Source Code for Module rdkit.Chem.ShowMols

 1  # $Id: ShowMols.py 1528 2010-09-26 17:04:37Z glandrum $ 
 2  # 
 3  # Copyright (C) 2004-2006 Rational Discovery LLC 
 4  # 
 5  #   @@ All Rights Reserved @@ 
 6  #  This file is part of the RDKit. 
 7  #  The contents are covered by the terms of the BSD license 
 8  #  which is included in the file license.txt, found at the root 
 9  #  of the RDKit source tree. 
10  # 
11  from rdkit import RDConfig 
12   
13  # change this to use another viewer: 
14  if RDConfig.molViewer in ('WEBLAB','DSVIEWER'): 
15    from rdkit.Chem.DSViewer import * 
16  elif RDConfig.molViewer=='PYMOL': 
17    from rdkit.Chem.PyMol import * 
18  else: 
19    raise ValueError,'invalid RD_MOLVIEWER specified' 
20   
21     
22     
23  if __name__=='__main__': 
24    import AllChem 
25    import sys 
26    if len(sys.argv)<2: 
27      smi ='c1cccc2c1cccc2CC(=O)N' 
28    else: 
29      smi = sys.argv[1] 
30   
31    m = Chem.MolFromSmiles(smi) 
32    m = Chem.AddHs(m) 
33    AllChem.EmbedMolecule(m) 
34    v = MolViewer() 
35    v.ShowMol(m,'raw') 
36    AllChem.UFFOptimizeMolecule(m) 
37    v.ShowMol(m,'opt',showOnly=0,highlightFeatures=[(0,),(2,),(3,4)]) 
38