@cyanheads/protein-mcp-server 0.3.0 → 0.3.1

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Files changed (10) hide show
  1. package/AGENTS.md +3 -2
  2. package/CLAUDE.md +3 -2
  3. package/README.md +1 -1
  4. package/changelog/0.3.x/0.3.1.md +16 -0
  5. package/dist/mcp-server/tools/definitions/get-structure.tool.d.ts +2 -0
  6. package/dist/mcp-server/tools/definitions/get-structure.tool.d.ts.map +1 -1
  7. package/dist/mcp-server/tools/definitions/get-structure.tool.js +43 -12
  8. package/dist/mcp-server/tools/definitions/get-structure.tool.js.map +1 -1
  9. package/package.json +1 -1
  10. package/server.json +3 -3
package/AGENTS.md CHANGED
@@ -1,7 +1,7 @@
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  # Developer Protocol
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  **Server:** protein-mcp-server
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- **Version:** 0.3.0
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+ **Version:** 0.3.1
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  **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.10.10`
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  **Engines:** Bun ≥1.3.0, Node ≥24.0.0
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  **MCP SDK:** `@modelcontextprotocol/sdk` ^1.29.0
@@ -80,7 +80,8 @@ export const getAnnotations = tool('protein_get_annotations', {
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  async handler(input, ctx) {
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  let accession = input.uniprot?.toUpperCase();
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  if (!accession && input.pdb_id) {
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- accession = (await getRcsbService().resolveUniprot(input.pdb_id, ctx))[0];
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+ // entity-grained; the real handler picks deterministically by author chain
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+ accession = (await getRcsbService().resolveUniprotEntities(input.pdb_id, ctx))[0]?.accession;
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  }
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  if (!accession || !isUniProtAccession(accession)) {
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  throw ctx.fail('no_uniprot_mapping', 'Provide a UniProt accession, or a PDB ID with a modeled protein chain.');
package/CLAUDE.md CHANGED
@@ -1,7 +1,7 @@
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  # Developer Protocol
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  **Server:** protein-mcp-server
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- **Version:** 0.3.0
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+ **Version:** 0.3.1
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  **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.10.10`
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  **Engines:** Bun ≥1.3.0, Node ≥24.0.0
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  **MCP SDK:** `@modelcontextprotocol/sdk` ^1.29.0
@@ -80,7 +80,8 @@ export const getAnnotations = tool('protein_get_annotations', {
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  async handler(input, ctx) {
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  let accession = input.uniprot?.toUpperCase();
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  if (!accession && input.pdb_id) {
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- accession = (await getRcsbService().resolveUniprot(input.pdb_id, ctx))[0];
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+ // entity-grained; the real handler picks deterministically by author chain
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+ accession = (await getRcsbService().resolveUniprotEntities(input.pdb_id, ctx))[0]?.accession;
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  }
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  if (!accession || !isUniProtAccession(accession)) {
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  throw ctx.fail('no_uniprot_mapping', 'Provide a UniProt accession, or a PDB ID with a modeled protein chain.');
package/README.md CHANGED
@@ -7,7 +7,7 @@
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  <div align="center">
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- [![Version](https://img.shields.io/badge/Version-0.3.0-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/)
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+ [![Version](https://img.shields.io/badge/Version-0.3.1-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/)
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  </div>
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package/changelog/0.3.x/0.3.1.md ADDED
@@ -0,0 +1,16 @@
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+ ---
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+ summary: "best_available confidence scores are now scale-correct and self-describing instead of overloading meanPlddt; experimental best_available picks return the full cif/pdb/bcif coordinate set, matching source: experimental."
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+ breaking: false
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+ security: false
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+ ---
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+
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+ # 0.3.1 — 2026-07-03
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+
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+ ## Changed
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+
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+ - **`protein_get_structure` description** — clarifies that `best_available`'s experimental pick optimizes for resolution, not biological representativeness (it can return an engineered mutant over the wild-type entry). ([#16](https://github.com/cyanheads/protein-mcp-server/issues/16))
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+
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+ ## Fixed
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+
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+ - **`protein_get_structure` (`best_available`)** — a non-pLDDT provider score (e.g. SWISS-MODEL's QMEANDisCo, 0–1 scale) no longer populates the pLDDT-scaled `meanPlddt` field (0–100 scale). New `confidence` + `confidenceType` output fields carry the score on its native scale and name the metric; `meanPlddt` now populates only when `confidenceType` is `pLDDT`. ([#14](https://github.com/cyanheads/protein-mcp-server/issues/14))
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+ - **`protein_get_structure` (`best_available`)** — an experimental pick now returns the full `cif`/`pdb`/`bcif` coordinate-file URL set from RCSB, matching `source: experimental`, instead of the single 3D-Beacons `modelUrl`. ([#16](https://github.com/cyanheads/protein-mcp-server/issues/16))
package/dist/mcp-server/tools/definitions/get-structure.tool.d.ts CHANGED
@@ -31,6 +31,8 @@ export declare const getStructure: import("@cyanheads/mcp-ts-core").ToolDefiniti
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  resolution: z.ZodOptional<z.ZodNumber>;
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  organism: z.ZodOptional<z.ZodString>;
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  provider: z.ZodOptional<z.ZodString>;
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+ confidence: z.ZodOptional<z.ZodNumber>;
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+ confidenceType: z.ZodOptional<z.ZodString>;
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  meanPlddt: z.ZodOptional<z.ZodNumber>;
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  confidenceBuckets: z.ZodOptional<z.ZodObject<{
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  veryLow: z.ZodNumber;
package/dist/mcp-server/tools/definitions/get-structure.tool.d.ts.map CHANGED
@@ -1 +1 @@
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- {"version":3,"file":"get-structure.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-structure.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAsB,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAC/D,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAgEjE,eAAO,MAAM,YAAY;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAiQvB,CAAC"}
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+ {"version":3,"file":"get-structure.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-structure.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAsB,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAC/D,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAiFjE,eAAO,MAAM,YAAY;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAsQvB,CAAC"}
package/dist/mcp-server/tools/definitions/get-structure.tool.js CHANGED
@@ -40,7 +40,18 @@ const structureRecordSchema = z
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  resolution: z.number().optional().describe('Resolution in Å (experimental).'),
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  organism: z.string().optional().describe('Source organism.'),
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  provider: z.string().optional().describe('Model provider (predicted / best_available).'),
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- meanPlddt: z.number().optional().describe('Mean pLDDT confidence 0–100 (predicted).'),
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+ confidence: z
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+ .number()
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+ .optional()
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+ .describe('Model confidence on its native scale; confidenceType names the metric and range (e.g. pLDDT 0–100, QMEANDisCo 0–1). Present for predicted models that report a score.'),
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+ confidenceType: z
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+ .string()
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+ .optional()
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+ .describe('Name of the confidence metric carried in confidence (e.g. "pLDDT", "QMEANDisCo"). Providers score on different scales; this names the one in use.'),
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+ meanPlddt: z
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+ .number()
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+ .optional()
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+ .describe('Mean pLDDT confidence (0–100); present only for pLDDT-scored models. For other metrics read confidence + confidenceType.'),
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  confidenceBuckets: confidenceBucketsSchema
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  .optional()
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  .describe('pLDDT confidence-band fractions (predicted).'),
@@ -69,10 +80,12 @@ export const getStructure = tool('protein_get_structure', {
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  title: 'protein-mcp-server: get structure',
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  description: 'Fetch structures with metadata and coordinate-file URLs. source "experimental" takes PDB entry IDs ' +
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  '(batched in one call); "predicted" takes UniProt accessions (AlphaFold, with pLDDT/PAE confidence); ' +
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- '"best_available" takes UniProt accessions and returns the top federated model (experimental if one ' +
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- 'exists, else the best prediction). Resolves up to the configured batch cap per call with per-ID partial ' +
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- 'success — missed IDs are listed in failed[]. Set include_coords to inline coordinate content; if that ' +
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- 'overflows, a section outline is returned — re-call with sections:[ids] to inline specific structures.',
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+ '"best_available" takes UniProt accessions and returns the top federated model — the highest-resolution ' +
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+ 'experimental structure if one exists (optimizing resolution, not biological representativeness, so it can ' +
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+ 'return an engineered mutant over the wild-type entry), else the best prediction. Resolves up to the ' +
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+ 'configured batch cap per call with per-ID partial success — missed IDs are listed in failed[]. Set ' +
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+ 'include_coords to inline coordinate content; if that overflows, a section outline is returned — re-call ' +
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+ 'with sections:[ids] to inline specific structures.',
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  annotations: { readOnlyHint: true, openWorldHint: true },
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  errors: [
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  {
@@ -230,6 +243,9 @@ export const getStructure = tool('protein_get_structure', {
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  typeof s.resolution === 'number' ? `**Resolution:** ${s.resolution} Å` : null,
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  s.organism ? `**Organism:** ${s.organism}` : null,
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  s.provider ? `**Provider:** ${s.provider}` : null,
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+ typeof s.confidence === 'number'
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+ ? `**Confidence:** ${s.confidence}${s.confidenceType ? ` (${s.confidenceType})` : ''}`
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+ : null,
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  typeof s.meanPlddt === 'number' ? `**Mean pLDDT:** ${s.meanPlddt.toFixed(1)}` : null,
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  ].filter(Boolean);
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  if (meta.length > 0)
@@ -348,16 +364,16 @@ async function fetchBest(accession, ctx) {
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  return null;
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  const isExperimental = /experimentally/i.test(best.modelCategory ?? '');
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  // For an experimental pick the federated id is the chosen PDB entry; surface it
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- // explicitly so the agent can cite the structure, and fetch its title for parity
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- // with source "experimental". The title is best-effort — a failed lookup must
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- // not drop the structure the agent already has.
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+ // explicitly so the agent can cite the structure, fetch its title for parity with
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+ // source "experimental", and emit the full cif/pdb/bcif set from RCSB (matching
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+ // fetchExperimental) instead of the single beacon modelUrl. The title is
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+ // best-effort — a failed lookup must not drop the structure the agent already has.
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+ const rcsb = getRcsbService();
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  let pdbId;
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  let title;
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  if (isExperimental && best.modelIdentifier) {
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  pdbId = best.modelIdentifier.toUpperCase();
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- const entries = await getRcsbService()
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- .getEntries([pdbId], ctx)
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- .catch(() => []);
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+ const entries = await rcsb.getEntries([pdbId], ctx).catch(() => []);
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  title = entries[0]?.title;
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  }
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  return {
@@ -368,10 +384,25 @@ async function fetchBest(accession, ctx) {
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  ...(best.provider ? { provider: best.provider } : {}),
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  ...(typeof best.resolution === 'number' ? { resolution: best.resolution } : {}),
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  ...(best.experimentalMethod ? { method: best.experimentalMethod } : {}),
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+ ...(best.confidenceType ? { confidenceType: best.confidenceType } : {}),
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  ...(typeof best.confidenceAvgLocalScore === 'number'
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+ ? { confidence: best.confidenceAvgLocalScore }
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+ : {}),
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+ // meanPlddt is pLDDT-only (0–100); never surface another provider's metric
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+ // (e.g. QMEANDisCo, 0–1) under it. Non-pLDDT scores stay in confidence.
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+ ...(typeof best.confidenceAvgLocalScore === 'number' &&
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+ best.confidenceType?.toLowerCase() === 'plddt'
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  ? { meanPlddt: best.confidenceAvgLocalScore }
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  : {}),
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- coordinateUrls: best.modelUrl ? coordinateUrlFor(best.modelUrl) : {},
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+ coordinateUrls: pdbId
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+ ? {
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+ cif: rcsb.coordinateFileUrl(pdbId, 'cif'),
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+ pdb: rcsb.coordinateFileUrl(pdbId, 'pdb'),
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+ bcif: rcsb.coordinateFileUrl(pdbId, 'bcif'),
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+ }
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+ : best.modelUrl
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+ ? coordinateUrlFor(best.modelUrl)
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+ : {},
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  };
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  }
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  /** Slot a single federated model URL into the right format key. */
package/dist/mcp-server/tools/definitions/get-structure.tool.js.map CHANGED
@@ -1 +1 @@
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- 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package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@cyanheads/protein-mcp-server",
3
- "version": "0.3.0",
3
+ "version": "0.3.1",
4
4
  "mcpName": "io.github.cyanheads/protein-mcp-server",
5
5
  "description": "Federated protein structure & annotation across experimental (PDB) and predicted (AlphaFold) models via MCP. STDIO or Streamable HTTP.",
6
6
  "type": "module",
package/server.json CHANGED
@@ -6,7 +6,7 @@
6
6
  "url": "https://github.com/cyanheads/protein-mcp-server",
7
7
  "source": "github"
8
8
  },
9
- "version": "0.3.0",
9
+ "version": "0.3.1",
10
10
  "remotes": [
11
11
  {
12
12
  "type": "streamable-http",
@@ -19,7 +19,7 @@
19
19
  "registryBaseUrl": "https://registry.npmjs.org",
20
20
  "identifier": "@cyanheads/protein-mcp-server",
21
21
  "runtimeHint": "node",
22
- "version": "0.3.0",
22
+ "version": "0.3.1",
23
23
  "packageArguments": [
24
24
  {
25
25
  "type": "positional",
@@ -48,7 +48,7 @@
48
48
  "registryBaseUrl": "https://registry.npmjs.org",
49
49
  "identifier": "@cyanheads/protein-mcp-server",
50
50
  "runtimeHint": "node",
51
- "version": "0.3.0",
51
+ "version": "0.3.1",
52
52
  "packageArguments": [
53
53
  {
54
54
  "type": "positional",