@cyanheads/protein-mcp-server 0.8.4 → 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 (35) hide show
  1. package/AGENTS.md +15 -18
  2. package/CLAUDE.md +15 -18
  3. package/Dockerfile +92 -36
  4. package/README.md +75 -90
  5. package/changelog/0.8.x/0.8.5.md +16 -0
  6. package/changelog/0.8.x/0.8.6.md +22 -0
  7. package/dist/mcp-server/tools/definitions/analyze-collection.tool.d.ts.map +1 -1
  8. package/dist/mcp-server/tools/definitions/analyze-collection.tool.js +2 -2
  9. package/dist/mcp-server/tools/definitions/analyze-collection.tool.js.map +1 -1
  10. package/dist/mcp-server/tools/definitions/compare-structures.tool.d.ts.map +1 -1
  11. package/dist/mcp-server/tools/definitions/compare-structures.tool.js +3 -5
  12. package/dist/mcp-server/tools/definitions/compare-structures.tool.js.map +1 -1
  13. package/dist/mcp-server/tools/definitions/find-similar.tool.js +5 -7
  14. package/dist/mcp-server/tools/definitions/find-similar.tool.js.map +1 -1
  15. package/dist/mcp-server/tools/definitions/get-annotations.tool.d.ts.map +1 -1
  16. package/dist/mcp-server/tools/definitions/get-annotations.tool.js +4 -10
  17. package/dist/mcp-server/tools/definitions/get-annotations.tool.js.map +1 -1
  18. package/dist/mcp-server/tools/definitions/get-structure.tool.d.ts.map +1 -1
  19. package/dist/mcp-server/tools/definitions/get-structure.tool.js +3 -3
  20. package/dist/mcp-server/tools/definitions/get-structure.tool.js.map +1 -1
  21. package/dist/mcp-server/tools/definitions/search-structures.tool.d.ts.map +1 -1
  22. package/dist/mcp-server/tools/definitions/search-structures.tool.js +3 -5
  23. package/dist/mcp-server/tools/definitions/search-structures.tool.js.map +1 -1
  24. package/dist/mcp-server/tools/definitions/track-ligands.tool.d.ts +4 -0
  25. package/dist/mcp-server/tools/definitions/track-ligands.tool.d.ts.map +1 -1
  26. package/dist/mcp-server/tools/definitions/track-ligands.tool.js +78 -31
  27. package/dist/mcp-server/tools/definitions/track-ligands.tool.js.map +1 -1
  28. package/dist/services/rcsb/rcsb-service.d.ts +13 -3
  29. package/dist/services/rcsb/rcsb-service.d.ts.map +1 -1
  30. package/dist/services/rcsb/rcsb-service.js +50 -12
  31. package/dist/services/rcsb/rcsb-service.js.map +1 -1
  32. package/dist/services/rcsb/types.d.ts +22 -4
  33. package/dist/services/rcsb/types.d.ts.map +1 -1
  34. package/package.json +10 -9
  35. package/server.json +10 -24
package/package.json CHANGED
@@ -1,6 +1,6 @@
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  {
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  "name": "@cyanheads/protein-mcp-server",
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- "version": "0.8.4",
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+ "version": "0.8.6",
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  "mcpName": "io.github.cyanheads/protein-mcp-server",
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  "description": "Federated protein structure & annotation across experimental (PDB) and predicted (AlphaFold) models via MCP. STDIO or Streamable HTTP.",
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  "type": "module",
@@ -12,6 +12,7 @@
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  "files": [
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  "changelog/",
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  "dist/",
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+ "!dist/*.mcpb",
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  "README.md",
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  "LICENSE",
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  "CLAUDE.md",
@@ -83,7 +84,7 @@
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  }
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  ],
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  "license": "Apache-2.0",
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- "packageManager": "bun@1.4.0",
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+ "packageManager": "bun@1.4.2",
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  "engines": {
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  "bun": ">=1.4.0",
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  "node": ">=24.0.0"
@@ -92,18 +93,18 @@
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  "access": "public"
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  },
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  "dependencies": {
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- "@cyanheads/mcp-ts-core": "^0.13.6",
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+ "@cyanheads/mcp-ts-core": "^0.13.13",
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  "pino-pretty": "^13.1.3",
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  "zod": "^4.6.5"
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  },
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  "devDependencies": {
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- "@biomejs/biome": "2.5.14",
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- "@socketsecurity/bun-security-scanner": "^1.1.2",
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- "@types/node": "26.6.2",
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+ "@biomejs/biome": "2.5.15",
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+ "@socketsecurity/bun-security-scanner": "^1.1.3",
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+ "@types/node": "26.6.4",
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  "depcheck": "^1.4.7",
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- "ignore": "^7.0.9",
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- "tsc-alias": "^1.9.5",
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+ "ignore": "^7.0.12",
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+ "tsc-alias": "^1.9.7",
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  "typescript": "^7.0.2",
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- "vitest": "^5.0.1"
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+ "vitest": "^5.0.3"
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  }
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  }
package/server.json CHANGED
@@ -6,7 +6,7 @@
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  "url": "https://github.com/cyanheads/protein-mcp-server",
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  "source": "github"
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  },
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- "version": "0.8.4",
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+ "version": "0.8.6",
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  "remotes": [
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  {
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  "type": "streamable-http",
@@ -18,18 +18,8 @@
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  "registryType": "npm",
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  "registryBaseUrl": "https://registry.npmjs.org",
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  "identifier": "@cyanheads/protein-mcp-server",
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- "runtimeHint": "node",
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- "version": "0.8.4",
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- "packageArguments": [
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- {
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- "type": "positional",
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- "value": "run"
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- },
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- {
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- "type": "positional",
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- "value": "start:stdio"
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- }
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- ],
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+ "runtimeHint": "npx",
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+ "version": "0.8.6",
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  "environmentVariables": [
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  {
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  "name": "MCP_LOG_LEVEL",
@@ -47,19 +37,15 @@
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  "registryType": "npm",
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  "registryBaseUrl": "https://registry.npmjs.org",
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  "identifier": "@cyanheads/protein-mcp-server",
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- "runtimeHint": "node",
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- "version": "0.8.4",
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- "packageArguments": [
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+ "runtimeHint": "npx",
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+ "version": "0.8.6",
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+ "environmentVariables": [
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  {
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- "type": "positional",
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- "value": "run"
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+ "name": "MCP_TRANSPORT_TYPE",
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+ "description": "Selects the HTTP transport.",
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+ "format": "string",
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+ "value": "http"
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  },
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- {
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- "type": "positional",
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- "value": "start:http"
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- }
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- ],
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- "environmentVariables": [
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  {
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  "name": "MCP_HTTP_HOST",
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  "description": "The hostname for the HTTP server.",