Visualize pharmacophore in RDKit #RDKit

RDKit has pharmacophore feature assignment function. The function can retrieve molecular features based on pre-defined ph4core.
And RDKit IPythonconsole can draw molecules on ipython notebook.
Today I tried to visualize ph4core on notebook.
Code is very simple.

from rdkit import Chem
from rdkit.Chem import ChemicalFeatures
from rdkit import rdBase
from rdkit.RDPaths import RDDocsDir
from rdkit.RDPaths import RDDataDir
from rdkit.Chem.Draw import IPythonConsole
from rdkit.Chem import Draw
from rdkit.Chem import AllChem
import os
> 2018.09.1

First, load feature definition.

fdefFile = os.path.join(RDDataDir,'BaseFeatures.fdef')
featFact = ChemicalFeatures.BuildFeatureFactory(fdefFile)

Then calculate pharmacophore. And compute 2D cordes.

mols = [m for m in Chem.SDMolSupplier(os.path.join(RDDocsDir,"Book/data/cdk2.sdf"))]
featslists = [featFact.GetFeaturesForMol(mol) for mol in mols]
for mol in mols:

Next I defined drawing function. To highlight ph4core, highlightAtomLists and legends are used as optional arguments of MolsToGridImage.

def drawp4core(mol, feats):
    atoms_list = {}
    for feat in feats:
        atom_ids = feat.GetAtomIds()
        feat_type = feat.GetType()
        atoms_list[feat_type] = atom_ids
    return Draw.MolsToGridImage([mol]*len(atoms_list), legends=list(atoms_list.keys()), highlightAtomLists=list(atoms_list.values()))

Test the function.

im = drawp4core(mols[1], featslists[1])

I could get following image.

The function worked and it could pick up pharmacophore of given molecule. ;-)


Published by iwatobipen

I'm medicinal chemist in mid size of pharmaceutical company. I love chemoinfo, cording, organic synthesis, my family.

One thought on “Visualize pharmacophore in RDKit #RDKit

  1. Is it possible to visualize the Pharma2Dfp ? as a circle or whatever with different colors for different features? form a small list of smiles

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