@cyanheads/protein-mcp-server 0.8.5 → 0.8.6

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 (27) hide show
  1. package/AGENTS.md +15 -18
  2. package/CLAUDE.md +15 -18
  3. package/Dockerfile +92 -36
  4. package/README.md +75 -92
  5. package/changelog/0.8.x/0.8.6.md +22 -0
  6. package/dist/mcp-server/tools/definitions/analyze-collection.tool.d.ts.map +1 -1
  7. package/dist/mcp-server/tools/definitions/analyze-collection.tool.js +2 -2
  8. package/dist/mcp-server/tools/definitions/analyze-collection.tool.js.map +1 -1
  9. package/dist/mcp-server/tools/definitions/compare-structures.tool.d.ts.map +1 -1
  10. package/dist/mcp-server/tools/definitions/compare-structures.tool.js +3 -5
  11. package/dist/mcp-server/tools/definitions/compare-structures.tool.js.map +1 -1
  12. package/dist/mcp-server/tools/definitions/find-similar.tool.js +5 -7
  13. package/dist/mcp-server/tools/definitions/find-similar.tool.js.map +1 -1
  14. package/dist/mcp-server/tools/definitions/get-annotations.tool.d.ts.map +1 -1
  15. package/dist/mcp-server/tools/definitions/get-annotations.tool.js +4 -10
  16. package/dist/mcp-server/tools/definitions/get-annotations.tool.js.map +1 -1
  17. package/dist/mcp-server/tools/definitions/get-structure.tool.d.ts.map +1 -1
  18. package/dist/mcp-server/tools/definitions/get-structure.tool.js +3 -3
  19. package/dist/mcp-server/tools/definitions/get-structure.tool.js.map +1 -1
  20. package/dist/mcp-server/tools/definitions/search-structures.tool.d.ts.map +1 -1
  21. package/dist/mcp-server/tools/definitions/search-structures.tool.js +3 -5
  22. package/dist/mcp-server/tools/definitions/search-structures.tool.js.map +1 -1
  23. package/dist/mcp-server/tools/definitions/track-ligands.tool.d.ts.map +1 -1
  24. package/dist/mcp-server/tools/definitions/track-ligands.tool.js +3 -9
  25. package/dist/mcp-server/tools/definitions/track-ligands.tool.js.map +1 -1
  26. package/package.json +10 -9
  27. package/server.json +10 -24
package/dist/mcp-server/tools/definitions/find-similar.tool.js.map CHANGED
@@ -1 +1 @@
1
- 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package/dist/mcp-server/tools/definitions/get-annotations.tool.d.ts.map CHANGED
@@ -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;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAoSzB,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;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA6RzB,CAAC"}
package/dist/mcp-server/tools/definitions/get-annotations.tool.js CHANGED
@@ -156,14 +156,10 @@ export const getAnnotations = tool('protein_get_annotations', {
156
156
  // here rather than by a Zod refine so the rejection carries `data.reason` and
157
157
  // the declared recovery hint.
158
158
  if (!input.uniprot && !input.pdb_id) {
159
- throw ctx.fail('missing_identifier', 'Provide uniprot (e.g. P69905) or pdb_id (e.g. 4HHB).', {
160
- ...ctx.recoveryFor('missing_identifier'),
161
- });
159
+ throw ctx.fail('missing_identifier', 'Provide uniprot (e.g. P69905) or pdb_id (e.g. 4HHB).');
162
160
  }
163
161
  if (input.uniprot && !isUniProtAccession(input.uniprot)) {
164
- throw ctx.fail('invalid_accession', `"${input.uniprot}" is not a valid UniProt accession.`, {
165
- ...ctx.recoveryFor('invalid_accession'),
166
- });
162
+ throw ctx.fail('invalid_accession', `"${input.uniprot}" is not a valid UniProt accession.`);
167
163
  }
168
164
  let accession = input.uniprot?.toUpperCase();
169
165
  let resolvedFrom;
@@ -203,12 +199,10 @@ export const getAnnotations = tool('protein_get_annotations', {
203
199
  // malformed `uniprot` input was rejected before any lookup ran, so reaching
204
200
  // either means a supplied pdb_id resolved to nothing usable.
205
201
  if (!accession) {
206
- throw ctx.fail('no_uniprot_mapping', 'The supplied PDB ID carries no UniProt-mapped protein chain.', { ...ctx.recoveryFor('no_uniprot_mapping') });
202
+ throw ctx.fail('no_uniprot_mapping', 'The supplied PDB ID carries no UniProt-mapped protein chain.');
207
203
  }
208
204
  if (!isUniProtAccession(accession)) {
209
- throw ctx.fail('no_uniprot_mapping', `"${accession}" is not a valid UniProt accession.`, {
210
- ...ctx.recoveryFor('no_uniprot_mapping'),
211
- });
205
+ throw ctx.fail('no_uniprot_mapping', `"${accession}" is not a valid UniProt accession.`);
212
206
  }
213
207
  const include = input.include;
214
208
  const wantInterPro = include === 'domains' || include === 'all';
package/dist/mcp-server/tools/definitions/get-annotations.tool.js.map CHANGED
@@ -1 +1 @@
1
- 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package/dist/mcp-server/tools/definitions/get-structure.tool.d.ts.map CHANGED
@@ -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;;;;;;;;;;;GAWG;AAEH,OAAO,EAAsB,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAC/D,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAoHjE,eAAO,MAAM,YAAY;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAsUvB,CAAC"}
1
+ {"version":3,"file":"get-structure.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-structure.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;GAWG;AAEH,OAAO,EAAsB,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAC/D,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAoHjE,eAAO,MAAM,YAAY;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAmUvB,CAAC"}
package/dist/mcp-server/tools/definitions/get-structure.tool.js CHANGED
@@ -187,17 +187,17 @@ export const getStructure = tool('protein_get_structure', {
187
187
  }
188
188
  if (input.source === 'experimental') {
189
189
  if (ids.some((id) => isUniProtAccession(id) && !isPdbId(id))) {
190
- throw ctx.fail('mixed_id_types', 'source experimental expects PDB entry IDs, but UniProt accessions were present.', { ...ctx.recoveryFor('mixed_id_types') });
190
+ throw ctx.fail('mixed_id_types', 'source experimental expects PDB entry IDs, but UniProt accessions were present.');
191
191
  }
192
192
  }
193
193
  else if (ids.some((id) => isPdbId(id) && !isUniProtAccession(id))) {
194
- throw ctx.fail('mixed_id_types', `source ${input.source} expects UniProt accessions, but PDB IDs were present.`, { ...ctx.recoveryFor('mixed_id_types') });
194
+ throw ctx.fail('mixed_id_types', `source ${input.source} expects UniProt accessions, but PDB IDs were present.`);
195
195
  }
196
196
  const { structures, failed, notices: resolutionNotices, } = input.source === 'experimental'
197
197
  ? await fetchExperimental(ids, cfg.fanoutConcurrency, ctx)
198
198
  : await fetchPredictedOrBest(ids, input.source, cfg.fanoutConcurrency, ctx);
199
199
  if (structures.length === 0) {
200
- throw ctx.fail('all_failed', `None of the ${ids.length} requested IDs resolved to a structure.`, { ...ctx.recoveryFor('all_failed') });
200
+ throw ctx.fail('all_failed', `None of the ${ids.length} requested IDs resolved to a structure.`);
201
201
  }
202
202
  if (failed.length > 0) {
203
203
  notices.push(`${failed.length} of ${ids.length} IDs did not resolve: ${failed.map((f) => f.id).join(', ')}.`);
package/dist/mcp-server/tools/definitions/get-structure.tool.js.map CHANGED
@@ -1 +1 @@
1
- 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package/dist/mcp-server/tools/definitions/search-structures.tool.d.ts.map CHANGED
@@ -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;AAmDjE,eAAO,MAAM,gBAAgB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAqR3B,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;AAmDjE,eAAO,MAAM,gBAAgB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAgR3B,CAAC"}
package/dist/mcp-server/tools/definitions/search-structures.tool.js CHANGED
@@ -174,9 +174,7 @@ export const searchStructures = tool('protein_search_structures', {
174
174
  !input.organism &&
175
175
  !input.method &&
176
176
  typeof input.max_resolution !== 'number') {
177
- throw ctx.fail('no_criteria', 'Provide a query, sequence, organism, method, or maximum resolution to search on.', {
178
- ...ctx.recoveryFor('no_criteria'),
179
- });
177
+ throw ctx.fail('no_criteria', 'Provide a query, sequence, organism, method, or maximum resolution to search on.');
180
178
  }
181
179
  // buildQuery() reads these two only inside its sequence branch, so without a
182
180
  // sequence they never reach RCSB and the response looks like a filtered search
@@ -188,14 +186,14 @@ export const searchStructures = tool('protein_search_structures', {
188
186
  ].filter((name) => name !== undefined);
189
187
  if (!input.sequence && sequenceModifiers.length > 0) {
190
188
  const many = sequenceModifiers.length > 1;
191
- throw ctx.fail('sequence_modifier_without_sequence', `${sequenceModifiers.join(' and ')} ${many ? 'are sequence-search thresholds' : 'is a sequence-search threshold'}, but this request has no sequence — ${many ? 'they' : 'it'} would never reach RCSB.`, { ...ctx.recoveryFor('sequence_modifier_without_sequence') });
189
+ throw ctx.fail('sequence_modifier_without_sequence', `${sequenceModifiers.join(' and ')} ${many ? 'are sequence-search thresholds' : 'is a sequence-search threshold'}, but this request has no sequence — ${many ? 'they' : 'it'} would never reach RCSB.`);
192
190
  }
193
191
  // RCSB collapses two identically-named facet requests into one raw facet, and
194
192
  // the attribute-keyed lookup maps both specs back onto it — a repeated
195
193
  // dimension would return the same breakdown twice and double-count on any sum.
196
194
  const duplicate = input.facets?.find((d, i, all) => all.indexOf(d) !== i);
197
195
  if (duplicate)
198
- throw ctx.fail('duplicate_dimension', `facets lists "${duplicate}" more than once; each dimension is summarized once.`, { ...ctx.recoveryFor('duplicate_dimension') });
196
+ throw ctx.fail('duplicate_dimension', `facets lists "${duplicate}" more than once; each dimension is summarized once.`);
199
197
  const cfg = getServerConfig();
200
198
  const rcsb = getRcsbService();
201
199
  const facetSpecs = input.facets?.map((d) => buildFacetSpec(d));
package/dist/mcp-server/tools/definitions/search-structures.tool.js.map CHANGED
@@ -1 +1 @@
1
- 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package/dist/mcp-server/tools/definitions/track-ligands.tool.d.ts.map CHANGED
@@ -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;AAwEjE,eAAO,MAAM,YAAY;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA4SvB,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;AAwEjE,eAAO,MAAM,YAAY;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAqSvB,CAAC"}
package/dist/mcp-server/tools/definitions/track-ligands.tool.js CHANGED
@@ -155,9 +155,7 @@ export const trackLigands = tool('protein_track_ligands', {
155
155
  const cfg = getServerConfig();
156
156
  if (input.mode === 'find_ligand') {
157
157
  if (!input.query)
158
- throw ctx.fail('missing_param', 'mode find_ligand requires a name or formula in "query".', {
159
- ...ctx.recoveryFor('missing_param'),
160
- });
158
+ throw ctx.fail('missing_param', 'mode find_ligand requires a name or formula in "query".');
161
159
  // Over-fetch a candidate pool larger than the display limit, then re-rank by
162
160
  // deposition frequency and slice to the limit. The canonical component (e.g.
163
161
  // HEM for "heme") is the most-deposited but RCSB name-ranks it low, so a small
@@ -197,9 +195,7 @@ export const trackLigands = tool('protein_track_ligands', {
197
195
  if (input.mode === 'structures_with_ligand') {
198
196
  const compId = input.comp_id?.toUpperCase();
199
197
  if (!compId)
200
- throw ctx.fail('missing_param', 'mode structures_with_ligand requires a "comp_id".', {
201
- ...ctx.recoveryFor('missing_param'),
202
- });
198
+ throw ctx.fail('missing_param', 'mode structures_with_ligand requires a "comp_id".');
203
199
  const result = await rcsb.searchByLigand(compId, { limit: input.limit, start: input.start }, ctx);
204
200
  ctx.enrich.total(result.total);
205
201
  const nextStart = input.start + result.hits.length;
@@ -237,9 +233,7 @@ export const trackLigands = tool('protein_track_ligands', {
237
233
  // binding_site
238
234
  const compId = input.comp_id?.toUpperCase();
239
235
  if (!input.pdb_id)
240
- throw ctx.fail('missing_param', 'mode binding_site requires a "pdb_id".', {
241
- ...ctx.recoveryFor('missing_param'),
242
- });
236
+ throw ctx.fail('missing_param', 'mode binding_site requires a "pdb_id".');
243
237
  const sites = await rcsb.getBindingSites(input.pdb_id, compId, ctx);
244
238
  if (sites.length === 0) {
245
239
  throw ctx.fail('not_found', `No binding-site contacts found in ${input.pdb_id.toUpperCase()}${compId ? ` for ligand ${compId}` : ''}.`, {
package/dist/mcp-server/tools/definitions/track-ligands.tool.js.map CHANGED
@@ -1 +1 @@
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package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@cyanheads/protein-mcp-server",
3
- "version": "0.8.5",
3
+ "version": "0.8.6",
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",
@@ -12,6 +12,7 @@
12
12
  "files": [
13
13
  "changelog/",
14
14
  "dist/",
15
+ "!dist/*.mcpb",
15
16
  "README.md",
16
17
  "LICENSE",
17
18
  "CLAUDE.md",
@@ -83,7 +84,7 @@
83
84
  }
84
85
  ],
85
86
  "license": "Apache-2.0",
86
- "packageManager": "bun@1.4.0",
87
+ "packageManager": "bun@1.4.2",
87
88
  "engines": {
88
89
  "bun": ">=1.4.0",
89
90
  "node": ">=24.0.0"
@@ -92,18 +93,18 @@
92
93
  "access": "public"
93
94
  },
94
95
  "dependencies": {
95
- "@cyanheads/mcp-ts-core": "^0.13.6",
96
+ "@cyanheads/mcp-ts-core": "^0.13.13",
96
97
  "pino-pretty": "^13.1.3",
97
98
  "zod": "^4.6.5"
98
99
  },
99
100
  "devDependencies": {
100
- "@biomejs/biome": "2.5.14",
101
- "@socketsecurity/bun-security-scanner": "^1.1.2",
102
- "@types/node": "26.6.2",
101
+ "@biomejs/biome": "2.5.15",
102
+ "@socketsecurity/bun-security-scanner": "^1.1.3",
103
+ "@types/node": "26.6.4",
103
104
  "depcheck": "^1.4.7",
104
- "ignore": "^7.0.9",
105
- "tsc-alias": "^1.9.5",
105
+ "ignore": "^7.0.12",
106
+ "tsc-alias": "^1.9.7",
106
107
  "typescript": "^7.0.2",
107
- "vitest": "^5.0.1"
108
+ "vitest": "^5.0.3"
108
109
  }
109
110
  }