Chem.ShowMols

Package Chem :: Module ShowMols |
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# Source Code for Module Chem.ShowMols

     1  # $Id: ShowMols.py 2 2006-05-06 22:54:39Z glandrum $

     2  #

     3  # Copyright (C) 2004-2006 Rational Discovery LLC

     4  #

     5  #   @@ All Rights Reserved  @@

     6  #

     7  import RDConfig
     8

     9  # change this to use another viewer:

    10  if RDConfig.molViewer in ('WEBLAB','DSVIEWER'):
    11    from Chem.DSViewer import *
    12  elif RDConfig.molViewer=='PYMOL':
    13    from Chem.PyMol import *
    14  else:
    15    raise ValueError,'invalid RD_MOLVIEWER specified'
    16

    17

    18

    19  if __name__=='__main__':
    20    import AllChem
    21    import sys
    22    if len(sys.argv)<2:
    23      smi ='c1cccc2c1cccc2CC(=O)N'
    24    else:
    25      smi = sys.argv[1]
    26

    27    m = Chem.MolFromSmiles(smi)
    28    m = Chem.AddHs(m)
    29    AllChem.EmbedMolecule(m)
    30    v = MolViewer()
    31    v.ShowMol(m,'raw')
    32    AllChem.UFFOptimizeMolecule(m)
    33    v.ShowMol(m,'opt',showOnly=0,highlightFeatures=[(0,),(2,),(3,4)])
    34