{"$schema":"https://wellknown.network/schemas/agent-record-v1.json","schemaVersion":"1","id":"ag_kpnzqc4yncbq","handle":"iflow-mcp-chatmol-molecule-mcp","url":"https://wellknown.network/agents/iflow-mcp-chatmol-molecule-mcp","links":{"self":"https://wellknown.network/agents/iflow-mcp-chatmol-molecule-mcp/record.json","html":"https://wellknown.network/agents/iflow-mcp-chatmol-molecule-mcp","markdown":"https://wellknown.network/agents/iflow-mcp-chatmol-molecule-mcp/record.md","api":"https://wellknown.network/api/v1/agents/iflow-mcp-chatmol-molecule-mcp","status":"https://wellknown.network/api/v1/agents/iflow-mcp-chatmol-molecule-mcp/status","claim":"https://wellknown.network/agents/iflow-mcp-chatmol-molecule-mcp/claim","claimApi":"https://wellknown.network/api/v1/claims","claimDescriptor":"https://wellknown.network/agents/iflow-mcp-chatmol-molecule-mcp/claim.json","badge":"https://wellknown.network/agents/iflow-mcp-chatmol-molecule-mcp/badge.svg","openapi":"https://wellknown.network/openapi.json","history":"https://wellknown.network/api/v1/agents/iflow-mcp-chatmol-molecule-mcp/history","tools":"https://wellknown.network/api/v1/agents/iflow-mcp-chatmol-molecule-mcp/tools"},"ard":{"identifier":"urn:air::server:iflow-mcp-chatmol-molecule-mcp","type":"application/mcp-server-card+json"},"kind":"mcp_server","declared":{"name":"iflow-mcp_chatmol-molecule-mcp","summary":"Molecule-MCP: A Model Context Protocol server for molecules","description":"# Molecule-MCP\n**Molecule-MCP**: A model-context-protocol server for molecules.\nMolecule-MCP connects molecule science releated tools to Claude AI through the Model Context Protocol (MCP), allowing Claude to **directly interact with and control these tools and act as a co-scientist**. This integration enables prompt assisted molecule modeling.\n\n![Molecule MCP](./assets/chimerax.jpg)\n\n## Installation\n⚠️ **Note**: Molecule-MCP requires Claude Desktop to be installed and running.\n1. Go to Claude > Settings > Developer > Edit Config > claude_desktop_config.json to include the following:\n```json\n{\n  \"mcpServers\": {\n    \"pymol\": {\n      \"command\": \"/path/to/mcp\",\n      \"args\": [\n        \"run\",\n        \"/path/to/molecule-mcp/pymol_server.py\"\n      ]\n    },\n    \"chimerax\": {\n      \"command\": \"/path/to/mcp\",\n      \"args\": [\n        \"run\",\n        \"/path/to/molecule-mcp/ChimeraX_server.py\"\n      ]\n    },\n    \"gromacs_copilot\": {\n      \"command\": \"/path/to/mcp\",\n      \"args\": [\n        \"run\",\n        \"/path/to/molecule-mcp/mcp_server.py\"\n      ]\n    }\n  }\n}\n```\n2. Install mcp and get the script\n```bash\npip install \"mcp[cli]\" chatmol\npip install git+https://github.com/ChatMol/gromacs_copilot.git # optional, for running gromacs_copilot\nwhich mcp\n```\nthe path to mcp will be displayed. Copy this path for the next step and replace `/path/to/mcp` with the path to mcp.\n```\ngit clone https://github.com/ChatMol/molecule-mcp.git\ncd molecule-mcp\npwd\n```\nthe path to molecule-mcp will be displayed. Copy this path for the next step and replace `/path/to/molecule-mcp` with the path to molecule-mcp.\n\n## Disclaimer\nMolecule-MCP is provided \"as is\" without warranty of any kind, express or implied. The authors and contributors disclaim all warranties including, but not limited to, the implied warranties of merchantability and fitness for a particular purpose. Users employ this software at their own risk.\n\nThe authors bear no responsibility for any consequences arising from the use, misuse, or m…","publisher":null,"homepage":null,"repository":null,"version":"0.1.0","license":null,"protocols":["mcp"],"tags":["mcp"],"pricing":null,"endpoints":[{"url":"pypi:iflow-mcp_chatmol-molecule-mcp","type":"package_pypi","auth":null,"probeable":false}],"skills":null,"tools":null,"extra":null,"attribution":{"kind":"pypi","name":"pypi","summary":"pypi","version":"pypi","description":"pypi"}},"derived":{"capabilities":[{"slug":"dev.version-control","name":"Version Control","confidence":0.745,"provenance":"derived"}],"categories":["dev"],"language":"en"},"observed":{"status":"unknown","statusReason":"Distributed as a package to run locally; no network endpoint to check.","lastOkAt":null,"lastProbedAt":null,"statusComputedAt":null,"reliability30d":null,"latestObservations":[],"tools":null,"package":{"name":"iflow-mcp_chatmol-molecule-mcp","registry":"pypi","observedAt":"2026-09-15T17:23:10.295Z","publishedAt":"2026-02-08T01:27:16.425078Z","latestVersion":"0.1.0"},"toolSurface":null,"endpointFacts":[]},"verification":{"claimed":false,"claimedAt":null,"proofs":[]},"provenance":{"sources":[{"source":"pypi","key":"iflow-mcp_chatmol-molecule-mcp","url":"https://pypi.org/project/iflow-mcp_chatmol-molecule-mcp/","firstSeenAt":"2026-09-09T18:21:10.141Z","fetchedAt":"2026-09-15T17:21:44.018Z","normalizedAt":"2026-09-15T17:21:44.018Z"}]},"firstSeenAt":"2026-09-09T18:21:10.141Z","updatedAt":"2026-09-15T17:23:10.295Z"}