Lotus Tools

Configuration File: lotus_tools.json Tool Type: Local Tools Count: 3

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

Available Tools

LOTUS_get_compound (Type: BaseRESTTool)

Get detailed information about a specific natural product from LOTUS by its internal compound ID….

LOTUS_get_compound tool specification

Tool Information:

  • Name: LOTUS_get_compound

  • Type: BaseRESTTool

  • Description: Get detailed information about a specific natural product from LOTUS by its internal compound ID. Returns comprehensive data including structure (SMILES, InChI), molecular properties (weight, formula, LogP, PSA), drug-likeness metrics (Lipinski violations, H-bond donors/acceptors), chemical taxonomy (NPClassifier and ClassyFire classifications), and source organism data. Use LOTUS_search_natural_products to find the compound ID first.

Parameters:

  • compound_id (string) (required) LOTUS internal compound ID (MongoDB ObjectId, e.g., ‘604b8da112e4996162764b83’ for caffeine). Obtain from LOTUS_search_natural_products.

Example Usage:

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

LOTUS_search_by_inchikey (Type: BaseRESTTool)

Search the LOTUS natural products database specifically by InChIKey, which provides exact structu…

LOTUS_search_by_inchikey tool specification

Tool Information:

  • Name: LOTUS_search_by_inchikey

  • Type: BaseRESTTool

  • Description: Search the LOTUS natural products database specifically by InChIKey, which provides exact structural matching. InChIKey is a 27-character hash that uniquely identifies a chemical structure. This is the most precise way to look up a natural product in LOTUS. Returns the same results as LOTUS_search_natural_products but is optimized for InChIKey lookups.

Parameters:

  • inchikey (string) (required) InChIKey to search for (e.g., ‘RYYVLZVUVIJVGH-UHFFFAOYSA-N’ for caffeine, ‘IQBMWEYFKNVACH-MEBVLIOMSA-N’ for quercetin)

Example Usage:

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

LOTUS_search_natural_products (Type: BaseRESTTool)

Search the LOTUS (naturaL prOducTs occUrrenceS) database for natural products by name, SMILES, or…

LOTUS_search_natural_products tool specification

Tool Information:

  • Name: LOTUS_search_natural_products

  • Type: BaseRESTTool

  • Description: Search the LOTUS (naturaL prOducTs occUrrenceS) database for natural products by name, SMILES, or InChIKey. LOTUS is the largest open natural products database, containing 750,000+ structure-organism pairs from 35,000+ references. Returns compound IDs, structures (SMILES, InChI), molecular properties, and chemical taxonomy classifications. Supports searching by common name (e.g., ‘caffeine’), SMILES string, or InChIKey.

Parameters:

  • query (string) (required) Search query: compound name (e.g., ‘caffeine’, ‘quercetin’), SMILES string, or InChIKey

Example Usage:

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