@cyanheads/protein-mcp-server 0.4.0 → 0.4.2

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 (70) hide show
  1. package/AGENTS.md +32 -25
  2. package/CLAUDE.md +32 -25
  3. package/Dockerfile +16 -7
  4. package/LICENSE +1 -1
  5. package/README.md +8 -6
  6. package/changelog/0.4.x/0.4.1.md +32 -0
  7. package/changelog/0.4.x/0.4.2.md +16 -0
  8. package/changelog/template.md +60 -19
  9. package/dist/mcp-server/resources/definitions/af-summary.resource.d.ts.map +1 -1
  10. package/dist/mcp-server/resources/definitions/af-summary.resource.js +8 -1
  11. package/dist/mcp-server/resources/definitions/af-summary.resource.js.map +1 -1
  12. package/dist/mcp-server/tools/definitions/_schemas.d.ts +34 -6
  13. package/dist/mcp-server/tools/definitions/_schemas.d.ts.map +1 -1
  14. package/dist/mcp-server/tools/definitions/_schemas.js +149 -9
  15. package/dist/mcp-server/tools/definitions/_schemas.js.map +1 -1
  16. package/dist/mcp-server/tools/definitions/analyze-collection.tool.d.ts +9 -4
  17. package/dist/mcp-server/tools/definitions/analyze-collection.tool.d.ts.map +1 -1
  18. package/dist/mcp-server/tools/definitions/analyze-collection.tool.js +42 -13
  19. package/dist/mcp-server/tools/definitions/analyze-collection.tool.js.map +1 -1
  20. package/dist/mcp-server/tools/definitions/compare-structures.tool.d.ts +6 -4
  21. package/dist/mcp-server/tools/definitions/compare-structures.tool.d.ts.map +1 -1
  22. package/dist/mcp-server/tools/definitions/compare-structures.tool.js +24 -7
  23. package/dist/mcp-server/tools/definitions/compare-structures.tool.js.map +1 -1
  24. package/dist/mcp-server/tools/definitions/get-annotations.tool.d.ts +1 -1
  25. package/dist/mcp-server/tools/definitions/get-structure.tool.d.ts +2 -2
  26. package/dist/mcp-server/tools/definitions/get-structure.tool.d.ts.map +1 -1
  27. package/dist/mcp-server/tools/definitions/get-structure.tool.js +30 -7
  28. package/dist/mcp-server/tools/definitions/get-structure.tool.js.map +1 -1
  29. package/dist/mcp-server/tools/definitions/search-structures.tool.d.ts +5 -3
  30. package/dist/mcp-server/tools/definitions/search-structures.tool.d.ts.map +1 -1
  31. package/dist/mcp-server/tools/definitions/search-structures.tool.js +22 -15
  32. package/dist/mcp-server/tools/definitions/search-structures.tool.js.map +1 -1
  33. package/dist/mcp-server/tools/definitions/track-ligands.tool.d.ts +2 -2
  34. package/dist/services/alignment/alignment-service.d.ts +7 -0
  35. package/dist/services/alignment/alignment-service.d.ts.map +1 -1
  36. package/dist/services/alignment/alignment-service.js +22 -3
  37. package/dist/services/alignment/alignment-service.js.map +1 -1
  38. package/dist/services/alphafold/alphafold-service.d.ts.map +1 -1
  39. package/dist/services/alphafold/alphafold-service.js +1 -0
  40. package/dist/services/alphafold/alphafold-service.js.map +1 -1
  41. package/dist/services/beacons/beacons-service.d.ts.map +1 -1
  42. package/dist/services/foldseek/foldseek-service.d.ts +1 -1
  43. package/dist/services/foldseek/foldseek-service.d.ts.map +1 -1
  44. package/dist/services/foldseek/foldseek-service.js +5 -1
  45. package/dist/services/foldseek/foldseek-service.js.map +1 -1
  46. package/dist/services/rcsb/facets.d.ts +19 -19
  47. package/dist/services/rcsb/facets.d.ts.map +1 -1
  48. package/dist/services/rcsb/rcsb-service.d.ts +2 -2
  49. package/dist/services/rcsb/rcsb-service.d.ts.map +1 -1
  50. package/dist/services/rcsb/rcsb-service.js +24 -4
  51. package/dist/services/rcsb/rcsb-service.js.map +1 -1
  52. package/dist/services/rcsb/types.d.ts +14 -3
  53. package/dist/services/rcsb/types.d.ts.map +1 -1
  54. package/dist/services/shared/attribution.d.ts +6 -3
  55. package/dist/services/shared/attribution.d.ts.map +1 -1
  56. package/dist/services/shared/attribution.js +12 -2
  57. package/dist/services/shared/attribution.js.map +1 -1
  58. package/dist/services/shared/http.d.ts +7 -2
  59. package/dist/services/shared/http.d.ts.map +1 -1
  60. package/dist/services/shared/http.js +8 -18
  61. package/dist/services/shared/http.js.map +1 -1
  62. package/dist/services/shared/identifiers.d.ts +7 -0
  63. package/dist/services/shared/identifiers.d.ts.map +1 -1
  64. package/dist/services/shared/identifiers.js +14 -1
  65. package/dist/services/shared/identifiers.js.map +1 -1
  66. package/dist/services/uniprot/uniprot-service.d.ts.map +1 -1
  67. package/dist/services/uniprot/uniprot-service.js +1 -0
  68. package/dist/services/uniprot/uniprot-service.js.map +1 -1
  69. package/package.json +11 -10
  70. package/server.json +3 -3
package/dist/services/shared/identifiers.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"identifiers.d.ts","sourceRoot":"","sources":["../../../src/services/shared/identifiers.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAQH,oEAAoE;AACpE,wBAAgB,kBAAkB,CAAC,KAAK,EAAE,MAAM,GAAG,OAAO,CAEzD;AAED,+DAA+D;AAC/D,wBAAgB,OAAO,CAAC,KAAK,EAAE,MAAM,GAAG,OAAO,CAE9C;AAED,6EAA6E;AAC7E,wBAAgB,SAAS,CAAC,UAAU,EAAE,MAAM,GAAG,MAAM,CAGpD"}
1
+ {"version":3,"file":"identifiers.d.ts","sourceRoot":"","sources":["../../../src/services/shared/identifiers.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAcH,oEAAoE;AACpE,wBAAgB,kBAAkB,CAAC,KAAK,EAAE,MAAM,GAAG,OAAO,CAEzD;AAED;;;;;GAKG;AACH,wBAAgB,kBAAkB,CAAC,KAAK,EAAE,MAAM,GAAG,OAAO,CAEzD;AAED,+DAA+D;AAC/D,wBAAgB,OAAO,CAAC,KAAK,EAAE,MAAM,GAAG,OAAO,CAE9C;AAED,6EAA6E;AAC7E,wBAAgB,SAAS,CAAC,UAAU,EAAE,MAAM,GAAG,MAAM,CAGpD"}
package/dist/services/shared/identifiers.js CHANGED
@@ -3,14 +3,27 @@
3
3
  * (PDB) and predicted (UniProt-keyed) halves of the federation. Pure, no I/O.
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  * @module services/shared/identifiers
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5
  */
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+ /** UniProt accession body (6- or 10-character forms), unanchored. */
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+ const UNIPROT_BODY = '(?:[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9](?:[A-Z][A-Z0-9]{2}[0-9]){1,2})';
6
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  /** UniProt accession pattern (6- or 10-character forms). */
7
- const UNIPROT_RE = /^(?:[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9](?:[A-Z][A-Z0-9]{2}[0-9]){1,2})$/i;
9
+ const UNIPROT_RE = new RegExp(`^${UNIPROT_BODY}$`, 'i');
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+ /** AlphaFold DB entry ID pattern: `AF-<accession>-F<fragment>` (e.g. AF-P69905-F1). */
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+ const AF_ENTRY_RE = new RegExp(`^AF-${UNIPROT_BODY}-F\\d+$`, 'i');
8
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  /** PDB entry ID pattern: 4 alphanumerics, first character a digit (e.g. 4HHB, 1IEP). */
9
13
  const PDB_RE = /^[0-9][A-Za-z0-9]{3}$/;
10
14
  /** True when `value` is a syntactically valid UniProt accession. */
11
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  export function isUniProtAccession(value) {
12
16
  return UNIPROT_RE.test(value.trim());
13
17
  }
18
+ /**
19
+ * True when `value` is an AlphaFold DB entry ID (`AF-P69905-F1`). Both AlphaFold's
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+ * prediction endpoint and 3D-Beacons accept this form alongside the bare accession,
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+ * and the `af://` resource emits it as `entryId`, so a caller can hand it straight
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+ * back to a predicted-source lookup.
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+ */
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+ export function isAlphaFoldEntryId(value) {
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+ return AF_ENTRY_RE.test(value.trim());
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+ }
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  /** True when `value` is a syntactically valid PDB entry ID. */
15
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  export function isPdbId(value) {
16
29
  return PDB_RE.test(value.trim());
package/dist/services/shared/identifiers.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"identifiers.js","sourceRoot":"","sources":["../../../src/services/shared/identifiers.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,4DAA4D;AAC5D,MAAM,UAAU,GAAG,+EAA+E,CAAC;AAEnG,wFAAwF;AACxF,MAAM,MAAM,GAAG,uBAAuB,CAAC;AAEvC,oEAAoE;AACpE,MAAM,UAAU,kBAAkB,CAAC,KAAa;IAC9C,OAAO,UAAU,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC,CAAC;AACvC,CAAC;AAED,+DAA+D;AAC/D,MAAM,UAAU,OAAO,CAAC,KAAa;IACnC,OAAO,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC,CAAC;AACnC,CAAC;AAED,6EAA6E;AAC7E,MAAM,UAAU,SAAS,CAAC,UAAkB;IAC1C,MAAM,IAAI,GAAG,UAAU,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,IAAI,UAAU,CAAC;IACvD,OAAO,IAAI,CAAC,WAAW,EAAE,CAAC;AAC5B,CAAC"}
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package/dist/services/uniprot/uniprot-service.d.ts.map CHANGED
@@ -1 +1 @@
1
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1
+ {"version":3,"file":"uniprot-service.d.ts","sourceRoot":"","sources":["../../../src/services/uniprot/uniprot-service.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,wBAAwB,CAAC;AACtD,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,+BAA+B,CAAC;AAE/D,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,gCAAgC,CAAC;AACrE,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,2BAA2B,CAAC;AAG9D,yCAAyC;AACzC,MAAM,MAAM,iBAAiB,GAAG,UAAU,GAAG,SAAS,GAAG,UAAU,GAAG,KAAK,CAAC;AAE5E,6EAA6E;AAC7E,MAAM,WAAW,eAAe;IAC9B,sDAAsD;IACtD,QAAQ,EAAE,SAAS,GAAG,SAAS,CAAC;IAChC,6BAA6B;IAC7B,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,6BAA6B;IAC7B,GAAG,CAAC,EAAE,MAAM,CAAC;IACb,+BAA+B;IAC/B,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,+EAA+E;IAC/E,IAAI,EAAE,MAAM,CAAC;CACd;AAED,gCAAgC;AAChC,MAAM,WAAW,YAAY;IAC3B,SAAS,EAAE,MAAM,CAAC;IAClB,QAAQ,EAAE,eAAe,EAAE,CAAC;IAC5B,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,SAAS,EAAE,MAAM,EAAE,CAAC;IACpB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,cAAc,CAAC,EAAE,MAAM,CAAC;IACxB,OAAO,CAAC,EAAE,MAAM,CAAC;CAClB;AAED,4BAA4B;AAC5B,MAAM,WAAW,MAAM;IACrB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,EAAE,EAAE,MAAM,CAAC;IACX,IAAI,EAAE,MAAM,CAAC;CACd;AAED,0DAA0D;AAC1D,MAAM,WAAW,aAAa;IAC5B,SAAS,EAAE,MAAM,CAAC;IAClB,OAAO,EAAE,MAAM,EAAE,CAAC;IAClB,eAAe,EAAE,MAAM,EAAE,CAAC;IAC1B,IAAI,EAAE,MAAM,CAAC;IACb,IAAI,EAAE,MAAM,CAAC;CACd;AAyBD,qBAAa,cAAc;IACzB,OAAO,CAAC,QAAQ,CAAC,WAAW,CAAS;IACrC,OAAO,CAAC,QAAQ,CAAC,YAAY,CAAS;IAEtC,YAAY,OAAO,EAAE,SAAS,EAAE,QAAQ,EAAE,cAAc,EAAE,YAAY,EAAE,YAAY,EAGnF;IAED,gFAAgF;IAC1E,QAAQ,CACZ,SAAS,EAAE,MAAM,EACjB,OAAO,EAAE,iBAAiB,EAC1B,GAAG,EAAE,OAAO,GACX,OAAO,CAAC,YAAY,CAAC,CAWvB;IAED,wEAAwE;IAClE,WAAW,CAAC,SAAS,EAAE,MAAM,EAAE,GAAG,EAAE,OAAO,GAAG,OAAO,CAAC,MAAM,GAAG,IAAI,CAAC,CAQzE;IAED,wEAAwE;IAClE,WAAW,CAAC,SAAS,EAAE,MAAM,EAAE,GAAG,EAAE,OAAO,GAAG,OAAO,CAAC,aAAa,EAAE,CAAC,CAmB3E;CACF;AA2FD,wBAAgB,kBAAkB,CAChC,MAAM,EAAE,SAAS,EACjB,OAAO,EAAE,cAAc,EACvB,YAAY,EAAE,YAAY,GACzB,IAAI,CAEN;AAED,wBAAgB,iBAAiB,IAAI,cAAc,CAIlD"}
package/dist/services/uniprot/uniprot-service.js CHANGED
@@ -70,6 +70,7 @@ export class UniProtService {
70
70
  operation: 'UniProtService.getInterPro',
71
71
  label: 'InterPro',
72
72
  baseDelayMs: 400,
73
+ expectedStatuses: [404],
73
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  });
74
75
  }
75
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  catch (err) {
package/dist/services/uniprot/uniprot-service.js.map CHANGED
@@ -1 +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": "0.4.0",
3
+ "version": "0.4.2",
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",
@@ -70,7 +70,7 @@
70
70
  "url": "https://github.com/cyanheads/protein-mcp-server/issues"
71
71
  },
72
72
  "homepage": "https://github.com/cyanheads/protein-mcp-server#readme",
73
- "author": "cyanheads <casey@caseyjhand.com> (https://github.com/cyanheads/protein-mcp-server#readme)",
73
+ "author": "Casey Hand <casey@caseyjhand.com> (https://caseyjhand.com)",
74
74
  "funding": [
75
75
  {
76
76
  "type": "github",
@@ -82,7 +82,7 @@
82
82
  }
83
83
  ],
84
84
  "license": "Apache-2.0",
85
- "packageManager": "bun@1.3.2",
85
+ "packageManager": "bun@1.3.14",
86
86
  "engines": {
87
87
  "bun": ">=1.3.0",
88
88
  "node": ">=24.0.0"
@@ -91,17 +91,18 @@
91
91
  "access": "public"
92
92
  },
93
93
  "dependencies": {
94
- "@cyanheads/mcp-ts-core": "^0.10.10",
94
+ "@cyanheads/mcp-ts-core": "^0.11.5",
95
95
  "pino-pretty": "^13.1.3",
96
96
  "zod": "^4.4.3"
97
97
  },
98
98
  "devDependencies": {
99
- "@biomejs/biome": "2.5.2",
100
- "@types/node": "26.1.0",
99
+ "@biomejs/biome": "2.5.8",
100
+ "@socketsecurity/bun-security-scanner": "^1.1.2",
101
+ "@types/node": "26.2.0",
101
102
  "depcheck": "^1.4.7",
102
- "ignore": "^7.0.5",
103
- "tsc-alias": "^1.8.17",
104
- "typescript": "^6.0.3",
105
- "vitest": "^4.1.9"
103
+ "ignore": "^7.0.6",
104
+ "tsc-alias": "^1.9.1",
105
+ "typescript": "^7.0.2",
106
+ "vitest": "^4.1.10"
106
107
  }
107
108
  }
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": "0.4.0",
9
+ "version": "0.4.2",
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": "0.4.0",
22
+ "version": "0.4.2",
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": "0.4.0",
51
+ "version": "0.4.2",
52
52
  "packageArguments": [
53
53
  {
54
54
  "type": "positional",