Call rdkit from pymol

PyMol is one of major tool for visualisation of protein, ligand, etc.
You know ‘Py’ means that pymol is written using python.
I want to embed pymol to web app but it’s difficult for me (technical reason..)
If anyone have advice to do it, please leave comment. ;-)

Next, I have one question that, pymol can call rdkit ?
If it possible, it will be good information for me.
Think drug design based 3D structure is key for design, and lots of tools for visualise 3D structures.
….But complicated tools is not familiar for medchem.(really ?)
I wrote simple test script to call rdkit from pymol.
Script is following.

 from rdkit import Chem
 from rdkit.Chem import AllChem
 from pymol import cmd
 #from __future__ import print_function
 mol = Chem.MolFromSmiles( 'CCCS(=O)(=O)Nc1ccc(F)c(c1F)C(=O)c2c[nH]c3c2cc(cn3    )c4ccc(Cl)cc4' )
 hmol = Chem.AddHs( mol )
 AllChem.EmbedMolecule( hmol )
 AllChem.MMFFOptimizeMolecule( hmol )    
 #print( hmol.GetNumConformers( ))
 pdbstring = Chem.MolToPDBBlock( hmol )
 cmd.read_pdbstr( pdbstring, 'vemrafenib' )

Next, run script via pymol

iwatobipen$ pymol 
 PyMOL(TM) Molecular Graphics System, Version
 Copyright (c) Schrodinger, LLC.
 All Rights Reserved.

Work fine.!
Screen Shot 2015-11-23 at 10.08.14 PM
I’ll research more details about pymol api.

I went to tobuzoo yesterday.
I and my family enjoyed.


Published by iwatobipen

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

2 thoughts on “Call rdkit from pymol

Leave a Reply

Fill in your details below or click an icon to log in: Logo

You are commenting using your account. Log Out /  Change )

Twitter picture

You are commenting using your Twitter account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )

Connecting to %s

This site uses Akismet to reduce spam. Learn how your comment data is processed.

%d bloggers like this: