chemSearch/.mcp_config.json at main · Robaina/chemSearch · GitHub

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{
  "name": "chemsearch",
  "description": "ChemSearch MCP Server - Query genomes for chemical synthetic potential",
  "version": "1.0.0",
  "author": "Semidán Robaina Estévez",
  "license": "GPL-3.0",

  "server": {
    "command": "python",
    "args": ["mcp_server.py"],
    "env": {
      "PYTHONPATH": "./src"
    }
  },

  "capabilities": {
    "resources": {
      "provides": ["chemsearch://database-info"]
    },
    "tools": {
      "provides": [
        "search_compounds_by_smiles",
        "search_compounds_by_chebi_ids",
        "get_database_info"
      ]
    }
  },

  "data_requirements": {
    "description": "ChemSearch requires preprocessed biochemical databases",
    "required_files": [
      "tests/data/rhea-compounds.tsv",
      "tests/data/rhea_fingerprints.h5"
    ],
    "optional_files": [
      "data/compound_ec_database_plus_rhea.tsv",
      "data/genomes_ec/*.tsv"
    ]
  },

  "usage_examples": [
    {
      "description": "Search for organisms that can synthesize caffeine",
      "tool": "search_compounds_by_smiles",
      "parameters": {
        "smiles": ["CN1C=NC2=C1C(=O)N(C(=O)N2C)C"],
        "threshold": 0.7
      }
    },
    {
      "description": "Find genomes with potential to produce glucose",
      "tool": "search_compounds_by_chebi_ids",
      "parameters": {
        "chebi_ids": ["CHEBI:17634"],
        "include_similar_structures": true
      }
    }
  ]
}