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.
#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 126.96.36.199. Copyright (c) Schrodinger, LLC. All Rights Reserved. .....
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