Zinc Tools

Configuration File: zinc_tools.json Tool Type: Local Tools Count: 5

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

Available Tools

ZINC_get_compound (Type: ZincTool)

Get detailed information for a ZINC compound by its ID, including SMILES structure, molecular pro…

ZINC_get_compound tool specification

Tool Information:

  • Name: ZINC_get_compound

  • Type: ZincTool

  • Description: Get detailed information for a ZINC compound by its ID, including SMILES structure, molecular properties (MW, LogP, HBD, HBA, rotatable bonds), and vendor/catalog availability. Returns the list of vendors with purchasability tiers and the best available tier. Use after ZINC_search_compounds to get full details.

Parameters:

  • operation (string) (required) Operation type

  • zinc_id (string) (required) ZINC compound identifier, e.g., ZINC000000000053 (aspirin), ZINC000000001084 (caffeine), ZINC000000113398 (ibuprofen)

Example Usage:

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

ZINC_get_purchasable (Type: ZincTool)

Browse ZINC compounds by purchasability tier. Returns compounds available at a specific availabil…

ZINC_get_purchasable tool specification

Tool Information:

  • Name: ZINC_get_purchasable

  • Type: ZincTool

  • Description: Browse ZINC compounds by purchasability tier. Returns compounds available at a specific availability level with SMILES and molecular properties. Tiers: in-stock (ready to ship), for-sale (from vendor), on-demand (custom synthesis), agent (via broker), world (all purchasable), fda (FDA-approved). Use to find readily available compounds for screening.

Parameters:

  • operation (string) (required) Operation type

  • tier (string) (required) Purchasability tier. in-stock = ready to ship, for-sale = from vendor, on-demand = custom synthesis, agent = via broker, world = all purchasable, fda = FDA-approved drugs

  • count (integer) (optional) Maximum number of results (default: 10, max: 100)

Example Usage:

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

ZINC_search_by_properties (Type: ZincTool)

Filter ZINC compounds by molecular properties (Lipinski Rule of Five, Veber rules). Specify range…

ZINC_search_by_properties tool specification

Tool Information:

  • Name: ZINC_search_by_properties

  • Type: ZincTool

  • Description: Filter ZINC compounds by molecular properties (Lipinski Rule of Five, Veber rules). Specify ranges for molecular weight, LogP, hydrogen bond donors/acceptors, and rotatable bonds. Optionally restrict to a purchasability tier. Useful for finding drug-like compounds: Lipinski (MW<500, LogP<5, HBD<5, HBA<10), fragment-like (MW<250, LogP<3), or lead-like (MW 250-350, LogP 1-3).

Parameters:

  • operation (string) (required) Operation type

  • mwt_min ([‘number’, ‘null’]) (optional) Minimum molecular weight in Da (e.g., 150 for fragments, 250 for leads)

  • mwt_max ([‘number’, ‘null’]) (optional) Maximum molecular weight in Da (e.g., 500 for Lipinski, 250 for fragments)

  • logp_min ([‘number’, ‘null’]) (optional) Minimum LogP (e.g., -1 for hydrophilic compounds)

  • logp_max ([‘number’, ‘null’]) (optional) Maximum LogP (e.g., 5 for Lipinski rule, 3 for lead-like)

  • hbd_max ([‘integer’, ‘null’]) (optional) Maximum hydrogen bond donors (e.g., 5 for Lipinski)

  • hba_max ([‘integer’, ‘null’]) (optional) Maximum hydrogen bond acceptors (e.g., 10 for Lipinski)

  • rb_max ([‘integer’, ‘null’]) (optional) Maximum rotatable bonds (e.g., 10 for Veber rule)

  • purchasability ([‘string’, ‘null’]) (optional) Restrict to a purchasability tier

  • count (integer) (optional) Maximum number of results (default: 20, max: 100)

Example Usage:

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

ZINC_search_by_smiles (Type: ZincTool)

Search the ZINC database by SMILES structure string. Finds exact or similar compounds matching th…

ZINC_search_by_smiles tool specification

Tool Information:

  • Name: ZINC_search_by_smiles

  • Type: ZincTool

  • Description: Search the ZINC database by SMILES structure string. Finds exact or similar compounds matching the given SMILES. Useful for finding purchasable analogs of a lead compound or checking if a specific structure is commercially available. Returns ZINC IDs, SMILES, and molecular properties.

Parameters:

  • operation (string) (required) Operation type

  • smiles (string) (required) SMILES string to search for. Examples: CC(=O)Oc1ccccc1C(=O)O (aspirin), Cn1c(=O)c2c(ncn2C)n(C)c1=O (caffeine), c1ccccc1 (benzene)

  • count (integer) (optional) Maximum number of results (default: 10, max: 100)

Example Usage:

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

ZINC_search_compounds (Type: ZincTool)

Search the ZINC database for commercially available compounds by name or keyword. Returns ZINC ID…

ZINC_search_compounds tool specification

Tool Information:

  • Name: ZINC_search_compounds

  • Type: ZincTool

  • Description: Search the ZINC database for commercially available compounds by name or keyword. Returns ZINC IDs, SMILES structures, and molecular properties (MW, LogP, HBD, HBA, rotatable bonds). ZINC contains 750M+ purchasable compounds for virtual screening and drug discovery. Optionally filter by purchasability tier (in-stock, for-sale, on-demand, agent). Use this as the first step in a virtual screening workflow.

Parameters:

  • operation (string) (required) Operation type

  • query (string) (required) Search query: drug name (aspirin, ibuprofen, metformin), keyword, or partial name

  • count (integer) (optional) Maximum number of results to return (default: 10, max: 100)

  • purchasability ([‘string’, ‘null’]) (optional) Filter by purchasability tier. in-stock = ready to ship, for-sale = from vendor, on-demand = custom synthesis, agent = via broker

Example Usage:

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