Package rdkit :: Package Chem :: Module ShowMols
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Source Code for Module rdkit.Chem.ShowMols

 1  # $Id$ 
 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  if __name__ == '__main__': 
22    import AllChem 
23    import sys 
24    if len(sys.argv) < 2: 
25      smi = 'c1cccc2c1cccc2CC(=O)N' 
26    else: 
27      smi = sys.argv[1] 
28   
29    m = Chem.MolFromSmiles(smi) 
30    m = Chem.AddHs(m) 
31    AllChem.EmbedMolecule(m) 
32    v = MolViewer() 
33    v.ShowMol(m, 'raw') 
34    AllChem.UFFOptimizeMolecule(m) 
35    v.ShowMol(m, 'opt', showOnly=0, highlightFeatures=[(0, ), (2, ), (3, 4)]) 
36