Draw similarity network #RDKit #Cyjupyter

Recently Kei Ono who is developer of cytoscape developed cyjupyter.
It seems attractive for me because the library can draw network diagram on jupyter notebook.
There are many network structured data in chemoinformatics. For example molecule, molecular similarity map and MMP etc… I used the library to draw similarity map of molecules today.
I am newbie of the library, so following code is very simple but there are several useful examples are provided in official repository.
At first, load modules.

import os
import numpy as np
import igraph
from py2cytoscape import util
from cyjupyter import Cytoscape
from rdkit import Chem
from rdkit.Chem import DataStructs
from rdkit.Chem import AllChem
from rdkit import RDConfig
from rdkit.Chem import Draw
from rdkit.Chem.Draw import IPythonConsole

I used CDK2.sdf as a sample dataset

filedir = os.path.join(RDConfig.RDDocsDir,'Book/data/cdk2.sdf')
mols = [mol for mol in Chem.SDMolSupplier(filedir) if mol != None]
for mol in mols:
fps = [AllChem.GetMorganFingerprintAsBitVect(mol, 2) for mol in mols]
smiles_list = [Chem.MolToSmiles(mol) for mol in mols]

Then make graph object, node as an each molecule and make edge if tanimoto similarity more 0.5.

g = igraph.Graph()
for smiles in smiles_list:
for i in range(len(mols)):
    for j in range(i):
        tc = DataStructs.TanimotoSimilarity(fps[i], fps[j])
        if tc >= 0.5:
            g.add_edge(smiles_list[i], smiles_list[j])

Finally convert graph object to json by using py2cytoscape and Draw graph with default settings.

graph_data = util.from_igraph(g)

I could get following image.

And check network

Cyjupyter is useful network drawing tool for jupyter notebook user. I would like to check the way to control visualization.
My example code is uploaded my repository. URL is below.

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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