New function of RDKit 2017.09 #RDKit

Recently I updated my rdkit env from 201703 to 201709 by using conda.
New version of rdkit was implemented cool function named rdRGroupDeompositon.
The function enable us to render RGroups as DataFrame.
I tried to visualize cdk2.sdf dataset.
Code that I wrote is bellow.(using jupyter notebook)

from rdkit import Chem
from rdkit.Chem import Draw, AllChem
from rdkit.Chem import PandasTools
from rdkit.Chem import rdBase
from rdkit.Chem import RDConfig
from rdkit.Chem.Draw import IPythonConsole
import os
base = RDConfig.RDDocsDir
datapath = os.path.join( base, "Book/data/cdk2.sdf")
mols = [ mol for mol in Chem.SDMolSupplier( datapath ) if mol != None ]
# mol object that has 3D conformer information did not work well. So I remove the conformation info.
for m in mols: tmp = m.RemoveAllConformers()
# define core to RG decomposition.
core = Chem.MolFromSmiles('[nH]1cnc2cncnc21')
from rdkit.Chem import rdRGroupDecomposition
tables = PandasTools.LoadSDF( datapath )
rg = rdRGroupDecomposition.RGroupDecomposition( core )
for mol in mols[:5]:
    rg.Add( mol )
# Do RG deconpositon.

Then visualize RGdecomp result.

import pandas as pd
modlf = PandasTools.LoadSDF( datapath )
frame = pd.DataFrame( rg.GetRGroupsAsColumns() )

Result is following image. ;-)
New version of RDKit is cool & powerful tool for chemoinformatics. I really respect the developer of rdkit.


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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