@cyanheads/protein-mcp-server 0.8.1 → 0.8.3

package/dist/mcp-server/tools/definitions/get-structure.tool.js

@@ -14,7 +14,7 @@ import { tool, z } from '@cyanheads/mcp-ts-core';
 import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
 import { DEFAULT_OUTLINE_BUDGET_BYTES } from '@cyanheads/mcp-ts-core/utils';
 import { getServerConfig } from '../../../config/server-config.js';
-import { getAlphaFoldService } from '../../../services/alphafold/alphafold-service.js';
+import { getAlphaFoldService, } from '../../../services/alphafold/alphafold-service.js';
 import { getBeaconsService } from '../../../services/beacons/beacons-service.js';
 import { getRcsbService } from '../../../services/rcsb/rcsb-service.js';
 import { mapWithConcurrency } from '../../../services/shared/async.js';
@@ -37,7 +37,7 @@ const structureRecordSchema = z
     pdbId: z
         .string()
         .optional()
-        .describe('Chosen PDB entry ID when a best_available query resolved to an experimental structure (id stays the queried UniProt accession). Lets an agent cite the structure without parsing the coordinate URL.'),
+        .describe('Chosen PDB entry ID when a best_available query resolved to an experimental structure (id stays the queried UniProt accession), so the structure can be cited without parsing the coordinate URL.'),
     title: z.string().optional().describe('Structure / protein title.'),
     method: z.string().optional().describe('Experimental method(s).'),
     resolution: z.number().optional().describe('Resolution in Å (experimental).'),
@@ -45,19 +45,19 @@ const structureRecordSchema = z
     molecularWeight: z
         .number()
         .optional()
-        .describe('Deposited structure molecular weight in kDa, from the RCSB entry record. Omitted when the record does not report one.'),
+        .describe('Deposited structure molecular weight in kDa. Present only when the call used source experimental; omitted when the record does not report one.'),
     releaseDate: z
         .string()
         .optional()
-        .describe('Initial release date (ISO 8601), from the RCSB entry record. Omitted when the record does not report one.'),
+        .describe('Initial release date (ISO 8601). Present only when the call used source experimental; omitted when the record does not report one.'),
     polymerEntities: z
         .array(polymerEntitySchema)
         .optional()
-        .describe('Modeled polymer entities, each with both chain namespaces — authAsymIds for protein_get_annotations.chain, labelAsymIds for protein_compare_structures.chain. Present for records served by the RCSB entry endpoint (source experimental, computed models included); omitted for predicted / best_available records and for entries with none.'),
+        .describe('Modeled polymer entities, each with both chain namespaces — authAsymIds for protein_get_annotations.chain, labelAsymIds for protein_compare_structures.chain. Present when the call used source experimental (computed-model IDs included); omitted under source predicted or best_available and for entries with none.'),
     ligands: z
         .array(ligandSchema)
         .optional()
-        .describe('Bound non-polymer components. Present for records served by the RCSB entry endpoint; omitted when the entry binds none or the record carries no ligand data.'),
+        .describe('Bound non-polymer components. Present when the call used source experimental; omitted under source predicted or best_available, when the entry binds none, or when the record carries no ligand data.'),
     provider: z.string().optional().describe('Model provider (predicted / best_available).'),
     confidence: z
         .number()
@@ -84,7 +84,7 @@ const structureRecordSchema = z
         pdb: z.string().optional().describe('PDB-format coordinate file URL.'),
         bcif: z.string().optional().describe('Binary CIF coordinate file URL.'),
     })
-        .describe('Coordinate file download URLs.'),
+        .describe('Coordinate file download URLs. A format with no published file is omitted — e.g. pdb for large entries archived as mmCIF only.'),
     coordinateFormat: z
         .enum(['cif', 'pdb', 'bcif'])
         .optional()
@@ -97,7 +97,7 @@ const structureRecordSchema = z
     .describe('A resolved structure with metadata and coordinate-file URLs.');
 export const getStructure = tool('protein_get_structure', {
     title: 'protein-mcp-server: get structure',
-    description: `Fetch structures with metadata and coordinate-file URLs. source "experimental" takes PDB entry IDs (batched in one call), and also resolves the computed-model IDs protein_search_structures returns (AF_*/MA_*), which come back marked source "predicted" with their modelling provider; "predicted" takes UniProt accessions (AlphaFold, with pLDDT/PAE confidence); "best_available" takes UniProt accessions and returns the top federated model — the highest-resolution experimental structure if one exists (optimizing resolution, not biological representativeness, so it can return an engineered mutant over the wild-type entry), else the best prediction. Records served by the RCSB entry endpoint also carry polymer entities with both chain namespaces (labelAsymIds for protein_compare_structures, authAsymIds for protein_get_annotations), bound ligands, molecular weight, and release date. Resolves up to the configured batch cap per call with per-ID partial success — missed IDs are listed in failed[], and IDs beyond the cap are reported in the notice. Set include_coords to inline coordinate content; if the inlined bytes exceed the response budget the content is withheld and overflow lists each structure's size — re-call with sections:[ids] for specific structures, or for a single oversized file download it from that record's coordinateUrls.`,
+    description: `Fetch structures with metadata and coordinate-file URLs. source "experimental" takes PDB entry IDs, and also resolves the computed-model IDs protein_search_structures returns (AF_*/MA_*), which come back marked source "predicted" with their modelling provider; "predicted" takes UniProt accessions (AlphaFold, with pLDDT/PAE confidence); "best_available" takes UniProt accessions and returns the top federated model — the highest-resolution experimental structure if one exists (optimizing resolution, not biological representativeness, so it can return an engineered mutant over the wild-type entry), else the best prediction. Records fetched under source "experimental", computed models included, also carry polymer entities with both chain namespaces (labelAsymIds for protein_compare_structures, authAsymIds for protein_get_annotations), bound ligands, molecular weight, and release date. Resolves up to the configured batch cap per call with per-ID partial success — missed IDs are listed in failed[], and IDs beyond the cap are reported in the notice. Set include_coords to inline coordinate content; if the inlined bytes exceed the response budget the content is withheld and overflow lists each structure's size — re-call with sections:[ids] for specific structures, or for a single oversized file download it from that record's coordinateUrls.`,
     annotations: { readOnlyHint: true, openWorldHint: true },
     errors: [
         {
@@ -125,7 +125,7 @@ export const getStructure = tool('protein_get_structure', {
         include_coords: z
             .boolean()
             .default(false)
-            .describe('Inline coordinate-file content (cif). Off by default — URLs are always returned.'),
+            .describe('Inline coordinate-file content — mmCIF, or PDB format when no mmCIF URL is available; coordinateFormat names which. Off by default — URLs are always returned.'),
         sections: z
             .array(z.string())
             .optional()
@@ -166,7 +166,7 @@ export const getStructure = tool('protein_get_structure', {
     enrichment: {
         requested: z
             .number()
-            .describe('Number of IDs in the original request (input.ids.length), before the batch cap was applied.'),
+            .describe('Number of IDs in the original request, before the batch cap was applied.'),
         processed: z
             .number()
             .describe('Number of IDs actually processed after the batch cap. Lower than requested means the excess IDs were ignored and never looked up — re-submit them in a follow-up call.'),
@@ -174,7 +174,7 @@ export const getStructure = tool('protein_get_structure', {
         notice: z
             .string()
             .optional()
-            .describe('Every applicable advisory joined into one string: batch cap, partial failures, coordinate-budget overflow, and failed coordinate inlining.'),
+            .describe('Every applicable advisory joined into one string: batch cap, partial failures, a computed model whose provider coordinate lookup failed (only its BinaryCIF URL listed), coordinate-budget overflow, and failed coordinate inlining.'),
     },
     async handler(input, ctx) {
         const cfg = getServerConfig();
@@ -193,8 +193,8 @@ export const getStructure = tool('protein_get_structure', {
         else if (ids.some((id) => isPdbId(id) && !isUniProtAccession(id))) {
             throw ctx.fail('mixed_id_types', `source ${input.source} expects UniProt accessions, but PDB IDs were present.`, { ...ctx.recoveryFor('mixed_id_types') });
         }
-        const { structures, failed } = input.source === 'experimental'
-            ? await fetchExperimental(ids, ctx)
+        const { structures, failed, notices: resolutionNotices, } = input.source === 'experimental'
+            ? await fetchExperimental(ids, cfg.fanoutConcurrency, ctx)
             : await fetchPredictedOrBest(ids, input.source, cfg.fanoutConcurrency, ctx);
         if (structures.length === 0) {
             throw ctx.fail('all_failed', `None of the ${ids.length} requested IDs resolved to a structure.`, { ...ctx.recoveryFor('all_failed') });
@@ -202,6 +202,8 @@ export const getStructure = tool('protein_get_structure', {
         if (failed.length > 0) {
             notices.push(`${failed.length} of ${ids.length} IDs did not resolve: ${failed.map((f) => f.id).join(', ')}.`);
         }
+        if (resolutionNotices)
+            notices.push(...resolutionNotices);
         // Inline coordinates when requested (all, or only the re-called sections).
         const inlineSet = input.sections?.length
             ? new Set(input.sections.map((s) => s.toUpperCase()))
@@ -364,12 +366,13 @@ export const getStructure = tool('protein_get_structure', {
 function pct(fraction) {
     return `${Math.round(fraction * 100)}%`;
 }
-async function fetchExperimental(ids, ctx) {
+async function fetchExperimental(ids, concurrency, ctx) {
     const rcsb = getRcsbService();
     const entries = await rcsb.getEntries(ids, ctx);
     const byId = new Map(entries.map((e) => [e.id.toUpperCase(), e]));
     const structures = [];
     const failed = [];
+    const csms = [];
     for (const id of ids) {
         const meta = byId.get(id.toUpperCase());
         if (!meta) {
@@ -381,7 +384,7 @@ async function fetchExperimental(ids, ctx) {
         // their IDs under the default content_type. Read the provenance rather than
         // stamping every resolved ID experimental — that would both contradict the
         // record and credit an AlphaFold/ModelArchive model to the PDB's CC0.
-        structures.push({
+        const record = {
             id: meta.id,
             source: meta.computedModelProvider ? 'predicted' : 'experimental',
             ...(meta.computedModelProvider ? { provider: meta.computedModelProvider } : {}),
@@ -397,14 +400,62 @@ async function fetchExperimental(ids, ctx) {
             // emitted empty, so a sparse entry does not read as "this entry has none".
             ...(meta.polymerEntities.length > 0 ? { polymerEntities: meta.polymerEntities } : {}),
             ...(meta.ligands.length > 0 ? { ligands: meta.ligands } : {}),
-            coordinateUrls: {
-                cif: rcsb.coordinateFileUrl(meta.id, 'cif'),
-                pdb: rcsb.coordinateFileUrl(meta.id, 'pdb'),
-                bcif: rcsb.coordinateFileUrl(meta.id, 'bcif'),
-            },
-        });
+            coordinateUrls: rcsb.coordinateUrls(meta),
+        };
+        structures.push(record);
+        if (meta.computedModelProvider)
+            csms.push({ meta, record });
     }
-    return { structures, failed };
+    // RCSB publishes only BinaryCIF for a computed model; its provider publishes the
+    // text formats. Each lookup degrades to the RCSB BinaryCIF URL on its own row.
+    const notices = [];
+    await mapWithConcurrency(csms, concurrency, async ({ meta, record }) => {
+        const provider = await providerCoordinateUrls(meta, ctx);
+        if (provider === 'unresolved') {
+            notices.push(`AlphaFold DB coordinate lookup did not resolve for ${meta.id}; only its RCSB BinaryCIF URL is listed — fetch the model by UniProt accession with source "predicted" for mmCIF and PDB files.`);
+            return;
+        }
+        record.coordinateUrls = { ...record.coordinateUrls, ...provider };
+    });
+    return { structures, failed, notices };
+}
+/**
+ * Text-format coordinate URLs from a computed model's own provider, keyed on the
+ * provider entry ID RCSB records. AlphaFold DB file names carry a model version,
+ * so they come from its prediction record — the same URLs `source: "predicted"`
+ * returns. A ModelArchive download is addressed by entry ID alone. `'unresolved'`
+ * marks an AlphaFold model whose lookup failed or found nothing; any other
+ * provider has no known download route and contributes nothing.
+ */
+async function providerCoordinateUrls(meta, ctx) {
+    const entryId = meta.computedModelEntryId;
+    if (meta.computedModelProvider === 'ModelArchive' && entryId) {
+        return {
+            cif: `${getServerConfig().modelArchiveBaseUrl}/api/projects/${encodeURIComponent(entryId)}?type=basic__model_file_name`,
+        };
+    }
+    if (meta.computedModelProvider !== 'AlphaFold DB')
+        return {};
+    if (!entryId)
+        return 'unresolved';
+    const model = await getAlphaFoldService()
+        .getPrediction(entryId, ctx)
+        .catch((err) => {
+        ctx.log.warning('AlphaFold coordinate lookup failed', {
+            id: meta.id,
+            error: err instanceof Error ? err.message : err,
+        });
+        return null;
+    });
+    return model ? alphaFoldCoordinateUrls(model) : 'unresolved';
+}
+/** The coordinate URLs an AlphaFold DB prediction record publishes. */
+function alphaFoldCoordinateUrls(model) {
+    return {
+        ...(model.cifUrl ? { cif: model.cifUrl } : {}),
+        ...(model.pdbUrl ? { pdb: model.pdbUrl } : {}),
+        ...(model.bcifUrl ? { bcif: model.bcifUrl } : {}),
+    };
 }
 /**
  * Per-ID failure reason for an identifier that is not accession-shaped. Kept
@@ -449,11 +500,7 @@ async function fetchPrediction(accession, ctx) {
         ...(typeof model.meanPlddt === 'number' ? { meanPlddt: model.meanPlddt } : {}),
         ...(model.confidenceBuckets ? { confidenceBuckets: model.confidenceBuckets } : {}),
         ...(model.paeDocUrl ? { paeDocUrl: model.paeDocUrl } : {}),
-        coordinateUrls: {
-            ...(model.cifUrl ? { cif: model.cifUrl } : {}),
-            ...(model.pdbUrl ? { pdb: model.pdbUrl } : {}),
-            ...(model.bcifUrl ? { bcif: model.bcifUrl } : {}),
-        },
+        coordinateUrls: alphaFoldCoordinateUrls(model),
     };
 }
 async function fetchBest(accession, ctx) {
@@ -474,12 +521,12 @@ async function fetchBest(accession, ctx) {
     // best-effort — a failed lookup must not drop the structure the agent already has.
     const rcsb = getRcsbService();
     let pdbId;
-    let title;
+    let entry;
     if (isExperimental && best.modelIdentifier) {
         pdbId = best.modelIdentifier.toUpperCase();
-        const entries = await rcsb.getEntries([pdbId], ctx).catch(() => []);
-        title = entries[0]?.title;
+        entry = (await rcsb.getEntries([pdbId], ctx).catch(() => []))[0];
     }
+    const title = entry?.title;
     return {
         id: summary.accession,
         source: isExperimental ? 'experimental' : 'predicted',
@@ -498,12 +545,10 @@ async function fetchBest(accession, ctx) {
             best.confidenceType?.toLowerCase() === 'plddt'
             ? { meanPlddt: best.confidenceAvgLocalScore }
             : {}),
+        // The entry record (when the best-effort lookup succeeded) says whether a
+        // PDB-format file exists; without it the URL set matches an unreported entry.
         coordinateUrls: pdbId
-            ? {
-                cif: rcsb.coordinateFileUrl(pdbId, 'cif'),
-                pdb: rcsb.coordinateFileUrl(pdbId, 'pdb'),
-                bcif: rcsb.coordinateFileUrl(pdbId, 'bcif'),
-            }
+            ? rcsb.coordinateUrls(entry ?? { id: pdbId })
             : best.modelUrl
                 ? coordinateUrlFor(best.modelUrl)
                 : {},
@@ -532,8 +577,11 @@ async function inlineCoordinates(structures, inline, concurrency, ctx) {
             : s.coordinateUrls.pdb
                 ? ['pdb', s.coordinateUrls.pdb]
                 : null;
-        if (!pick)
+        // BinaryCIF is binary, so a record with no text format cannot be inlined.
+        if (!pick) {
+            failures.push(s.id);
             return;
+        }
         try {
             s.coordinates = await fetchText(pick[1], ctx, {
                 operation: 'getStructure.inlineCoordinates',

package/dist/mcp-server/tools/definitions/get-structure.tool.js.map

@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/search-structures.tool.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"search-structures.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/search-structures.tool.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAmDjE,eAAO,MAAM,gBAAgB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAqR3B,CAAC"}

package/dist/mcp-server/tools/definitions/search-structures.tool.js

@@ -10,7 +10,7 @@ import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
 import { getServerConfig } from '../../../config/server-config.js';
 import { buildFacetSpec, FACET_DIMENSION_NAMES } from '../../../services/rcsb/facets.js';
 import { getRcsbService } from '../../../services/rcsb/rcsb-service.js';
-import { entryIdOf } from '../../../services/shared/identifiers.js';
+import { entryIdOf, isComputedModelId } from '../../../services/shared/identifiers.js';
 import { CONTENT_TYPE_SCOPES, coverageNotices, flatFacetDimensionSchema, renderFacets, toFacetOutput, } from './_schemas.js';
 /**
  * Zero-hit advice, per scope. Only the two single-universe scopes have a wider
@@ -22,10 +22,6 @@ const ZERO_HIT_NOTICE = {
     predicted: 'No predicted models matched. Predicted search covers computed models indexed by RCSB; widen content_type to "all" to include experimental structures.',
     all: 'No structures matched in either the experimental or computed-model universe — content_type "all" is already the widest scope. Broaden the query or drop filters.',
 };
-/** A computed-model identifier (AlphaFold / ModelArchive) vs an experimental PDB entry. */
-function isPredictedId(id) {
-    return /^(AF|MA)_/i.test(id);
-}
 /** Pull a UniProt accession out of a computed-model identifier when present (`AF_AFP69905F1` → `P69905`). */
 function accessionFromCsm(id) {
     return /AF_AF([A-Z0-9]+?)F\d+$/i.exec(id)?.[1]?.toUpperCase();
@@ -50,15 +46,7 @@ function truncationNotice(dimensions, cap, sequenceSearch) {
 }
 export const searchStructures = tool('protein_search_structures', {
     title: 'protein-mcp-server: search structures',
-    description: 'Search experimental (PDB) and predicted (computed-model) protein structures by free text, ' +
-        'protein sequence (triggers an mmseqs2 similarity search), and/or organism, method, and ' +
-        'resolution filters. Returns ranked hits; the experimental page is enriched with title, method, ' +
-        'resolution, and organism. Chain hit IDs into protein_get_structure. Optionally returns a facet ' +
-        'breakdown (counts by method / organism / release year / …) alongside the hits at no extra call. ' +
-        'A facet on a dimension you are already filtering (e.g. the organism facet while organism is set) ' +
-        'lists unfiltered alternatives by design — it does not constrain by its own active filter, so you ' +
-        'can see sibling values to pivot to. Numeric histogram buckets (resolution, molecular weight) carry ' +
-        'explicit rangeFrom/rangeTo bounds so a boundary label is unambiguous.',
+    description: 'Search experimental (PDB) and predicted (computed-model) protein structures by free text, protein sequence (triggers an mmseqs2 similarity search), and/or organism, method, and resolution filters. Returns ranked hits; the experimental page is enriched with title, method, resolution, and organism. Chain hit IDs into protein_get_structure. Optionally returns a facet breakdown (counts by method / organism / release year / …) alongside the hits in the same response. A facet on a dimension you are already filtering (e.g. the organism facet while organism is set) lists unfiltered alternatives by design — it does not constrain by its own active filter, so you can see sibling values to pivot to. Numeric histogram buckets (resolution, molecular weight) carry explicit rangeFrom/rangeTo bounds so a boundary label is unambiguous.',
     annotations: { readOnlyHint: true, openWorldHint: true },
     errors: [
         {
@@ -107,12 +95,12 @@ export const searchStructures = tool('protein_search_structures', {
             .min(0)
             .max(1)
             .optional()
-            .describe('Minimum sequence identity (0–1) for a sequence search. Requires sequence — supplying it without one is rejected, since the threshold would never reach RCSB. Default 0.'),
+            .describe('Minimum sequence identity (0–1) for a sequence search. Requires sequence — supplying it without one is rejected, since the threshold filters only a sequence search. Default 0.'),
         max_evalue: z
             .number()
             .positive()
             .optional()
-            .describe('Maximum E-value for a sequence search. Requires sequence — supplying it without one is rejected, since the threshold would never reach RCSB. Default 1.'),
+            .describe('Maximum E-value for a sequence search. Requires sequence — supplying it without one is rejected, since the threshold filters only a sequence search. Default 1.'),
         content_type: z
             .enum(['experimental', 'predicted', 'all'])
             .default('all')
@@ -137,7 +125,7 @@ export const searchStructures = tool('protein_search_structures', {
             entityId: z
                 .string()
                 .optional()
-                .describe('Matched polymer-entity ID for experimental sequence hits; id remains the chainable PDB entry ID.'),
+                .describe('Matched polymer-entity ID for sequence hits (e.g. 4HHB_1, AF_AFP69905F1_1); id remains the chainable entry ID.'),
             source: z
                 .enum(['experimental', 'predicted'])
                 .describe('Which universe the hit came from.'),
@@ -226,7 +214,7 @@ export const searchStructures = tool('protein_search_structures', {
             start: input.start,
         }, ctx, facetSpecs);
         const experimentalIds = [
-            ...new Set(result.hits.filter((h) => !isPredictedId(h.id)).map((h) => entryIdOf(h.id))),
+            ...new Set(result.hits.filter((h) => !isComputedModelId(h.id)).map((h) => entryIdOf(h.id))),
         ];
         const metaById = new Map();
         if (experimentalIds.length > 0) {
@@ -246,8 +234,12 @@ export const searchStructures = tool('protein_search_structures', {
         // `notice` is a single last-wins field, so the zero-hit advice, the capped-facet
         // advice, and one fragment per under-covered facet dimension compose into ONE string.
         const notices = [];
+        // An empty page with a nonzero total is an offset past the end, not a query
+        // that matched nothing — the two need opposite next moves.
         if (hits.length === 0)
-            notices.push(ZERO_HIT_NOTICE[input.content_type]);
+            notices.push(result.total === 0
+                ? ZERO_HIT_NOTICE[input.content_type]
+                : `start ${input.start} is past the end of the ${result.total} matches. Re-call with a lower start to read a populated page.`);
         if (facets) {
             const capped = facets.filter((f) => f.truncated).map((f) => f.dimension);
             if (capped.length > 0)
@@ -284,20 +276,25 @@ export const searchStructures = tool('protein_search_structures', {
 });
 /** Build one output hit, folding in enrichment metadata when available. */
 function toHit(hit, metaById, sequenceSearch) {
-    if (isPredictedId(hit.id)) {
-        const accession = accessionFromCsm(hit.id);
+    // A sequence search returns polymer entities in both universes (4HHB_1,
+    // AF_AFP69905F1_1); `id` is the chainable entry and `entityId` the matched entity.
+    const entryId = entryIdOf(hit.id);
+    const identity = {
+        id: sequenceSearch ? entryId : hit.id,
+        ...(sequenceSearch ? { entityId: hit.id } : {}),
+    };
+    if (isComputedModelId(hit.id)) {
+        const accession = accessionFromCsm(identity.id);
         return {
-            id: hit.id,
+            ...identity,
             source: 'predicted',
             score: hit.score,
             ...(accession ? { uniprotAccession: accession } : {}),
         };
     }
-    const entryId = entryIdOf(hit.id);
     const meta = metaById.get(entryId);
     return {
-        id: sequenceSearch ? entryId : hit.id,
-        ...(sequenceSearch ? { entityId: hit.id } : {}),
+        ...identity,
         source: 'experimental',
         score: hit.score,
         ...(meta?.title ? { title: meta.title } : {}),

package/dist/mcp-server/tools/definitions/search-structures.tool.js.map

@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/track-ligands.tool.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"track-ligands.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/track-ligands.tool.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA0CjE,eAAO,MAAM,YAAY;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA6PvB,CAAC"}

package/dist/mcp-server/tools/definitions/track-ligands.tool.js

@@ -42,14 +42,7 @@ const bindingSiteSchema = z
     .describe('A ligand instance and the protein residues lining its pocket.');
 export const trackLigands = tool('protein_track_ligands', {
     title: 'protein-mcp-server: track ligands',
-    description: 'Ligand discovery and binding-site analysis across the PDB. mode "find_ligand" resolves a name or ' +
-        'formula to chemical component IDs with metadata (formula, weight, SMILES), ranked by deposition ' +
-        'frequency — most-deposited component first, so the top hit is the most common match for the name, ' +
-        'not necessarily an exact name-string match. mode "structures_with_ligand" returns PDB entries ' +
-        'containing a ligand (by exact component ID — get the ID from find_ligand first), highest-resolution ' +
-        'first, each with its resolution in Å. mode "binding_site" returns the protein residues lining a ' +
-        "ligand's pocket in a given structure, with contact distances. Binding sites are experimental-only " +
-        '(computed from deposited coordinates; predicted models carry no bound ligands).',
+    description: `Ligand discovery and binding-site analysis across the PDB. mode "find_ligand" resolves a name or formula to chemical component IDs with metadata (formula, weight, SMILES), ranked by deposition frequency — most-deposited component first, so the top hit is the most common match for the name, not necessarily an exact name-string match. mode "structures_with_ligand" returns PDB entries containing a ligand (by exact component ID — get the ID from find_ligand first), highest-resolution first, each with its resolution in Å. mode "binding_site" returns the protein residues lining a ligand's pocket in a given structure, with contact distances. Binding sites are experimental-only (computed from deposited coordinates; predicted models carry no bound ligands).`,
     annotations: { readOnlyHint: true, openWorldHint: true },
     errors: [
         {
@@ -131,7 +124,7 @@ export const trackLigands = tool('protein_track_ligands', {
         notice: z
             .string()
             .optional()
-            .describe('Advisory note when a mode-specific input is missing or absent.'),
+            .describe('Advisory note: a structures_with_ligand page that is empty because no entry contains the component or because start is past the end, or binding-site instances beyond limit that were left out.'),
     },
     async handler(input, ctx) {
         const rcsb = getRcsbService();
@@ -185,8 +178,11 @@ export const trackLigands = tool('protein_track_ligands', {
             });
             // A valid component with zero containing structures is an empty result set,
             // not a not-found — mirrors protein_search_structures' empty-hits behavior.
+            // An empty page over a nonzero total is an offset past the end instead.
             if (result.hits.length === 0) {
-                ctx.enrich.notice(`No PDB entries contain ${compId}. Verify the component ID via mode find_ligand.`);
+                ctx.enrich.notice(result.total === 0
+                    ? `No PDB entries contain ${compId}. Verify the component ID via mode find_ligand.`
+                    : `start ${input.start} is past the end of the ${result.total} PDB entries containing ${compId}. Re-call with a lower start to read a populated page.`);
             }
             // Replace RCSB's uniform containment score (noise for a boolean filter) with
             // each entry's resolution, enriched via the same batched entry-metadata path