Mcule Tools

Configuration File: mcule_tools.json Tool Type: Local Tools Count: 4

This page contains all tools defined in the mcule_tools.json configuration file.

Available Tools

Mcule_get_compound (Type: MculeTool)

Get detailed compound information from Mcule by its Mcule ID. Returns SMILES, InChIKey, standard …

Mcule_get_compound tool specification

Tool Information:

  • Name: Mcule_get_compound

  • Type: MculeTool

  • Description: Get detailed compound information from Mcule by its Mcule ID. Returns SMILES, InChIKey, standard InChI, molecular formula, CAS numbers, stereo type, and molecular properties (molecular mass, LogP, H-bond donors/acceptors, rotatable bonds, polar surface area, Lipinski Rule-of-5 violations, ring count, heavy atoms, stereocenters). Use after Mcule_lookup_compound to get full chemical data. Public endpoint, no auth required (rate limit: 10/min).

Parameters:

  • operation (string) (required) Operation type

  • mcule_id (string) (required) Mcule compound identifier, e.g., MCULE-3199019536 (aspirin), MCULE-9475454445 (ibuprofen racemic)

Example Usage:

query = {
    "name": "Mcule_get_compound",
    "arguments": {
        "operation": "example_value",
        "mcule_id": "example_value"
    }
}
result = tu.run(query)

Mcule_get_database (Type: MculeTool)

Get detailed information for a specific Mcule compound database file by its ID. Returns database …

Mcule_get_database tool specification

Tool Information:

  • Name: Mcule_get_database

  • Type: MculeTool

  • Description: Get detailed information for a specific Mcule compound database file by its ID. Returns database name, description, entry count, last updated date, and download file links with checksums. Known database IDs: 1 (Mcule Full, 139M+ compounds), 2 (Mcule In Stock, 7M+), 15 (Building Blocks, 6.4M+), 3 (Known Stock Amounts, 4.4M+), 16 (Virtual, 132M+). Public endpoint, no auth required.

Parameters:

  • operation (string) (required) Operation type

  • database_id (integer) (required) Database file ID. Known IDs: 1 (Full), 2 (In Stock), 15 (Building Blocks), 3 (Known Stock Amounts), 16 (Virtual)

Example Usage:

query = {
    "name": "Mcule_get_database",
    "arguments": {
        "operation": "example_value",
        "database_id": 10
    }
}
result = tu.run(query)

Mcule_list_databases (Type: MculeTool)

List available compound database files from Mcule for bulk download. Mcule provides pre-built dat…

Mcule_list_databases tool specification

Tool Information:

  • Name: Mcule_list_databases

  • Type: MculeTool

  • Description: List available compound database files from Mcule for bulk download. Mcule provides pre-built databases of purchasable compounds including: Full (139M+ entries), In Stock (7M+), Building Blocks (6.4M+), Virtual (132M+), Known Stock Amounts, Bioactive, and more. Returns database names, descriptions, entry counts, last updated dates, and download links (SDF.gz and SMILES.gz formats). Useful for setting up local compound databases for virtual screening. Public endpoint, no auth required.

Parameters:

  • operation (string) (required) Operation type

  • public_only ([‘boolean’, ‘null’]) (optional) If true (default), only return publicly accessible databases

Example Usage:

query = {
    "name": "Mcule_list_databases",
    "arguments": {
        "operation": "example_value"
    }
}
result = tu.run(query)

Mcule_lookup_compound (Type: MculeTool)

Look up purchasable compounds on Mcule by SMILES, InChIKey, or Mcule ID. Mcule aggregates 30M+ co…

Mcule_lookup_compound tool specification

Tool Information:

  • Name: Mcule_lookup_compound

  • Type: MculeTool

  • Description: Look up purchasable compounds on Mcule by SMILES, InChIKey, or Mcule ID. Mcule aggregates 30M+ compounds from multiple chemical suppliers. Returns matching Mcule IDs and SMILES structures. Accepts any chemical identifier: SMILES string (e.g., CC(=O)Oc1ccccc1C(=O)O for aspirin), InChIKey (e.g., BSYNRYMUTXBXSQ-UHFFFAOYSA-N), or Mcule ID (e.g., MCULE-3199019536). Use this as the first step to find a compound’s Mcule ID, then use Mcule_get_compound for full details. Public endpoint, no auth required (rate limit: 10/min).

Parameters:

  • operation (string) (required) Operation type

  • query (string) (required) Chemical identifier to look up: SMILES string, InChIKey, or Mcule ID (e.g., CC(=O)Oc1ccccc1C(=O)O, BSYNRYMUTXBXSQ-UHFFFAOYSA-N, or MCULE-3199019536)

Example Usage:

query = {
    "name": "Mcule_lookup_compound",
    "arguments": {
        "operation": "example_value",
        "query": "example_value"
    }
}
result = tu.run(query)