npm - @cyanheads/protein-mcp-server - Versions diffs - 0.2.0 → 0.2.1 - Mend

@cyanheads/protein-mcp-server 0.2.0 → 0.2.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (29) hide show

package/AGENTS.md CHANGED Viewed

@@ -1,7 +1,7 @@
 # Developer Protocol
 **Server:** protein-mcp-server
-**Version:** 0.2.0
+**Version:** 0.2.1
 **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.10.10`
 **Engines:** Bun ≥1.3.0, Node ≥24.0.0
 **MCP SDK:** `@modelcontextprotocol/sdk` ^1.29.0

package/CLAUDE.md CHANGED Viewed

@@ -1,7 +1,7 @@
 # Developer Protocol
 **Server:** protein-mcp-server
-**Version:** 0.2.0
+**Version:** 0.2.1
 **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.10.10`
 **Engines:** Bun ≥1.3.0, Node ≥24.0.0
 **MCP SDK:** `@modelcontextprotocol/sdk` ^1.29.0

package/README.md CHANGED Viewed

@@ -7,7 +7,7 @@
 <div align="center">
-[![Version](https://img.shields.io/badge/Version-0.2.0-blue.svg?style=flat-square)](./CHANGELOG.md) [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![Docker](https://img.shields.io/badge/Docker-ghcr.io-2496ED?style=flat-square&logo=docker&logoColor=white)](https://github.com/users/cyanheads/packages/container/package/protein-mcp-server) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.29.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/) [![npm](https://img.shields.io/npm/v/@cyanheads/protein-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/protein-mcp-server) [![TypeScript](https://img.shields.io/badge/TypeScript-^6.0.3-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-v1.3.2-blueviolet.svg?style=flat-square)](https://bun.sh/)
+[![Version](https://img.shields.io/badge/Version-0.2.1-blue.svg?style=flat-square)](./CHANGELOG.md) [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![Docker](https://img.shields.io/badge/Docker-ghcr.io-2496ED?style=flat-square&logo=docker&logoColor=white)](https://github.com/users/cyanheads/packages/container/package/protein-mcp-server) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.29.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/) [![npm](https://img.shields.io/npm/v/@cyanheads/protein-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/protein-mcp-server) [![TypeScript](https://img.shields.io/badge/TypeScript-^6.0.3-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-v1.3.2-blueviolet.svg?style=flat-square)](https://bun.sh/)
 </div>

package/changelog/0.2.x/0.2.1.md ADDED Viewed

@@ -0,0 +1,16 @@
+---
+summary: "Nested cross-tab facet children now carry a truncated flag; declared error recovery hints reach the wire; protein_track_ligands binding_site honors limit."
+breaking: false
+security: false
+---
+# 0.2.1 — 2026-07-03
+## Added
+- **`protein_analyze_collection` / `protein_search_structures`** — nested cross-tab facet child dimensions now carry a `truncated` boolean when their bucket list is capped by `bucket_limit`; `renderFacets` appends `(truncated)` to the nested line in `content[]`. ([#13](https://github.com/cyanheads/protein-mcp-server/issues/13))
+## Fixed
+- **`protein_track_ligands` `binding_site`** — now caps returned instances to `limit` and emits a truncation notice, instead of returning every instance regardless of `limit`. ([#9](https://github.com/cyanheads/protein-mcp-server/issues/9))
+- **Declared recovery hints** — `errors[].recovery` now reaches the wire (`data.recovery.hint`, mirrored into `content[]`) at throw sites across `protein_search_structures`, `protein_get_annotations`, `protein_get_structure`, `protein_find_similar`, `protein_track_ligands`, and `protein_analyze_collection`. ([#10](https://github.com/cyanheads/protein-mcp-server/issues/10))

package/dist/mcp-server/tools/definitions/_schemas.d.ts CHANGED Viewed

@@ -19,6 +19,7 @@ export declare const facetDimensionSchema: z.ZodObject<{
                 label: z.ZodString;
                 count: z.ZodNumber;
             }, z.core.$strip>>;
+            truncated: z.ZodOptional<z.ZodBoolean>;
         }, z.core.$strip>>>;
     }, z.core.$strip>>;
     truncated: z.ZodOptional<z.ZodBoolean>;

package/dist/mcp-server/tools/definitions/_schemas.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"_schemas.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/_schemas.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAC3C,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,0BAA0B,CAAC;AAoC/D,yCAAyC;AACzC,eAAO,MAAM,oBAAoB;;;;;;;;;;;;;;;iBAW4B,CAAC;AAE9D,MAAM,MAAM,oBAAoB,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,oBAAoB,CAAC,CAAC;AAExE,oFAAoF;AACpF,wBAAgB,aAAa,CAAC,KAAK,EAAE,cAAc,EAAE,GAAG,EAAE,MAAM,GAAG,oBAAoB,CAmBtF;AAED,iFAAiF;AACjF,wBAAgB,YAAY,CAAC,MAAM,EAAE,oBAAoB,EAAE,GAAG,MAAM,EAAE,CAarE"}

package/dist/mcp-server/tools/definitions/_schemas.js CHANGED Viewed

@@ -18,6 +18,10 @@ const childDimensionSchema = z
     .object({
     dimension: z.string().describe('Nested dimension name.'),
     buckets: z.array(leafBucketSchema).describe('Nested buckets within the parent bucket.'),
+    truncated: z
+        .boolean()
+        .optional()
+        .describe('True when this nested bucket list was capped by the per-dimension bucket limit.'),
 })
     .describe('A nested cross-tab dimension within a parent bucket.');
 /** A top-level facet bucket, optionally carrying a nested cross-tab dimension. */
@@ -57,6 +61,7 @@ export function toFacetOutput(facet, cap) {
                     children: b.children.map((c) => ({
                         dimension: c.dimension,
                         buckets: c.buckets.slice(0, cap).map((cb) => ({ label: cb.label, count: cb.count })),
+                        ...(c.buckets.length > cap ? { truncated: true } : {}),
                     })),
                 }
                 : {}),
@@ -73,7 +78,7 @@ export function renderFacets(facets) {
             lines.push(`- ${b.label}: ${b.count}`);
             for (const c of b.children ?? []) {
                 const inner = c.buckets.map((cb) => `${cb.label}: ${cb.count}`).join(', ');
-                lines.push(`  - ${c.dimension} → ${inner}`);
+                lines.push(`  - ${c.dimension} → ${inner}${c.truncated ? ' (truncated)' : ''}`);
             }
         }
     }

package/dist/mcp-server/tools/definitions/_schemas.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/analyze-collection.tool.d.ts CHANGED Viewed

@@ -45,6 +45,7 @@ export declare const analyzeCollection: import("@cyanheads/mcp-ts-core").ToolDef
                     label: z.ZodString;
                     count: z.ZodNumber;
                 }, z.core.$strip>>;
+                truncated: z.ZodOptional<z.ZodBoolean>;
             }, z.core.$strip>>>;
         }, z.core.$strip>>;
         truncated: z.ZodOptional<z.ZodBoolean>;

package/dist/mcp-server/tools/definitions/analyze-collection.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"analyze-collection.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/analyze-collection.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAOjE,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAyH5B,CAAC"}

package/dist/mcp-server/tools/definitions/analyze-collection.tool.js CHANGED Viewed

@@ -86,7 +86,9 @@ export const analyzeCollection = tool('protein_analyze_collection', {
                 : 'experimental';
         const [primary, secondary] = input.group_by;
         if (!primary)
-            throw ctx.fail('unknown_dimension', 'group_by requires at least one dimension.');
+            throw ctx.fail('unknown_dimension', 'group_by requires at least one dimension.', {
+                ...ctx.recoveryFor('unknown_dimension'),
+            });
         const spec = buildFacetSpec(primary, input.interval, secondary);
         const { total, facets } = await rcsb.analyzeFacets({
             ...(input.query ? { text: input.query } : {}),

package/dist/mcp-server/tools/definitions/analyze-collection.tool.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/find-similar.tool.js CHANGED Viewed

@@ -253,16 +253,18 @@ async function resolveSequence(input, ctx) {
     if (input.pdb_id) {
         const seq = await getRcsbService().getSequence(input.pdb_id, ctx);
         if (!seq)
-            throw ctx.fail('no_sequence', `No protein sequence found for PDB entry ${input.pdb_id.toUpperCase()}.`);
+            throw ctx.fail('no_sequence', `No protein sequence found for PDB entry ${input.pdb_id.toUpperCase()}.`, { ...ctx.recoveryFor('no_sequence') });
         return seq.sequence;
     }
     if (input.uniprot) {
         const seq = await getUniProtService().getSequence(input.uniprot, ctx);
         if (!seq)
-            throw ctx.fail('no_sequence', `No sequence found for UniProt accession ${input.uniprot.toUpperCase()}.`);
+            throw ctx.fail('no_sequence', `No sequence found for UniProt accession ${input.uniprot.toUpperCase()}.`, { ...ctx.recoveryFor('no_sequence') });
         return seq;
     }
-    throw ctx.fail('missing_query', 'Provide a sequence, pdb_id, or uniprot to search from.');
+    throw ctx.fail('missing_query', 'Provide a sequence, pdb_id, or uniprot to search from.', {
+        ...ctx.recoveryFor('missing_query'),
+    });
 }
 /** Resolve a query coordinate file (PDB-format text) from a PDB ID or UniProt accession. */
 async function resolveCoordinateFile(input, ctx) {
@@ -275,14 +277,14 @@ async function resolveCoordinateFile(input, ctx) {
     if (input.uniprot && isUniProtAccession(input.uniprot)) {
         const model = await getAlphaFoldService().getPrediction(input.uniprot, ctx);
         if (!model?.pdbUrl) {
-            throw ctx.fail('no_sequence', `No predicted model with coordinates found for ${input.uniprot.toUpperCase()}.`);
+            throw ctx.fail('no_sequence', `No predicted model with coordinates found for ${input.uniprot.toUpperCase()}.`, { ...ctx.recoveryFor('no_sequence') });
         }
         return {
             content: await fetchCoordinateText(model.pdbUrl, ctx),
             fileName: `${input.uniprot.toUpperCase()}.pdb`,
         };
     }
-    throw ctx.fail('missing_query', 'by:structure requires a pdb_id or uniprot accession to derive coordinates.');
+    throw ctx.fail('missing_query', 'by:structure requires a pdb_id or uniprot accession to derive coordinates.', { ...ctx.recoveryFor('missing_query') });
 }
 function fetchCoordinateText(url, ctx) {
     return fetchText(url, ctx, {

package/dist/mcp-server/tools/definitions/find-similar.tool.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/mcp-server/tools/definitions/get-annotations.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"get-annotations.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-annotations.tool.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA4CjE,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;~~EAwIzB~~,CAAC"}
1	+ {"version":3,"file":"get-annotations.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-annotations.tool.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA4CjE,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA2IzB,CAAC"}

package/dist/mcp-server/tools/definitions/get-annotations.tool.js CHANGED Viewed

@@ -98,10 +98,12 @@ export const getAnnotations = tool('protein_get_annotations', {
             resolvedFrom = input.pdb_id.toUpperCase();
         }
         if (!accession) {
-            throw ctx.fail('no_uniprot_mapping', 'Provide a UniProt accession, or a PDB ID with a modeled protein chain.');
+            throw ctx.fail('no_uniprot_mapping', 'Provide a UniProt accession, or a PDB ID with a modeled protein chain.', { ...ctx.recoveryFor('no_uniprot_mapping') });
         }
         if (!isUniProtAccession(accession)) {
-            throw ctx.fail('no_uniprot_mapping', `"${accession}" is not a valid UniProt accession.`);
+            throw ctx.fail('no_uniprot_mapping', `"${accession}" is not a valid UniProt accession.`, {
+                ...ctx.recoveryFor('no_uniprot_mapping'),
+            });
         }
         const include = input.include;
         const wantInterPro = include === 'domains' || include === 'all';

package/dist/mcp-server/tools/definitions/get-annotations.tool.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/mcp-server/tools/definitions/get-structure.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"get-structure.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-structure.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAsB,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAC/D,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA8DjE,eAAO,MAAM,YAAY;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;~~EAgOvB~~,CAAC"}
1	+ {"version":3,"file":"get-structure.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-structure.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAsB,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAC/D,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA8DjE,eAAO,MAAM,YAAY;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAmOvB,CAAC"}

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

@@ -145,17 +145,17 @@ export const getStructure = tool('protein_get_structure', {
         }
         if (input.source === 'experimental') {
             if (ids.some((id) => isUniProtAccession(id) && !isPdbId(id))) {
-                throw ctx.fail('mixed_id_types', 'source experimental expects PDB entry IDs, but UniProt accessions were present.');
+                throw ctx.fail('mixed_id_types', 'source experimental expects PDB entry IDs, but UniProt accessions were present.', { ...ctx.recoveryFor('mixed_id_types') });
             }
         }
         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.`);
+            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)
             : 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.`);
+            throw ctx.fail('all_failed', `None of the ${ids.length} requested IDs resolved to a structure.`, { ...ctx.recoveryFor('all_failed') });
         }
         // Inline coordinates when requested (all, or only the re-called sections).
         const inlineSet = input.sections?.length

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

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

@@ -54,6 +54,7 @@ export declare const searchStructures: import("@cyanheads/mcp-ts-core").ToolDefi
                     label: z.ZodString;
                     count: z.ZodNumber;
                 }, z.core.$strip>>;
+                truncated: z.ZodOptional<z.ZodBoolean>;
             }, z.core.$strip>>>;
         }, z.core.$strip>>;
         truncated: z.ZodOptional<z.ZodBoolean>;

package/dist/mcp-server/tools/definitions/search-structures.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"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;AAwBjE,eAAO,MAAM,gBAAgB~~;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA0L3B~~,CAAC"}
1	+ {"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;AAwBjE,eAAO,MAAM,gBAAgB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA4L3B,CAAC"}

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

@@ -128,7 +128,9 @@ export const searchStructures = tool('protein_search_structures', {
     },
     async handler(input, ctx) {
         if (!input.query && !input.sequence && !input.organism) {
-            throw ctx.fail('no_criteria', 'Provide a query, sequence, or organism to search on.');
+            throw ctx.fail('no_criteria', 'Provide a query, sequence, or organism to search on.', {
+                ...ctx.recoveryFor('no_criteria'),
+            });
         }
         const cfg = getServerConfig();
         const rcsb = getRcsbService();

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

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

	@@ -1 +1 @@
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1	+ {"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;AAqCjE,eAAO,MAAM,YAAY;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAiMvB,CAAC"}

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

@@ -116,7 +116,9 @@ export const trackLigands = tool('protein_track_ligands', {
         const cfg = getServerConfig();
         if (input.mode === 'find_ligand') {
             if (!input.query)
-                throw ctx.fail('missing_param', 'mode find_ligand requires a name or formula in "query".');
+                throw ctx.fail('missing_param', 'mode find_ligand requires a name or formula in "query".', {
+                    ...ctx.recoveryFor('missing_param'),
+                });
             const ids = await rcsb.findChemComps(input.query, input.limit, ctx);
             const ligands = (await mapWithConcurrency(ids, cfg.fanoutConcurrency, (id) => rcsb.getChemComp(id, ctx))).filter((c) => c != null);
             if (ligands.length === 0) {
@@ -131,7 +133,9 @@ export const trackLigands = tool('protein_track_ligands', {
         if (input.mode === 'structures_with_ligand') {
             const compId = input.comp_id?.toUpperCase();
             if (!compId)
-                throw ctx.fail('missing_param', 'mode structures_with_ligand requires a "comp_id".');
+                throw ctx.fail('missing_param', 'mode structures_with_ligand requires a "comp_id".', {
+                    ...ctx.recoveryFor('missing_param'),
+                });
             const result = await rcsb.searchByLigand(compId, { limit: input.limit }, ctx);
             ctx.enrich.total(result.total);
             ctx.enrich({ resolvedCompId: compId });
@@ -148,7 +152,9 @@ export const trackLigands = tool('protein_track_ligands', {
         // binding_site
         const compId = input.comp_id?.toUpperCase();
         if (!input.pdb_id)
-            throw ctx.fail('missing_param', 'mode binding_site requires a "pdb_id".');
+            throw ctx.fail('missing_param', 'mode binding_site requires a "pdb_id".', {
+                ...ctx.recoveryFor('missing_param'),
+            });
         const sites = await rcsb.getBindingSites(input.pdb_id, compId, ctx);
         if (sites.length === 0) {
             throw ctx.fail('not_found', `No binding-site contacts found in ${input.pdb_id.toUpperCase()}${compId ? ` for ligand ${compId}` : ''}.`, {
@@ -157,9 +163,15 @@ export const trackLigands = tool('protein_track_ligands', {
                 },
             });
         }
+        // Cap binding-site INSTANCES to the shared limit (mode-consistent top-N; the
+        // other two modes already bound their results). Disclose the drop via notice.
+        const bindingSites = sites.slice(0, input.limit);
+        if (sites.length > input.limit) {
+            ctx.enrich.notice(`Showing ${input.limit} of ${sites.length} binding-site instances in ${input.pdb_id.toUpperCase()}${compId ? ` for ${compId}` : ''}; raise limit to see more.`);
+        }
         if (compId)
             ctx.enrich({ resolvedCompId: compId });
-        return { mode: input.mode, bindingSites: sites };
+        return { mode: input.mode, bindingSites };
     },
     format: (result) => {
         const lines = [`## protein_track_ligands — ${result.mode}`];

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

	@@ -1 +1 @@
1	- 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package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "@cyanheads/protein-mcp-server",
-  "version": "0.2.0",
+  "version": "0.2.1",
   "mcpName": "io.github.cyanheads/protein-mcp-server",
   "description": "Federated protein structure & annotation across experimental (PDB) and predicted (AlphaFold) models via MCP. STDIO or Streamable HTTP.",
   "type": "module",

package/server.json CHANGED Viewed

@@ -6,7 +6,7 @@
     "url": "https://github.com/cyanheads/protein-mcp-server",
     "source": "github"
   },
-  "version": "0.2.0",
+  "version": "0.2.1",
   "remotes": [
     {
       "type": "streamable-http",
@@ -19,7 +19,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/protein-mcp-server",
       "runtimeHint": "node",
-      "version": "0.2.0",
+      "version": "0.2.1",
       "packageArguments": [
         {
           "type": "positional",
@@ -48,7 +48,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/protein-mcp-server",
       "runtimeHint": "node",
-      "version": "0.2.0",
+      "version": "0.2.1",
       "packageArguments": [
         {
           "type": "positional",