Rdkit Cheminfo Tools

Configuration File: rdkit_cheminfo_tools.json Tool Type: Local Tools Count: 2

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

Available Tools

RDKit_matched_molecular_pair (Type: RDKitCheminfoTool)

Find the Matched Molecular Pair (MMP) transformation between two SMILES compounds using the Hussa…

RDKit_matched_molecular_pair tool specification

Tool Information:

  • Name: RDKit_matched_molecular_pair

  • Type: RDKitCheminfoTool

  • Description: Find the Matched Molecular Pair (MMP) transformation between two SMILES compounds using the Hussain-Rea single-cut fragmentation algorithm (rdMMPA). Identifies the maximal common core scaffold and the side-chain substituents that differ between compound A and compound B. Returns: common core SMILES, side-chain A, side-chain B, transformation string (sidechain_A → sidechain_B), Tanimoto similarity (Morgan r=2), and property deltas (ΔMW, ΔcLogP, ΔHBD, ΔHBA, ΔTPSA). Essential for SAR analysis: understand what structural change caused a property improvement or potency shift.

Parameters:

  • smiles_a (string) (required) SMILES of compound A (reference/starting compound). Example: ‘CC(=O)Nc1ccc(O)cc1’ (paracetamol).

  • smiles_b (string) (required) SMILES of compound B (analog/modified compound). Example: ‘CC(=O)Nc1ccc(F)cc1’ (fluorine analog of paracetamol).

Example Usage:

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

RDKit_pharmacophore_features (Type: RDKitCheminfoTool)

Extract pharmacophore feature centers from a SMILES string using RDKit SMARTS matching. Identifie…

RDKit_pharmacophore_features tool specification

Tool Information:

  • Name: RDKit_pharmacophore_features

  • Type: RDKitCheminfoTool

  • Description: Extract pharmacophore feature centers from a SMILES string using RDKit SMARTS matching. Identifies and counts 6 pharmacophore feature types: HBD (hydrogen bond donors), HBA (hydrogen bond acceptors), Aromatic (aromatic atoms), Hydrophobic (hydrophobic atoms), PosIonizable (positively ionizable groups like amines), NegIonizable (negatively ionizable groups like carboxylates). Optionally generates 3D feature center coordinates using MMFF conformer optimization. Use to characterize compound binding hypotheses, compare pharmacophore profiles between hits, or guide scaffold decoration in drug design.

Parameters:

  • smiles (string) (required) SMILES string of the molecule. Examples: ‘CC(=O)Oc1ccccc1C(=O)O’ (aspirin), ‘c1ccc(cc1)C(=N)N’ (benzamidine, has PosIonizable + HBD).

  • include_features ([‘array’, ‘null’]) (optional) List of feature types to extract (default: all). Options: ‘HBD’, ‘HBA’, ‘Aromatic’, ‘Hydrophobic’, ‘PosIonizable’, ‘NegIonizable’.

Example Usage:

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