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.
pymoltest.py

 #test
 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 pymolrdkit.py 
 PyMOL(TM) Molecular Graphics System, Version 1.7.6.0.
 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.http://www.tobuzoo.com/
I and my family enjoyed.
IMG_1735

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