1
2
3
4
5
6
7
8
9
10
11 from rdkit import RDConfig
12
13
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