Visualize a given substructure in a given molecule using rdkit and python.

Given the smiles of a molecule and the smiles of a possible substructure, find the atoms of the substructure in the molecule. Visualize the molecule with the substructure atoms highlighted in green.

Functions to convert smiles to molecules, find maximum common substructure and visualize the atoms.

import rdkit
import rdkit.Chem as Chem
from rdkit.Chem import rdFMCS
from matplotlib import colors
from rdkit.Chem.Draw import MolToImage

def get_mol(smiles):
    mol = Chem.MolFromSmiles(smiles)
    if mol is None:
        return None
    Chem.Kekulize(mol)
    return mol


def find_matches_one(mol,submol):
    #find all matching atoms for each submol in submol_list in mol.
    match_dict = {}
    mols = [mol,submol] #pairwise search
    res=rdFMCS.FindMCS(mols) #,ringMatchesRingOnly=True)
    mcsp = Chem.MolFromSmarts(res.smartsString)
    matches = mol.GetSubstructMatches(mcsp)
    return matches

#Draw the molecule
def get_image(mol,atomset=None):    
    hcolor = colors.to_rgb('green')
    if atomset is not None:
        #highlight the atoms set while drawing the whole molecule.
        img = MolToImage(mol, size=(600, 600),fitImage=True, highlightAtoms=atomset,highlightColor=hcolor)
    else:
        img = MolToImage(mol, size=(400, 400),fitImage=True)
    return img

peptide_smi = 'CCCCCCCCCC(=O)NC(Cc1c[nH]c2ccccc12)C(=O)NC(CC(N)=O)C(=O)NC(CC(=O)O)C(=O)NC4C(C)OC(=O)C(CC(=O)c3ccccc3(N))NC(=O)C(NC(=O)C(CO)NC(=O)CNC(=O)C(CC(=O)O)NC(=O)C(C)NC(=O)C(CC(=O)O)NC(=O)C(CCCN)NC(=O)CNC4(=O))C(C)CC(=O)O'
monomer_smi = 'CCCCCCCCCC(=O)O'

peptide_mol = get_mol(peptide_smi) #whole molecule
monomer_mol = get_mol(monomer_smi) #substructure molecule

matches = find_matches_one(peptide_mol,monomer_mol)

atomset = list(matches[0])
#print(atomset)

Visualize the molecule with the atoms of the substructure in dark green.

Molecule with substructure(green)
an image alt text 
img = get_image(peptide_mol,atomset)
img #see the whole molecule with the substructure highlighted.

Visualize the substructure molecule alone.

img = get_image(monomer_mol)
img #see the whole molecule with the substructure highlighted.

Substructure alone | :—————-:| an image alt text |

Written on April 16, 2019