RDKit Pharmacophore Features

Overview

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.

Status

The most recent probe succeeded. Safe to call from the agent today.

Last probed

1d ago

Last success

1d ago

Last latency

85ms

Schema

JSON Schema the agent (or your API call) must match.

{
  "properties": {
    "include_features": {
      "description": "List of feature types to extract (default: all). Options: 'HBD', 'HBA', 'Aromatic', 'Hydrophobic', 'PosIonizable', 'NegIonizable'.",
      "items": {
        "type": "string"
      },
      "type": [
        "array",
        "null"
      ]
    },
    "smiles": {
      "description": "SMILES string of the molecule. Examples: 'CC(=O)Oc1ccccc1C(=O)O' (aspirin), 'c1ccc(cc1)C(=N)N' (benzamidine, has PosIonizable + HBD).",
      "type": "string"
    }
  },
  "required": [
    "smiles"
  ],
  "type": "object"
}

Examples (1)

{
  "smiles": "CC(=O)Oc1ccccc1C(=O)O"
}

Identifiers

Catalog ID

tu_RDKit_pharmacophore_features

Tool name

RDKit_pharmacophore_features

Added

2026-04-30 22:47Z

Tags

tooluniverse