@cyanheads/protein-mcp-server 0.1.0

package/package.json

@@ -0,0 +1,106 @@
+{
+  "name": "@cyanheads/protein-mcp-server",
+  "version": "0.1.0",
+  "mcpName": "io.github.cyanheads/protein-mcp-server",
+  "description": "Federated protein structure & function across experimental (PDB) and predicted (AlphaFold) models.",
+  "type": "module",
+  "main": "dist/index.js",
+  "types": "dist/index.d.ts",
+  "bin": {
+    "protein-mcp-server": "dist/index.js"
+  },
+  "files": [
+    "changelog/",
+    "dist/",
+    "README.md",
+    "LICENSE",
+    "CLAUDE.md",
+    "AGENTS.md",
+    "Dockerfile",
+    "server.json"
+  ],
+  "scripts": {
+    "build": "bun run scripts/build.ts",
+    "rebuild": "bun run scripts/clean.ts && bun run scripts/build.ts",
+    "clean": "bun run scripts/clean.ts",
+    "devcheck": "bun run scripts/devcheck.ts",
+    "audit:refresh": "rm -f bun.lock && bun install && bun audit",
+    "tree": "bun run scripts/tree.ts",
+    "list-skills": "bun run scripts/list-skills.ts",
+    "format": "biome check --write .",
+    "format:unsafe": "biome check --write --unsafe .",
+    "lint:mcp": "bun run scripts/lint-mcp.ts",
+    "lint:packaging": "bun run scripts/lint-packaging.ts",
+    "bundle": "bun run build && npx -y @anthropic-ai/mcpb pack . dist/protein-mcp-server.mcpb && bun run scripts/clean-mcpb.ts dist/protein-mcp-server.mcpb",
+    "changelog:build": "bun run scripts/build-changelog.ts",
+    "changelog:check": "bun run scripts/build-changelog.ts --check",
+    "release:github": "bun run scripts/release-github.ts",
+    "test": "vitest run",
+    "start": "node dist/index.js",
+    "start:stdio": "MCP_TRANSPORT_TYPE=stdio node dist/index.js",
+    "start:http": "MCP_TRANSPORT_TYPE=http node dist/index.js"
+  },
+  "keywords": [
+    "protein",
+    "protein-structure",
+    "structural-biology",
+    "pdb",
+    "alphafold",
+    "uniprot",
+    "interpro",
+    "foldseek",
+    "rcsb",
+    "bioinformatics",
+    "drug-discovery",
+    "mcp",
+    "mcp-server",
+    "model-context-protocol",
+    "typescript",
+    "bun",
+    "stdio",
+    "streamable-http",
+    "ai-agent"
+  ],
+  "repository": {
+    "type": "git",
+    "url": "git+https://github.com/cyanheads/protein-mcp-server.git"
+  },
+  "bugs": {
+    "url": "https://github.com/cyanheads/protein-mcp-server/issues"
+  },
+  "homepage": "https://github.com/cyanheads/protein-mcp-server#readme",
+  "author": "cyanheads <casey@caseyjhand.com> (https://github.com/cyanheads/protein-mcp-server#readme)",
+  "funding": [
+    {
+      "type": "github",
+      "url": "https://github.com/sponsors/cyanheads"
+    },
+    {
+      "type": "buy_me_a_coffee",
+      "url": "https://www.buymeacoffee.com/cyanheads"
+    }
+  ],
+  "license": "Apache-2.0",
+  "packageManager": "bun@1.3.2",
+  "engines": {
+    "bun": ">=1.3.0",
+    "node": ">=24.0.0"
+  },
+  "publishConfig": {
+    "access": "public"
+  },
+  "dependencies": {
+    "@cyanheads/mcp-ts-core": "^0.10.6",
+    "pino-pretty": "^13.1.3",
+    "zod": "^4.4.3"
+  },
+  "devDependencies": {
+    "@biomejs/biome": "2.5.0",
+    "@types/node": "25.9.3",
+    "depcheck": "^1.4.7",
+    "ignore": "^7.0.5",
+    "tsc-alias": "^1.8.17",
+    "typescript": "^6.0.3",
+    "vitest": "^4.1.9"
+  }
+}

package/server.json

@@ -0,0 +1,99 @@
+{
+  "$schema": "https://static.modelcontextprotocol.io/schemas/2025-12-11/server.schema.json",
+  "name": "io.github.cyanheads/protein-mcp-server",
+  "description": "Federated protein structure & function across experimental (PDB) and predicted (AlphaFold) models.",
+  "repository": {
+    "url": "https://github.com/cyanheads/protein-mcp-server",
+    "source": "github"
+  },
+  "version": "0.1.0",
+  "packages": [
+    {
+      "registryType": "npm",
+      "registryBaseUrl": "https://registry.npmjs.org",
+      "identifier": "@cyanheads/protein-mcp-server",
+      "runtimeHint": "node",
+      "version": "0.1.0",
+      "packageArguments": [
+        {
+          "type": "positional",
+          "value": "run"
+        },
+        {
+          "type": "positional",
+          "value": "start:stdio"
+        }
+      ],
+      "environmentVariables": [
+        {
+          "name": "MCP_LOG_LEVEL",
+          "description": "Sets the minimum log level for output (e.g., 'debug', 'info', 'warn').",
+          "format": "string",
+          "isRequired": false,
+          "default": "info"
+        }
+      ],
+      "transport": {
+        "type": "stdio"
+      }
+    },
+    {
+      "registryType": "npm",
+      "registryBaseUrl": "https://registry.npmjs.org",
+      "identifier": "@cyanheads/protein-mcp-server",
+      "runtimeHint": "node",
+      "version": "0.1.0",
+      "packageArguments": [
+        {
+          "type": "positional",
+          "value": "run"
+        },
+        {
+          "type": "positional",
+          "value": "start:http"
+        }
+      ],
+      "environmentVariables": [
+        {
+          "name": "MCP_HTTP_HOST",
+          "description": "The hostname for the HTTP server.",
+          "format": "string",
+          "isRequired": false,
+          "default": "127.0.0.1"
+        },
+        {
+          "name": "MCP_HTTP_PORT",
+          "description": "The port to run the HTTP server on.",
+          "format": "string",
+          "isRequired": false,
+          "default": "3010"
+        },
+        {
+          "name": "MCP_HTTP_ENDPOINT_PATH",
+          "description": "The endpoint path for the MCP server.",
+          "format": "string",
+          "isRequired": false,
+          "default": "/mcp"
+        },
+        {
+          "name": "MCP_AUTH_MODE",
+          "description": "Authentication mode to use: 'none', 'jwt', or 'oauth'.",
+          "format": "string",
+          "isRequired": false,
+          "default": "none"
+        },
+        {
+          "name": "MCP_LOG_LEVEL",
+          "description": "Sets the minimum log level for output (e.g., 'debug', 'info', 'warn').",
+          "format": "string",
+          "isRequired": false,
+          "default": "info"
+        }
+      ],
+      "transport": {
+        "type": "streamable-http",
+        "url": "http://localhost:3010/mcp"
+      }
+    }
+  ]
+}