mol2graph and graph2mol #rdkit #igraph

I posted about mol to graph object before.
In the blog post, I wrote example that convert RDKit mol object to igraph object. It was one way. There was no method igraph to rdkit mol object.
So I wrote very simple converter from graph to molecule.

First, import modules.

import numpy as np
import pandas as pd
import igraph
from rdkit import Chem
from rdkit.Chem.rdchem import RWMol
from rdkit.Chem import Draw
from rdkit.Chem import rdmolops
from rdkit.Chem.Draw import IPythonConsole
IPythonConsole.ipython_useSVG = True

Then define two way function, mol2graph and graph2mol. It is very simple.I did not sanitize process because I could not handle some compounds. RWMol method is very useful to do this work.

def mol2graph(mol):
    atoms_info = [ (atom.GetIdx(), atom.GetAtomicNum(), atom.GetSymbol()) for atom in mol.GetAtoms()]
    bonds_info = [(bond.GetBeginAtomIdx(), bond.GetEndAtomIdx(), bond.GetBondType(), bond.GetBondTypeAsDouble()) for bond in mol.GetBonds()]
    graph = igraph.Graph()
    for atom_info in atoms_info:
        graph.add_vertex(atom_info[0], AtomicNum=atom_info[1], AtomicSymbole=atom_info[2])
    for bond_info in bonds_info:
        graph.add_edge(bond_info[0], bond_info[1], BondType=bond_info[2], BondTypeAsDouble=bond_info[3])
    return graph

def graph2mol(graph): 
    emol = RWMol()
    for v in graph.vs():
    for e in
        emol.AddBond(e.source,, e['BondType'])
    mol = emol.GetMol()
    return mol

Finally, I checked my function on jupyter notebook. And It worked well.

All code is uploaded my repo and can check from following URL.

Published by iwatobipen

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

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