI,CAAA;AAE1B,SAAS,QAAQ,CAAC,KAAc;IAC9B,OAAO,OAAO,KAAK,KAAK,QAAQ,IAAI,KAAK,KAAK,IAAI,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;AAC7E,CAAC;AAED,SAAS,YAAY,CAAC,KAAc;IAClC,OAAO,OAAO,KAAK,KAAK,QAAQ,IAAI,MAAM,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,SAAS,CAAA;AAChF,CAAC;AAED,SAAS,OAAO,CAAC,KAAc;IAC7B,OAAO,KAAK,CAAC,OAAO,CAAC,KAAK,CAAC;QACzB,CAAC,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,EAAe,EAAE,CAAC,OAAO,CAAC,KAAK,QAAQ,CAAC;QACzD,CAAC,CAAC,EAAE,CAAA;AACR,CAAC;AAED;;;;GAIG;AACH,SAAgB,qBAAqB,CAAC,IAAa;IACjD,MAAM,UAAU,GAAG,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,UAAU,CAAC,CAAC,CAAC,SAAS,CAAA;IAC/D,MAAM,OAAO,GAAG,QAAQ,CAAC,UAAU,CAAC;QAClC,CAAC,CAAC,UAAU,CAAC,iBAAiB;QAC9B,CAAC,CAAC,SAAS,CAAA;IACb,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,OAAO,CAAC,EAAE,CAAC;QAC5B,OAAO,EAAE,CAAA;IACX,CAAC;IACD,OAAO,OAAO,CAAC,OAAO,CAAC,MAAM,CAAC,EAAE;QAC9B,IAAI,CAAC,QAAQ,CAAC,MAAM,CAAC,IAAI,OAAO,MAAM,CAAC,SAAS,KAAK,QAAQ,EAAE,CAAC;YAC9D,OAAO,EAAE,CAAA;QACX,CAAC;QACD,MAAM,CAAC,KAAK,CAAC,GAAG,MAAM,CAAC,SAAS,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;QAC3C,MAAM,QAAQ,GAAG,QAAQ,CAAC,MAAM,CAAC,QAAQ,CAAC;YACxC,CAAC,CAAC,YAAY,CAAC,MAAM,CAAC,QAAQ,CAAC,cAAc,CAAC;YAC9C,CAAC,CAAC,SAAS,CAAA;QACb,MAAM,OAAO,GAAG,KAAK,CAAC,OAAO,CAAC,MAAM,CAAC,eAAe,CAAC;YACnD,CAAC,CAAC,MAAM,CAAC,eAAe,CAAC,MAAM,CAAC,QAAQ,CAAC;YACzC,CAAC,CAAC,EAAE,CAAA;QACN,MAAM,MAAM,GAAG,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,YAAY,CAAC,CAAC,CAAC,WAAW,CAAC,CAAC,CAAA;QAC5D,MAAM,IAAI,GAAG,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,YAAY,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAA;QACxD,OAAO,KAAK,KAAK,SAAS;YACxB,IAAA,0BAAO,EAAC,KAAK,CAAC;YACd,QAAQ,KAAK,SAAS;YACtB,MAAM,CAAC,MAAM,GAAG,CAAC;YACjB,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,KAAK,SAAS,CAAC;YAClC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,KAAK,SAAS,CAAC;YAChC,CAAC,CAAC;gBACE;oBACE,QAAQ,EAAE,MAAM,CAAC,SAAS;oBAC1B,KAAK,EAAE,KAAK,CAAC,WAAW,EAAE;oBAC1B,KAAK,EAAE,IAAI,CAAC,GAAG,CAAC,GAAG,MAAM,CAAC;oBAC1B,GAAG,EAAE,IAAI,CAAC,GAAG,CAAC,GAAG,IAAI,CAAC;oBACtB,QAAQ;iBACT;aACF;YACH,CAAC,CAAC,EAAE,CAAA;IACR,CAAC,CAAC,CAAA;AACJ,CAAC;AAED,SAAgB,kBAAkB,CAAC,IAAa;IAC9C,MAAM,QAAQ,GAAG,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,gBAAgB,CAAC,CAAC,CAAC,SAAS,CAAA;IACnE,MAAM,OAAO,GAAG,IAAI,GAAG,EAAyB,CAAA;IAChD,KAAK,MAAM,MAAM,IAAI,KAAK,CAAC,OAAO,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC;QAC7D,IAAI,CAAC,QAAQ,CAAC,MAAM,CAAC,IAAI,OAAO,MAAM,CAAC,OAAO,KAAK,QAAQ,EAAE,CAAC;YAC5D,SAAQ;QACV,CAAC;QACD,MAAM,GAAG,GAAG,MAAM,CAAC,yCAAyC,CAAA;QAC5D,MAAM,IAAI,GAAG,QAAQ,CAAC,MAAM,CAAC,KAAK,CAAC;YACjC,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,eAAe;YAC9B,CAAC,CAAC,SAAS,CAAA;QACb,MAAM,WAAW,GAAG,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,mBAAmB,CAAC,CAAC,CAAC,SAAS,CAAA;QACzE,MAAM,UAAU,GAAG,KAAK,CAAC,OAAO,CAAC,WAAW,CAAC;YAC3C,CAAC,CAAC,YAAY,CAAC,WAAW,CAAC,CAAC,CAAC,CAAC;YAC9B,CAAC,CAAC,SAAS,CAAA;QACb,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,OAAO,EAAE;YAC1B,MAAM,EACJ,QAAQ,CAAC,IAAI,CAAC,IAAI,OAAO,IAAI,CAAC,mBAAmB,KAAK,QAAQ;gBAC5D,CAAC,CAAC,IAAI,CAAC,mBAAmB;gBAC1B,CAAC,CAAC,cAAc;YACpB,GAAG,CAAC,UAAU,KAAK,SAAS,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,UAAU,EAAE,CAAC;YACnD,MAAM,EAAE,OAAO,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,aAAa,CAAC,CAAC,CAAC,SAAS,CAAC;SAC/D,CAAC,CAAA;IACJ,CAAC;IACD,OAAO,OAAO,CAAA;AAChB,CAAC;AAED;;;;;GAKG;AACH,SAAgB,sBAAsB,CACpC,UAA6B,EAC7B,OAA2C;IAE3C,MAAM,OAAO,GAAG,IAAI,GAAG,EAAiC,CAAA;IACxD,KAAK,MAAM,CAAC,IAAI,UAAU,EAAE,CAAC;QAC3B,MAAM,CAAC,GAAG,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAA;QACjC,IAAI,CAAC,CAAC,EAAE,CAAC;YACP,SAAQ;QACV,CAAC;QACD,MAAM,QAAQ,GAAG,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,KAAK,CAAC,CAAA;QACrC,IAAI,CAAC,QAAQ,EAAE,CAAC;YACd,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,KAAK,EAAE;gBACnB,KAAK,EAAE,CAAC,CAAC,KAAK;gBACd,MAAM,EAAE,CAAC,CAAC,MAAM;gBAChB,GAAG,CAAC,CAAC,CAAC,UAAU,KAAK,SAAS,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,UAAU,EAAE,CAAC,CAAC,UAAU,EAAE,CAAC;gBACnE,KAAK,EAAE,CAAC,CAAC,KAAK;gBACd,GAAG,EAAE,CAAC,CAAC,GAAG;gBACV,QAAQ,EAAE,CAAC,CAAC,QAAQ;gBACpB,MAAM,EAAE,CAAC,GAAG,CAAC,CAAC,MAAM,CAAC;aACtB,CAAC,CAAA;YACF,SAAQ;QACV,CAAC;QACD,KAAK,MAAM,KAAK,IAAI,CAAC,CAAC,MAAM,EAAE,CAAC;YAC7B,IAAI,CAAC,QAAQ,CAAC,MAAM,CAAC,QAAQ,CAAC,KAAK,CAAC,EAAE,CAAC;gBACrC,QAAQ,CAAC,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;YAC7B,CAAC;QACH,CAAC;QACD,IAAI,CAAC,CAAC,QAAQ,GAAG,QAAQ,CAAC,QAAQ,EAAE,CAAC;YACnC,MAAM,CAAC,MAAM,CAAC,QAAQ,EAAE;gBACtB,KAAK,EAAE,CAAC,CAAC,KAAK;gBACd,GAAG,EAAE,CAAC,CAAC,GAAG;gBACV,QAAQ,EAAE,CAAC,CAAC,QAAQ;aACrB,CAAC,CAAA;QACJ,CAAC;IACH,CAAC;IACD,OAAO,CAAC,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC,CAAC,IAAI,CAC/B,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CACP,CAAC,CAAC,QAAQ,GAAG,CAAC,CAAC,QAAQ;QACvB,CAAC,CAAC,CAAC,UAAU,IAAI,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,UAAU,IAAI,QAAQ,CAAC,CAC1D,CAAA;AACH,CAAC;AAED,MAAM,cAAc,GAAG,OAAO,CAAA;AAE9B;;;;GAIG;AACI,KAAK,UAAU,2BAA2B,CAC/C,SAAiB,EACjB,IAAmB;IAEnB,MAAM,UAAU,GAAG,qBAAqB,CACtC,MAAM,IAAA,0BAAY,EAChB,qCAA6B,EAC7B,qBAAqB,CAAC,SAAS,CAAC,OAAO,CAAC,cAAc,EAAE,EAAE,CAAC,CAAC,EAC5D,SAAS,EACT,IAAI,CACL,CACF,CAAA;IACD,MAAM,GAAG,GAAG,UAAU,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAA;IAC3C,MAAM,OAAO,GAAG,IAAI,GAAG,EAAyB,CAAA;IAChD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,GAAG,CAAC,MAAM,EAAE,CAAC,IAAI,aAAa,EAAE,CAAC;QACnD,MAAM,KAAK,GAAG,kBAAkB,CAC9B,MAAM,IAAA,0BAAY,EAChB,mCAAqB,EACrB,4BAAoB,EACpB,EAAE,GAAG,EAAE,GAAG,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,GAAG,aAAa,CAAC,EAAE,EACxC,IAAI,CACL,CACF,CAAA;QACD,KAAK,MAAM,CAAC,EAAE,EAAE,CAAC,CAAC,IAAI,KAAK,EAAE,CAAC;YAC5B,OAAO,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC,CAAC,CAAA;QACpB,CAAC;IACH,CAAC;IACD,OAAO,sBAAsB,CAAC,UAAU,EAAE,OAAO,CAAC,CAAA;AACpD,CAAC"}

package/dist/structureUrls.d.ts

@@ -9,6 +9,8 @@ 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

package/dist/structureUrls.js

@@ -8,6 +8,8 @@ exports.uniprotFastaUrl = uniprotFastaUrl;
 exports.uniprotEntryUrl = uniprotEntryUrl;
 exports.getAlphaFoldStructureUrl = getAlphaFoldStructureUrl;
 exports.getPdbStructureUrl = getPdbStructureUrl;
+exports.isPdbId = isPdbId;
+exports.rcsbEntryUrl = rcsbEntryUrl;
 exports.resolveStructureUrl = resolveStructureUrl;
 exports.getPdbIdFromUrl = getPdbIdFromUrl;
 exports.getUniprotIdFromAlphaFoldTarget = getUniprotIdFromAlphaFoldTarget;
@@ -40,6 +42,15 @@ function getAlphaFoldStructureUrl(uniprotId, version = ALPHAFOLD_VERSION) {
 function getPdbStructureUrl(pdbId) {
     return `https://files.rcsb.org/download/${pdbId}.cif`;
 }
+// A PDB id is four characters, the first a digit: 1TUP, 6ZIO. Checked before
+// a typed one reaches a fetch, so three characters on the way to four are not
+// a 404 apiece.
+function isPdbId(value) {
+    return /^[1-9][A-Za-z0-9]{3}$/.test(value);
+}
+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

package/dist/structureUrls.js.map

@@ -1 +1 @@
-{"version":3,"file":"structureUrls.js","sourceRoot":"","sources":["../src/structureUrls.ts"],"names":[],"mappings":";AAAA,+EAA+E;AAC/E,kFAAkF;AAClF,gFAAgF;;AAQhF,sCAEC;AAED,0CAEC;AAED,0CAEC;AAQD,4DAKC;AAED,gDAEC;AAkBD,kDAiBC;AAYD,0CAiBC;AAUD,0EAGC;AAID,8DAUC;AAED,gEAOC;AAOD,sDA0BC;AAtKD,MAAM,iBAAiB,GAAG,IAAI,CAAA;AAE9B,+EAA+E;AAC/E,6EAA6E;AAC7E,6EAA6E;AAC7E,yEAAyE;AACzE,SAAgB,aAAa,CAAC,SAAiB;IAC7C,OAAO,sCAAsC,SAAS,MAAM,CAAA;AAC9D,CAAC;AAED,SAAgB,eAAe,CAAC,SAAiB;IAC/C,OAAO,sCAAsC,SAAS,QAAQ,CAAA;AAChE,CAAC;AAED,SAAgB,eAAe,CAAC,SAAiB;IAC/C,OAAO,qCAAqC,SAAS,QAAQ,CAAA;AAC/D,CAAC;AAED;;;;;GAKG;AACH,SAAgB,wBAAwB,CACtC,SAAiB,EACjB,OAAO,GAAG,iBAAiB;IAE3B,OAAO,wCAAwC,SAAS,aAAa,OAAO,MAAM,CAAA;AACpF,CAAC;AAED,SAAgB,kBAAkB,CAAC,KAAa;IAC9C,OAAO,mCAAmC,KAAK,MAAM,CAAA;AACvD,CAAC;AAED;;;;;;;;;;;;;;;GAeG;AACH,SAAgB,mBAAmB,CAAC,EAClC,GAAG,EACH,IAAI,EACJ,SAAS,EACT,KAAK,GAMN;IACC,IAAI,GAAG,KAAK,SAAS,IAAI,IAAI,KAAK,SAAS,EAAE,CAAC;QAC5C,OAAO,GAAG,CAAA;IACZ,CAAC;IACD,OAAO,SAAS,KAAK,SAAS,IAAI,KAAK,KAAK,SAAS;QACnD,CAAC,CAAC,SAAS;QACX,CAAC,CAAC,kBAAkB,CAAC,KAAK,CAAC,CAAA;AAC/B,CAAC;AAED,8EAA8E;AAC9E,iFAAiF;AACjF,8DAA8D;AAC9D,MAAM,iBAAiB,GAAG,CAAC,gBAAgB,EAAE,eAAe,EAAE,eAAe,CAAC,CAAA;AAE9E;;;;GAIG;AACH,SAAgB,eAAe,CAAC,GAAW;IACzC,MAAM,EAAE,IAAI,EAAE,IAAI,EAAE,GAAG,CAAC,GAAG,EAAE;QAC3B,IAAI,CAAC;YACH,MAAM,MAAM,GAAG,IAAI,GAAG,CAAC,GAAG,CAAC,CAAA;YAC3B,OAAO,EAAE,IAAI,EAAE,MAAM,CAAC,QAAQ,EAAE,IAAI,EAAE,MAAM,CAAC,QAAQ,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,GAAG,EAAE,EAAE,CAAA;QAC1E,CAAC;QAAC,MAAM,CAAC;YACP,OAAO,EAAE,IAAI,EAAE,SAAS,EAAE,IAAI,EAAE,SAAS,EAAE,CAAA;QAC7C,CAAC;IACH,CAAC,CAAC,EAAE,CAAA;IACJ,IAAI,IAAI,KAAK,SAAS,IAAI,CAAC,iBAAiB,CAAC,QAAQ,CAAC,IAAI,CAAC,EAAE,CAAC;QAC5D,OAAO,SAAS,CAAA;IAClB,CAAC;IACD,MAAM,KAAK,GACT,2EAA2E,CAAC,IAAI,CAC9E,IAAI,IAAI,EAAE,CACX,CAAA;IACH,OAAO,KAAK,EAAE,CAAC,CAAC,CAAC,EAAE,WAAW,EAAE,CAAA;AAClC,CAAC;AAED,yEAAyE;AACzE,yEAAyE;AACzE,SAAS,eAAe,CAAC,MAAc;IACrC,OAAO,MAAM,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAE,CAAA;AAC9B,CAAC;AAED;+EAC+E;AAC/E,SAAgB,+BAA+B,CAAC,MAAc;IAC5D,MAAM,KAAK,GAAG,8BAA8B,CAAC,IAAI,CAAC,eAAe,CAAC,MAAM,CAAC,CAAC,CAAA;IAC1E,OAAO,KAAK,EAAE,CAAC,CAAC,CAAC,CAAA;AACnB,CAAC;AAED,0EAA0E;AAC1E,wEAAwE;AACxE,SAAgB,yBAAyB,CAAC,MAAc,EAAE,EAAU;IAClE,MAAM,QAAQ,GAAG,eAAe,CAAC,MAAM,CAAC,CAAA;IACxC,IAAI,QAAQ,CAAC,UAAU,CAAC,KAAK,CAAC,EAAE,CAAC;QAC/B,OAAO,qCAAqC,QAAQ,MAAM,CAAA;IAC5D,CAAC;IACD,MAAM,KAAK,GACT,EAAE,KAAK,QAAQ;QACb,CAAC,CAAC,iCAAiC,CAAC,IAAI,CAAC,QAAQ,CAAC,EAAE,CAAC,CAAC,CAAC;QACvD,CAAC,CAAC,SAAS,CAAA;IACf,OAAO,KAAK,CAAC,CAAC,CAAC,kBAAkB,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;AACtD,CAAC;AAED,SAAgB,0BAA0B,CAAC,MAAc;IACvD,MAAM,QAAQ,GAAG,eAAe,CAAC,MAAM,CAAC,CAAA;IACxC,IAAI,QAAQ,CAAC,UAAU,CAAC,KAAK,CAAC,EAAE,CAAC;QAC/B,MAAM,YAAY,GAAG,QAAQ,CAAC,OAAO,CAAC,SAAS,EAAE,cAAc,CAAC,CAAA;QAChE,OAAO,qCAAqC,YAAY,OAAO,CAAA;IACjE,CAAC;IACD,OAAO,SAAS,CAAA;AAClB,CAAC;AAED;;;;GAIG;AACH,SAAgB,qBAAqB,CAAC,EACpC,GAAG,EACH,IAAI,EACJ,SAAS,GAKV;IACC,IAAI,GAAG,KAAK,SAAS,EAAE,CAAC;QACtB,OAAO,IAAI,KAAK,SAAS;YACvB,CAAC,CAAC,oBAAoB;YACtB,CAAC,CAAC,SAAS;gBACT,CAAC,CAAC,aAAa,SAAS,EAAE;gBAC1B,CAAC,CAAC,EAAE,CAAA;IACV,CAAC;IACD,MAAM,KAAK,GAAG,eAAe,CAAC,GAAG,CAAC,CAAA;IAClC,IAAI,KAAK,EAAE,CAAC;QACV,OAAO,KAAK,CAAC,WAAW,EAAE,CAAA;IAC5B,CAAC;IACD,MAAM,YAAY,GAAG,+BAA+B,CAAC,GAAG,CAAC,CAAA;IACzD,IAAI,YAAY,EAAE,CAAC;QACjB,OAAO,aAAa,YAAY,EAAE,CAAA;IACpC,CAAC;IACD,MAAM,IAAI,GAAG,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,GAAG,EAAE,EAAE,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAA;IAChD,OAAO,IAAI,KAAK,SAAS,IAAI,IAAI,KAAK,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAA;AACvD,CAAC"}
+{"version":3,"file":"structureUrls.js","sourceRoot":"","sources":["../src/structureUrls.ts"],"names":[],"mappings":";AAAA,+EAA+E;AAC/E,kFAAkF;AAClF,gFAAgF;;AAQhF,sCAEC;AAED,0CAEC;AAED,0CAEC;AAQD,4DAKC;AAED,gDAEC;AAKD,0BAEC;AAED,oCAEC;AAkBD,kDAiBC;AAYD,0CAiBC;AAUD,0EAGC;AAID,8DAUC;AAED,gEAOC;AAOD,sDA0BC;AAjLD,MAAM,iBAAiB,GAAG,IAAI,CAAA;AAE9B,+EAA+E;AAC/E,6EAA6E;AAC7E,6EAA6E;AAC7E,yEAAyE;AACzE,SAAgB,aAAa,CAAC,SAAiB;IAC7C,OAAO,sCAAsC,SAAS,MAAM,CAAA;AAC9D,CAAC;AAED,SAAgB,eAAe,CAAC,SAAiB;IAC/C,OAAO,sCAAsC,SAAS,QAAQ,CAAA;AAChE,CAAC;AAED,SAAgB,eAAe,CAAC,SAAiB;IAC/C,OAAO,qCAAqC,SAAS,QAAQ,CAAA;AAC/D,CAAC;AAED;;;;;GAKG;AACH,SAAgB,wBAAwB,CACtC,SAAiB,EACjB,OAAO,GAAG,iBAAiB;IAE3B,OAAO,wCAAwC,SAAS,aAAa,OAAO,MAAM,CAAA;AACpF,CAAC;AAED,SAAgB,kBAAkB,CAAC,KAAa;IAC9C,OAAO,mCAAmC,KAAK,MAAM,CAAA;AACvD,CAAC;AAED,6EAA6E;AAC7E,8EAA8E;AAC9E,gBAAgB;AAChB,SAAgB,OAAO,CAAC,KAAa;IACnC,OAAO,uBAAuB,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;AAC5C,CAAC;AAED,SAAgB,YAAY,CAAC,KAAa;IACxC,OAAO,kCAAkC,KAAK,CAAC,WAAW,EAAE,EAAE,CAAA;AAChE,CAAC;AAED;;;;;;;;;;;;;;;GAeG;AACH,SAAgB,mBAAmB,CAAC,EAClC,GAAG,EACH,IAAI,EACJ,SAAS,EACT,KAAK,GAMN;IACC,IAAI,GAAG,KAAK,SAAS,IAAI,IAAI,KAAK,SAAS,EAAE,CAAC;QAC5C,OAAO,GAAG,CAAA;IACZ,CAAC;IACD,OAAO,SAAS,KAAK,SAAS,IAAI,KAAK,KAAK,SAAS;QACnD,CAAC,CAAC,SAAS;QACX,CAAC,CAAC,kBAAkB,CAAC,KAAK,CAAC,CAAA;AAC/B,CAAC;AAED,8EAA8E;AAC9E,iFAAiF;AACjF,8DAA8D;AAC9D,MAAM,iBAAiB,GAAG,CAAC,gBAAgB,EAAE,eAAe,EAAE,eAAe,CAAC,CAAA;AAE9E;;;;GAIG;AACH,SAAgB,eAAe,CAAC,GAAW;IACzC,MAAM,EAAE,IAAI,EAAE,IAAI,EAAE,GAAG,CAAC,GAAG,EAAE;QAC3B,IAAI,CAAC;YACH,MAAM,MAAM,GAAG,IAAI,GAAG,CAAC,GAAG,CAAC,CAAA;YAC3B,OAAO,EAAE,IAAI,EAAE,MAAM,CAAC,QAAQ,EAAE,IAAI,EAAE,MAAM,CAAC,QAAQ,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,GAAG,EAAE,EAAE,CAAA;QAC1E,CAAC;QAAC,MAAM,CAAC;YACP,OAAO,EAAE,IAAI,EAAE,SAAS,EAAE,IAAI,EAAE,SAAS,EAAE,CAAA;QAC7C,CAAC;IACH,CAAC,CAAC,EAAE,CAAA;IACJ,IAAI,IAAI,KAAK,SAAS,IAAI,CAAC,iBAAiB,CAAC,QAAQ,CAAC,IAAI,CAAC,EAAE,CAAC;QAC5D,OAAO,SAAS,CAAA;IAClB,CAAC;IACD,MAAM,KAAK,GACT,2EAA2E,CAAC,IAAI,CAC9E,IAAI,IAAI,EAAE,CACX,CAAA;IACH,OAAO,KAAK,EAAE,CAAC,CAAC,CAAC,EAAE,WAAW,EAAE,CAAA;AAClC,CAAC;AAED,yEAAyE;AACzE,yEAAyE;AACzE,SAAS,eAAe,CAAC,MAAc;IACrC,OAAO,MAAM,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAE,CAAA;AAC9B,CAAC;AAED;+EAC+E;AAC/E,SAAgB,+BAA+B,CAAC,MAAc;IAC5D,MAAM,KAAK,GAAG,8BAA8B,CAAC,IAAI,CAAC,eAAe,CAAC,MAAM,CAAC,CAAC,CAAA;IAC1E,OAAO,KAAK,EAAE,CAAC,CAAC,CAAC,CAAA;AACnB,CAAC;AAED,0EAA0E;AAC1E,wEAAwE;AACxE,SAAgB,yBAAyB,CAAC,MAAc,EAAE,EAAU;IAClE,MAAM,QAAQ,GAAG,eAAe,CAAC,MAAM,CAAC,CAAA;IACxC,IAAI,QAAQ,CAAC,UAAU,CAAC,KAAK,CAAC,EAAE,CAAC;QAC/B,OAAO,qCAAqC,QAAQ,MAAM,CAAA;IAC5D,CAAC;IACD,MAAM,KAAK,GACT,EAAE,KAAK,QAAQ;QACb,CAAC,CAAC,iCAAiC,CAAC,IAAI,CAAC,QAAQ,CAAC,EAAE,CAAC,CAAC,CAAC;QACvD,CAAC,CAAC,SAAS,CAAA;IACf,OAAO,KAAK,CAAC,CAAC,CAAC,kBAAkB,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;AACtD,CAAC;AAED,SAAgB,0BAA0B,CAAC,MAAc;IACvD,MAAM,QAAQ,GAAG,eAAe,CAAC,MAAM,CAAC,CAAA;IACxC,IAAI,QAAQ,CAAC,UAAU,CAAC,KAAK,CAAC,EAAE,CAAC;QAC/B,MAAM,YAAY,GAAG,QAAQ,CAAC,OAAO,CAAC,SAAS,EAAE,cAAc,CAAC,CAAA;QAChE,OAAO,qCAAqC,YAAY,OAAO,CAAA;IACjE,CAAC;IACD,OAAO,SAAS,CAAA;AAClB,CAAC;AAED;;;;GAIG;AACH,SAAgB,qBAAqB,CAAC,EACpC,GAAG,EACH,IAAI,EACJ,SAAS,GAKV;IACC,IAAI,GAAG,KAAK,SAAS,EAAE,CAAC;QACtB,OAAO,IAAI,KAAK,SAAS;YACvB,CAAC,CAAC,oBAAoB;YACtB,CAAC,CAAC,SAAS;gBACT,CAAC,CAAC,aAAa,SAAS,EAAE;gBAC1B,CAAC,CAAC,EAAE,CAAA;IACV,CAAC;IACD,MAAM,KAAK,GAAG,eAAe,CAAC,GAAG,CAAC,CAAA;IAClC,IAAI,KAAK,EAAE,CAAC;QACV,OAAO,KAAK,CAAC,WAAW,EAAE,CAAA;IAC5B,CAAC;IACD,MAAM,YAAY,GAAG,+BAA+B,CAAC,GAAG,CAAC,CAAA;IACzD,IAAI,YAAY,EAAE,CAAC;QACjB,OAAO,aAAa,YAAY,EAAE,CAAA;IACpC,CAAC;IACD,MAAM,IAAI,GAAG,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,GAAG,EAAE,EAAE,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAA;IAChD,OAAO,IAAI,KAAK,SAAS,IAAI,IAAI,KAAK,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAA;AACvD,CAAC"}

package/esm/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/esm/coordinates.js.map

@@ -1 +1 @@
-{"version":3,"file":"coordinates.js","sourceRoot":"","sources":["../src/coordinates.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,+BAA+B,EAC/B,8BAA8B,EAC9B,gCAAgC,GACjC,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,SAAS,EAAE,MAAM,gBAAgB,CAAA;AAqB1C,MAAM,CAAC,MAAM,YAAY,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,CAAiB,CAAA;AAC5D,MAAM,CAAC,MAAM,aAAa,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,CAAkB,CAAA;AAC9D,MAAM,CAAC,MAAM,YAAY,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,CAAiB,CAAA;AA2B5D;;;;GAIG;AACH,MAAM,UAAU,oBAAoB,CAClC,iBAAoC;IAEpC,MAAM,EACJ,mCAAmC,EACnC,mCAAmC,GACpC,GAAG,8BAA8B,CAAC,iBAAiB,CAAC,CAAA;IACrD,MAAM,KAAK,GAAG,+BAA+B,CAAC,iBAAiB,CAAC,CAAA;IAChE,MAAM,KAAK,GAAG,gCAAgC,CAAC,iBAAiB,CAAC,CAAA;IACjE,MAAM,KAAK,GAAG,SAAS,CAAC,KAAK,CAAC,CAAA;IAC9B,MAAM,KAAK,GAAG,SAAS,CAAC,KAAK,CAAC,CAAA;IAE9B,uEAAuE;IACvE,6EAA6E;IAC7E,sEAAsE;IACtE,OAAO;QACL,qBAAqB,EAAE,CAAC,CAAC,EAAE,CACzB,mCAAmC,CAAC,CAAC,CAA8B;QACrE,qBAAqB,EAAE,CAAC,CAAC,EAAE,CACzB,mCAAmC,CAAC,CAAC,CAA6B;QACpE,oBAAoB,EAAE,CAAC,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC,CAA6B;QAC/D,oBAAoB,EAAE,CAAC,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC,CAA6B;QAC/D,qBAAqB,EAAE,CAAC,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC,CAA6B;QAChE,qBAAqB,EAAE,CAAC,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC,CAA8B;QACjE,IAAI,EAAE;YACJ,mCAAmC;YACnC,mCAAmC;YACnC,+BAA+B,EAAE,KAAK;YACtC,gCAAgC,EAAE,KAAK;YACvC,4BAA4B,EAAE,KAAK;YACnC,6BAA6B,EAAE,KAAK;SACrC;KACF,CAAA;AACH,CAAC;AAED;;;;;;GAMG;AACH,MAAM,UAAU,+BAA+B,CAC7C,MAAwB,EACxB,KAAqC;IAErC,IAAI,KAAyB,CAAA;IAC7B,IAAI,IAAwB,CAAA;IAC5B,KAAK,IAAI,OAAO,GAAG,KAAK,CAAC,KAAK,EAAE,OAAO,IAAI,KAAK,CAAC,GAAG,EAAE,OAAO,EAAE,EAAE,CAAC;QAChE,MAAM,GAAG,GAAG,MAAM,CAAC,qBAAqB,CAAC,aAAa,CAAC,OAAO,GAAG,CAAC,CAAC,CAAC,CAAA;QACpE,IAAI,GAAG,KAAK,SAAS,EAAE,CAAC;YACtB,KAAK,GAAG,KAAK,KAAK,SAAS,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,KAAK,EAAE,GAAG,CAAC,CAAA;YACxD,IAAI,GAAG,IAAI,KAAK,SAAS,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,IAAI,EAAE,GAAG,CAAC,CAAA;QACvD,CAAC;IACH,CAAC;IACD,OAAO,KAAK,KAAK,SAAS,IAAI,IAAI,KAAK,SAAS;QAC9C,CAAC,CAAC,SAAS;QACX,CAAC,CAAC,EAAE,KAAK,EAAE,KAAK,EAAE,GAAG,EAAE,IAAI,GAAG,CAAC,EAAE,CAAA;AACrC,CAAC"}
+{"version":3,"file":"coordinates.js","sourceRoot":"","sources":["../src/coordinates.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,+BAA+B,EAC/B,8BAA8B,EAC9B,gCAAgC,GACjC,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,SAAS,EAAE,MAAM,gBAAgB,CAAA;AAoB1C,MAAM,CAAC,MAAM,YAAY,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,CAAiB,CAAA;AAC5D,MAAM,CAAC,MAAM,aAAa,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,CAAkB,CAAA;AAC9D,MAAM,CAAC,MAAM,YAAY,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,CAAiB,CAAA;AA2B5D;;;;GAIG;AACH,MAAM,UAAU,oBAAoB,CAClC,iBAAoC;IAEpC,MAAM,EACJ,mCAAmC,EACnC,mCAAmC,GACpC,GAAG,8BAA8B,CAAC,iBAAiB,CAAC,CAAA;IACrD,MAAM,KAAK,GAAG,+BAA+B,CAAC,iBAAiB,CAAC,CAAA;IAChE,MAAM,KAAK,GAAG,gCAAgC,CAAC,iBAAiB,CAAC,CAAA;IACjE,MAAM,KAAK,GAAG,SAAS,CAAC,KAAK,CAAC,CAAA;IAC9B,MAAM,KAAK,GAAG,SAAS,CAAC,KAAK,CAAC,CAAA;IAE9B,uEAAuE;IACvE,6EAA6E;IAC7E,sEAAsE;IACtE,OAAO;QACL,qBAAqB,EAAE,CAAC,CAAC,EAAE,CACzB,mCAAmC,CAAC,CAAC,CAA8B;QACrE,qBAAqB,EAAE,CAAC,CAAC,EAAE,CACzB,mCAAmC,CAAC,CAAC,CAA6B;QACpE,oBAAoB,EAAE,CAAC,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC,CAA6B;QAC/D,oBAAoB,EAAE,CAAC,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC,CAA6B;QAC/D,qBAAqB,EAAE,CAAC,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC,CAA6B;QAChE,qBAAqB,EAAE,CAAC,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC,CAA8B;QACjE,IAAI,EAAE;YACJ,mCAAmC;YACnC,mCAAmC;YACnC,+BAA+B,EAAE,KAAK;YACtC,gCAAgC,EAAE,KAAK;YACvC,4BAA4B,EAAE,KAAK;YACnC,6BAA6B,EAAE,KAAK;SACrC;KACF,CAAA;AACH,CAAC;AAED;;;;;;GAMG;AACH,MAAM,UAAU,+BAA+B,CAC7C,MAAwB,EACxB,KAAqC;IAErC,IAAI,KAAyB,CAAA;IAC7B,IAAI,IAAwB,CAAA;IAC5B,KAAK,IAAI,OAAO,GAAG,KAAK,CAAC,KAAK,EAAE,OAAO,IAAI,KAAK,CAAC,GAAG,EAAE,OAAO,EAAE,EAAE,CAAC;QAChE,MAAM,GAAG,GAAG,MAAM,CAAC,qBAAqB,CAAC,aAAa,CAAC,OAAO,GAAG,CAAC,CAAC,CAAC,CAAA;QACpE,IAAI,GAAG,KAAK,SAAS,EAAE,CAAC;YACtB,KAAK,GAAG,KAAK,KAAK,SAAS,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,KAAK,EAAE,GAAG,CAAC,CAAA;YACxD,IAAI,GAAG,IAAI,KAAK,SAAS,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,IAAI,EAAE,GAAG,CAAC,CAAA;QACvD,CAAC;IACH,CAAC;IACD,OAAO,KAAK,KAAK,SAAS,IAAI,IAAI,KAAK,SAAS;QAC9C,CAAC,CAAC,SAAS;QACX,CAAC,CAAC,EAAE,KAAK,EAAE,KAAK,EAAE,GAAG,EAAE,IAAI,GAAG,CAAC,EAAE,CAAA;AACrC,CAAC"}

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

@@ -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/esm/fetchUtils.js

@@ -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);

package/esm/fetchUtils.js.map

@@ -1 +1 @@
-{"version":3,"file":"fetchUtils.js","sourceRoot":"","sources":["../src/fetchUtils.ts"],"names":[],"mappings":"AAAA,SAAS,MAAM,CAAC,GAAW;IACzB,IAAI,CAAC;QACH,OAAO,IAAI,GAAG,CAAC,GAAG,CAAC,CAAC,IAAI,CAAA;IAC1B,CAAC;IAAC,MAAM,CAAC;QACP,OAAO,GAAG,CAAA;IACZ,CAAC;AACH,CAAC;AAED,MAAM,UAAU,GAAG,GAAG,CAAA;AAEtB,SAAS,SAAS,CAAC,IAAY;IAC7B,MAAM,IAAI,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,IAAI,EAAE,IAAI,EAAE,CAAA;IACjD,OAAO,IAAI,CAAC,MAAM,GAAG,UAAU,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,CAAC,EAAE,UAAU,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAA;AAC1E,CAAC;AAED;;;;GAIG;AACH,MAAM,OAAO,SAAU,SAAQ,KAAK;IACzB,MAAM,CAAQ;IAEvB,YAAY,OAAe,EAAE,MAAc;QACzC,KAAK,CAAC,OAAO,CAAC,CAAA;QACd,IAAI,CAAC,IAAI,GAAG,WAAW,CAAA;QACvB,IAAI,CAAC,MAAM,GAAG,MAAM,CAAA;IACtB,CAAC;CACF;AAED;;UAEU;AACV,MAAM,UAAU,mBAAmB,CAAC,CAAU;IAC5C,OAAO,CAAC,YAAY,SAAS,IAAI,CAAC,CAAC,MAAM,IAAI,GAAG,IAAI,CAAC,CAAC,MAAM,GAAG,GAAG,CAAA;AACpE,CAAC;AAED;;;;GAIG;AACH,MAAM,CAAC,KAAK,UAAU,SAAS,CAAC,QAAkB,EAAE,GAAW;IAC7D,MAAM,MAAM,GAAG,SAAS,CAAC,MAAM,QAAQ,CAAC,IAAI,EAAE,CAAC,KAAK,CAAC,GAAG,EAAE,CAAC,EAAE,CAAC,CAAC,CAAA;IAC/D,MAAM,MAAM,GAAG,QAAQ,QAAQ,CAAC,MAAM,GAAG,QAAQ,CAAC,UAAU,CAAC,CAAC,CAAC,IAAI,QAAQ,CAAC,UAAU,EAAE,CAAC,CAAC,CAAC,EAAE,SAAS,MAAM,CAAC,GAAG,CAAC,EAAE,CAAA;IACnH,OAAO,IAAI,SAAS,CAClB,MAAM,CAAC,CAAC,CAAC,GAAG,MAAM,KAAK,MAAM,EAAE,CAAC,CAAC,CAAC,MAAM,EACxC,QAAQ,CAAC,MAAM,CAChB,CAAA;AACH,CAAC;AAED;;;;;GAKG;AACH,MAAM,UAAU,YAAY,CAAC,GAAW,EAAE,KAAc;IACtD,OAAO,KAAK,YAAY,SAAS;QAC/B,CAAC,CAAC,IAAI,KAAK,CACP,mBAAmB,MAAM,CAAC,GAAG,CAAC,wGAAwG,EACtI,EAAE,KAAK,EAAE,CACV;QACH,CAAC,CAAC,KAAK,CAAA;AACX,CAAC;AAaD,MAAM,CAAC,KAAK,UAAU,QAAQ,CAAC,GAAW,EAAE,IAAmB;IAC7D,MAAM,EAAE,KAAK,EAAE,CAAC,GAAG,UAAU,CAAC,KAAK,EAAE,GAAG,IAAI,EAAE,GAAG,IAAI,IAAI,EAAE,CAAA;IAC3D,IAAI,CAAC;QACH,OAAO,MAAM,CAAC,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;IAC3B,CAAC;IAAC,OAAO,CAAC,EAAE,CAAC;QACX,MAAM,YAAY,CAAC,GAAG,EAAE,CAAC,CAAC,CAAA;IAC5B,CAAC;AACH,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,OAAO,CAAC,GAAW,EAAE,IAAmB;IAC5D,MAAM,QAAQ,GAAG,MAAM,QAAQ,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;IAE1C,IAAI,CAAC,QAAQ,CAAC,EAAE,EAAE,CAAC;QACjB,MAAM,MAAM,SAAS,CAAC,QAAQ,EAAE,GAAG,CAAC,CAAA;IACtC,CAAC;IAED,OAAO,QAAQ,CAAA;AACjB,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,SAAS,CAC7B,GAAW,EACX,IAAmB;IAEnB,6EAA6E;IAC7E,4EAA4E;IAC5E,MAAM,QAAQ,GAA+B,MAAM,OAAO,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;IACrE,OAAO,QAAQ,CAAC,IAAI,EAAE,CAAA;AACxB,CAAC;AAED;;;;;GAKG;AACH,MAAM,UAAU,UAAU,CAAC,MAAmB;IAC5C,OAAO,MAAM,CAAC,MAAM,YAAY,KAAK;QACnC,CAAC,CAAC,MAAM,CAAC,MAAM;QACf,CAAC,CAAC,IAAI,KAAK,CAAC,SAAS,EAAE,EAAE,KAAK,EAAE,MAAM,CAAC,MAAM,EAAE,CAAC,CAAA;AACpD,CAAC;AAED,MAAM,UAAU,OAAO,CAAC,IAAY,EAAE,MAAoB;IACxD,OAAO,IAAI,OAAO,CAAO,CAAC,OAAO,EAAE,MAAM,EAAE,EAAE;QAC3C,IAAI,MAAM,EAAE,OAAO,EAAE,CAAC;YACpB,MAAM,CAAC,UAAU,CAAC,MAAM,CAAC,CAAC,CAAA;QAC5B,CAAC;aAAM,CAAC;YACN,MAAM,EAAE,GAAG,UAAU,CAAC,OAAO,EAAE,IAAI,CAAC,CAAA;YACpC,MAAM,EAAE,gBAAgB,CACtB,OAAO,EACP,GAAG,EAAE;gBACH,YAAY,CAAC,EAAE,CAAC,CAAA;gBAChB,MAAM,CAAC,UAAU,CAAC,MAAM,CAAC,CAAC,CAAA;YAC5B,CAAC,EACD,EAAE,IAAI,EAAE,IAAI,EAAE,CACf,CAAA;QACH,CAAC;IACH,CAAC,CAAC,CAAA;AACJ,CAAC"}
+{"version":3,"file":"fetchUtils.js","sourceRoot":"","sources":["../src/fetchUtils.ts"],"names":[],"mappings":"AAAA,SAAS,MAAM,CAAC,GAAW;IACzB,IAAI,CAAC;QACH,OAAO,IAAI,GAAG,CAAC,GAAG,CAAC,CAAC,IAAI,CAAA;IAC1B,CAAC;IAAC,MAAM,CAAC;QACP,OAAO,GAAG,CAAA;IACZ,CAAC;AACH,CAAC;AAED,MAAM,UAAU,GAAG,GAAG,CAAA;AAEtB,SAAS,SAAS,CAAC,IAAY;IAC7B,MAAM,IAAI,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,IAAI,EAAE,IAAI,EAAE,CAAA;IACjD,OAAO,IAAI,CAAC,MAAM,GAAG,UAAU,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,CAAC,EAAE,UAAU,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAA;AAC1E,CAAC;AAED;;;;GAIG;AACH,MAAM,OAAO,SAAU,SAAQ,KAAK;IACzB,MAAM,CAAQ;IAEvB,YAAY,OAAe,EAAE,MAAc;QACzC,KAAK,CAAC,OAAO,CAAC,CAAA;QACd,IAAI,CAAC,IAAI,GAAG,WAAW,CAAA;QACvB,IAAI,CAAC,MAAM,GAAG,MAAM,CAAA;IACtB,CAAC;CACF;AAED;;UAEU;AACV,MAAM,UAAU,mBAAmB,CAAC,CAAU;IAC5C,OAAO,CAAC,YAAY,SAAS,IAAI,CAAC,CAAC,MAAM,IAAI,GAAG,IAAI,CAAC,CAAC,MAAM,GAAG,GAAG,CAAA;AACpE,CAAC;AAED;;;;GAIG;AACH,MAAM,CAAC,KAAK,UAAU,SAAS,CAAC,QAAkB,EAAE,GAAW;IAC7D,MAAM,MAAM,GAAG,SAAS,CAAC,MAAM,QAAQ,CAAC,IAAI,EAAE,CAAC,KAAK,CAAC,GAAG,EAAE,CAAC,EAAE,CAAC,CAAC,CAAA;IAC/D,MAAM,MAAM,GAAG,QAAQ,QAAQ,CAAC,MAAM,GAAG,QAAQ,CAAC,UAAU,CAAC,CAAC,CAAC,IAAI,QAAQ,CAAC,UAAU,EAAE,CAAC,CAAC,CAAC,EAAE,SAAS,MAAM,CAAC,GAAG,CAAC,EAAE,CAAA;IACnH,OAAO,IAAI,SAAS,CAClB,MAAM,CAAC,CAAC,CAAC,GAAG,MAAM,KAAK,MAAM,EAAE,CAAC,CAAC,CAAC,MAAM,EACxC,QAAQ,CAAC,MAAM,CAChB,CAAA;AACH,CAAC;AAED;;;;;GAKG;AACH,MAAM,UAAU,YAAY,CAAC,GAAW,EAAE,KAAc;IACtD,OAAO,KAAK,YAAY,SAAS;QAC/B,CAAC,CAAC,IAAI,KAAK,CACP,mBAAmB,MAAM,CAAC,GAAG,CAAC,wGAAwG,EACtI,EAAE,KAAK,EAAE,CACV;QACH,CAAC,CAAC,KAAK,CAAA;AACX,CAAC;AAaD,MAAM,UAAU,GAAG,kDAAkD,CAAA;AAErE;;;;;GAKG;AACH,SAAS,aAAa,CAAC,IAAiB;IACtC,IACE,OAAO,SAAS,KAAK,WAAW;QAChC,SAAS,CAAC,SAAS,CAAC,UAAU,CAAC,SAAS,CAAC,EACzC,CAAC;QACD,OAAO,IAAI,CAAA;IACb,CAAC;IACD,MAAM,OAAO,GAAG,IAAI,OAAO,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;IACzC,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,YAAY,CAAC,EAAE,CAAC;QAC/B,OAAO,CAAC,GAAG,CAAC,YAAY,EAAE,UAAU,CAAC,CAAA;IACvC,CAAC;IACD,OAAO,EAAE,GAAG,IAAI,EAAE,OAAO,EAAE,CAAA;AAC7B,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,QAAQ,CAAC,GAAW,EAAE,IAAmB;IAC7D,MAAM,EAAE,KAAK,EAAE,CAAC,GAAG,UAAU,CAAC,KAAK,EAAE,GAAG,IAAI,EAAE,GAAG,IAAI,IAAI,EAAE,CAAA;IAC3D,IAAI,CAAC;QACH,OAAO,MAAM,CAAC,CAAC,GAAG,EAAE,aAAa,CAAC,IAAI,CAAC,CAAC,CAAA;IAC1C,CAAC;IAAC,OAAO,CAAC,EAAE,CAAC;QACX,MAAM,YAAY,CAAC,GAAG,EAAE,CAAC,CAAC,CAAA;IAC5B,CAAC;AACH,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,OAAO,CAAC,GAAW,EAAE,IAAmB;IAC5D,MAAM,QAAQ,GAAG,MAAM,QAAQ,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;IAE1C,IAAI,CAAC,QAAQ,CAAC,EAAE,EAAE,CAAC;QACjB,MAAM,MAAM,SAAS,CAAC,QAAQ,EAAE,GAAG,CAAC,CAAA;IACtC,CAAC;IAED,OAAO,QAAQ,CAAA;AACjB,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,SAAS,CAC7B,GAAW,EACX,IAAmB;IAEnB,6EAA6E;IAC7E,4EAA4E;IAC5E,MAAM,QAAQ,GAA+B,MAAM,OAAO,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;IACrE,OAAO,QAAQ,CAAC,IAAI,EAAE,CAAA;AACxB,CAAC;AAED;;;;;GAKG;AACH,MAAM,UAAU,UAAU,CAAC,MAAmB;IAC5C,OAAO,MAAM,CAAC,MAAM,YAAY,KAAK;QACnC,CAAC,CAAC,MAAM,CAAC,MAAM;QACf,CAAC,CAAC,IAAI,KAAK,CAAC,SAAS,EAAE,EAAE,KAAK,EAAE,MAAM,CAAC,MAAM,EAAE,CAAC,CAAA;AACpD,CAAC;AAED,MAAM,UAAU,OAAO,CAAC,IAAY,EAAE,MAAoB;IACxD,OAAO,IAAI,OAAO,CAAO,CAAC,OAAO,EAAE,MAAM,EAAE,EAAE;QAC3C,IAAI,MAAM,EAAE,OAAO,EAAE,CAAC;YACpB,MAAM,CAAC,UAAU,CAAC,MAAM,CAAC,CAAC,CAAA;QAC5B,CAAC;aAAM,CAAC;YACN,MAAM,EAAE,GAAG,UAAU,CAAC,OAAO,EAAE,IAAI,CAAC,CAAA;YACpC,MAAM,EAAE,gBAAgB,CACtB,OAAO,EACP,GAAG,EAAE;gBACH,YAAY,CAAC,EAAE,CAAC,CAAA;gBAChB,MAAM,CAAC,UAAU,CAAC,MAAM,CAAC,CAAC,CAAA;YAC5B,CAAC,EACD,EAAE,IAAI,EAAE,IAAI,EAAE,CACf,CAAA;QACH,CAAC;IACH,CAAC,CAAC,CAAA;AACJ,CAAC"}

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 @@
-{"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,QAAQ;AACR,cAAc,wBAAwB,CAAA;AACtC,cAAc,qBAAqB,CAAA;AAEnC,oBAAoB;AACpB,cAAc,sBAAsB,CAAA;AACpC,cAAc,yBAAyB,CAAA;AACvC,cAAc,yBAAyB,CAAA;AACvC,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"}
+{"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

@@ -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/esm/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/esm/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;