npm - @cyanheads/protein-mcp-server - Versions diffs - 0.8.0 → 0.8.2 - Mend

@cyanheads/protein-mcp-server 0.8.0 → 0.8.2

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

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1	- 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package/dist/mcp-server/tools/definitions/find-similar.tool.d.ts CHANGED Viewed

@@ -56,27 +56,32 @@ export declare const findSimilar: import("@cyanheads/mcp-ts-core").ToolDefinitio
     readonly code: JsonRpcErrorCode.InvalidParams;
     readonly when: "None of sequence, pdb_id, or uniprot was provided.";
     readonly recovery: "Provide a raw sequence, a PDB entry ID, or a UniProt accession to search from.";
+    readonly thrownBy: "service";
 }, {
     readonly reason: "mode_mismatched_field";
     readonly code: JsonRpcErrorCode.InvalidParams;
     readonly when: "An input field only the other by mode consumes was supplied: sequence, max_evalue or min_identity under by:\"structure\"; ticket_id or a non-empty databases list under by:\"sequence\".";
     readonly recovery: "Drop the field, or switch by to the mode that reads it — sequence, max_evalue and min_identity apply to by:\"sequence\"; ticket_id and databases apply to by:\"structure\".";
+    readonly thrownBy: "service";
 }, {
     readonly reason: "no_sequence";
     readonly code: JsonRpcErrorCode.NotFound;
     readonly when: "A sequence could not be resolved from the given PDB ID or UniProt accession.";
     readonly recovery: "Verify the identifier, or pass a raw one-letter sequence directly via the sequence parameter.";
+    readonly thrownBy: "service";
 }, {
     readonly reason: "search_failed";
     readonly code: JsonRpcErrorCode.ServiceUnavailable;
     readonly when: "The Foldseek search service rejected or failed the structure job.";
     readonly retryable: true;
     readonly recovery: "Retry shortly; if it persists, verify the source structure has coordinates via protein_get_structure.";
+    readonly thrownBy: "service";
 }, {
     readonly reason: "ticket_not_found";
     readonly code: JsonRpcErrorCode.NotFound;
     readonly when: "The supplied ticket_id was rejected by Foldseek as an invalid or expired ticket.";
     readonly recovery: "Tickets expire once results age out; drop ticket_id and re-run the by:structure search from pdb_id or uniprot to get a fresh one.";
+    readonly thrownBy: "service";
 }], {
     totalCount: z.ZodOptional<z.ZodNumber>;
     start: z.ZodOptional<z.ZodNumber>;

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

	@@ -1 +1 @@
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1	+ {"version":3,"file":"find-similar.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/find-similar.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;GAUG;AAEH,OAAO,EAA6B,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACtE,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA8HjE,eAAO,MAAM,WAAW;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAsFtB,CAAC"}

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

@@ -113,24 +113,28 @@ export const findSimilar = tool('protein_find_similar', {
     title: 'protein-mcp-server: find similar',
     description: `Find structurally or evolutionarily related proteins. by:"sequence" runs an RCSB mmseqs2 sequence-similarity search (synchronous) over a sequence — supplied directly, or pulled from a PDB ID or UniProt accession. by:"structure" runs a Foldseek fold-similarity search (asynchronous) against experimental and predicted databases; if the job is still computing when the poll budget elapses, the response reports status "computing" with a ticket — re-call with ticket_id set to that value to resume the same job instead of resubmitting, and a complete response carries the same ticket so a finished job can be re-paged with a different start. Each mode reads only its own controls: sequence, max_evalue and min_identity belong to by:"sequence"; ticket_id and databases belong to by:"structure"; pdb_id, uniprot, start and limit are shared. A field the selected mode cannot consume is rejected rather than silently ignored. Output names the engine and database each hit came from.`,
     annotations: { readOnlyHint: true, openWorldHint: true },
+    // Every reason is thrown by a helper below the handler, hence thrownBy on each entry.
     errors: [
         {
             reason: 'missing_query',
             code: JsonRpcErrorCode.InvalidParams,
             when: 'None of sequence, pdb_id, or uniprot was provided.',
             recovery: 'Provide a raw sequence, a PDB entry ID, or a UniProt accession to search from.',
+            thrownBy: 'service',
         },
         {
             reason: 'mode_mismatched_field',
             code: JsonRpcErrorCode.InvalidParams,
             when: 'An input field only the other by mode consumes was supplied: sequence, max_evalue or min_identity under by:"structure"; ticket_id or a non-empty databases list under by:"sequence".',
             recovery: 'Drop the field, or switch by to the mode that reads it — sequence, max_evalue and min_identity apply to by:"sequence"; ticket_id and databases apply to by:"structure".',
+            thrownBy: 'service',
         },
         {
             reason: 'no_sequence',
             code: JsonRpcErrorCode.NotFound,
             when: 'A sequence could not be resolved from the given PDB ID or UniProt accession.',
             recovery: 'Verify the identifier, or pass a raw one-letter sequence directly via the sequence parameter.',
+            thrownBy: 'service',
         },
         {
             reason: 'search_failed',
@@ -138,12 +142,14 @@ export const findSimilar = tool('protein_find_similar', {
             when: 'The Foldseek search service rejected or failed the structure job.',
             retryable: true,
             recovery: 'Retry shortly; if it persists, verify the source structure has coordinates via protein_get_structure.',
+            thrownBy: 'service',
         },
         {
             reason: 'ticket_not_found',
             code: JsonRpcErrorCode.NotFound,
             when: 'The supplied ticket_id was rejected by Foldseek as an invalid or expired ticket.',
             recovery: 'Tickets expire once results age out; drop ticket_id and re-run the by:structure search from pdb_id or uniprot to get a fresh one.',
+            thrownBy: 'service',
         },
     ],
     input: inputSchema,

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

	@@ -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;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAwEjE,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;~~EA8SzB~~,CAAC"}
1	+ {"version":3,"file":"get-annotations.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-annotations.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAwEjE,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAoSzB,CAAC"}

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

@@ -63,13 +63,7 @@ const ambiguitySchema = z
     .describe('Present only when a PDB ID mapped to more than one distinct UniProt accession and no chain was supplied. The returned accession is the deterministic lowest-chain pick — re-call with chain set to a specific author chain ID to select another.');
 export const getAnnotations = tool('protein_get_annotations', {
     title: 'protein-mcp-server: get annotations',
-    description: 'Sequence and functional annotation for a protein: UniProt features (domains, binding sites, PTMs), ' +
-        'natural variants, and InterPro domain/family memberships (Pfam, PROSITE, …) with GO terms. Provide a ' +
-        "UniProt accession directly, or a PDB ID — it is resolved to its UniProt accession via the structure's " +
-        'sequence cross-reference. A multi-chain PDB entry can map to several accessions; the default pick is ' +
-        'deterministic (lowest author chain ID) and the alternatives are listed in "ambiguity" — pass "chain" to ' +
-        'select a specific one. Use "include" to scope which annotation classes are fetched. Every response carries ' +
-        'an "attribution" block with the upstream data licenses and citations.',
+    description: `Sequence and functional annotation for a protein: UniProt features (domains, binding sites, PTMs), natural variants, and InterPro domain/family memberships (Pfam, PROSITE, …) with GO terms. Provide a UniProt accession directly, or a PDB ID — it is resolved to its UniProt accession via the structure's sequence cross-reference. A multi-chain PDB entry can map to several accessions; the default pick is deterministic (lowest author chain ID) and the alternatives are listed in "ambiguity" — pass "chain" to select a specific one. Use "include" to scope which annotation classes are fetched. Every response carries an "attribution" block with the upstream data licenses and citations.`,
     annotations: { readOnlyHint: true, openWorldHint: true },
     errors: [
         {
@@ -120,10 +114,7 @@ export const getAnnotations = tool('protein_get_annotations', {
             .min(1)
             .max(200)
             .default(50)
-            .describe('Per-class cap (1–200): features, natural variants, and InterPro domains are each independently ' +
-            'truncated to at most this many records. The default keeps a typical annotation set intact while ' +
-            'bounding a densely-annotated protein (a well-studied protein can carry 150+ natural variants); a ' +
-            'truncated class is disclosed in the response notice — raise it to retrieve more.'),
+            .describe('Per-class cap (1–200): features, natural variants, and InterPro domains are each independently truncated to at most this many records. The default keeps a typical annotation set intact while bounding a densely-annotated protein (a well-studied protein can carry 150+ natural variants); a truncated class is disclosed in the response notice — raise it to retrieve more.'),
     }),
     output: z.object({
         accession: z.string().describe('UniProt accession the annotations describe.'),

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/search-structures.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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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;AAwDjE,eAAO,MAAM,gBAAgB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA8Q3B,CAAC"}

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

@@ -50,15 +50,7 @@ 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 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.',
     annotations: { readOnlyHint: true, openWorldHint: true },
     errors: [
         {

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 @@
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;AA0CjE,eAAO,MAAM,YAAY;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;~~EAgQvB~~,CAAC"}
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;AA0CjE,eAAO,MAAM,YAAY;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAwPvB,CAAC"}

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

@@ -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: [
         {

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

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

@@ -1,6 +1,6 @@
 {
   "name": "@cyanheads/protein-mcp-server",
-  "version": "0.8.0",
+  "version": "0.8.2",
   "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",
@@ -24,6 +24,7 @@
     "rebuild": "bun run scripts/clean.ts && bun run scripts/build.ts",
     "clean": "bun run scripts/clean.ts",
     "devcheck": "bun run scripts/devcheck.ts",
+    "audit:fix": "bun audit fix",
     "audit:refresh": "rm -f bun.lock && bun install && bun audit",
     "tree": "bun run scripts/tree.ts",
     "list-skills": "bun run scripts/list-skills.ts",
@@ -84,25 +85,25 @@
   "license": "Apache-2.0",
   "packageManager": "bun@1.4.0",
   "engines": {
-    "bun": ">=1.3.0",
+    "bun": ">=1.4.0",
     "node": ">=24.0.0"
   },
   "publishConfig": {
     "access": "public"
   },
   "dependencies": {
-    "@cyanheads/mcp-ts-core": "^0.12.7",
+    "@cyanheads/mcp-ts-core": "^0.13.6",
     "pino-pretty": "^13.1.3",
-    "zod": "^4.5.4"
+    "zod": "^4.6.5"
   },
   "devDependencies": {
-    "@biomejs/biome": "2.5.12",
+    "@biomejs/biome": "2.5.14",
     "@socketsecurity/bun-security-scanner": "^1.1.2",
-    "@types/node": "26.4.1",
+    "@types/node": "26.6.2",
     "depcheck": "^1.4.7",
-    "ignore": "^7.0.8",
-    "tsc-alias": "^1.9.4",
+    "ignore": "^7.0.9",
+    "tsc-alias": "^1.9.5",
     "typescript": "^7.0.2",
-    "vitest": "^5.0.0"
+    "vitest": "^5.0.1"
   }
 }

package/server.json CHANGED Viewed

@@ -6,7 +6,7 @@
     "url": "https://github.com/cyanheads/protein-mcp-server",
     "source": "github"
   },
-  "version": "0.8.0",
+  "version": "0.8.2",
   "remotes": [
     {
       "type": "streamable-http",
@@ -19,7 +19,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/protein-mcp-server",
       "runtimeHint": "node",
-      "version": "0.8.0",
+      "version": "0.8.2",
       "packageArguments": [
         {
           "type": "positional",
@@ -48,7 +48,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/protein-mcp-server",
       "runtimeHint": "node",
-      "version": "0.8.0",
+      "version": "0.8.2",
       "packageArguments": [
         {
           "type": "positional",