Source Code for Module Chem.Descriptors

 1  # $Id: Descriptors.py 2 2006-05-06 22:54:39Z glandrum $ 
 2  # 
 3  # Copyright (C) 2001-2006 greg Landrum and Rational Discovery LLC 
 4  # 
 5  #   @@ All Rights Reserved  @@ 
 6  # 
 7  import Chem 
 8   
 9 -def MolWt(mol,heavyAtomsOnly=0): 
10    """ The average molecular weight of the molecule 
11   
12    >>> '%.2f'%MolWt(Chem.MolFromSmiles('CC')) 
13    '30.07' 
14    >>> '%.2f'%MolWt(Chem.MolFromSmiles('CC'),1) 
15    '24.02' 
16    >>> '%.2f'%MolWt(Chem.MolFromSmiles('[NH4+].[Cl-]')) 
17    '53.49' 
18    """ 
19    hMass = Chem.GetPeriodicTable().GetAtomicWeight(1) 
20    accum = 0.0 
21    for atom in mol.GetAtoms(): 
22      accum += atom.GetMass() 
23      if not heavyAtomsOnly: 
24        accum += atom.GetTotalNumHs()*hMass 
25    return accum 
26  MolWt.version="1.0.0" 
27   
28  HeavyAtomMolWt=lambda x:MolWt(x,1) 
29  HeavyAtomMolWt.__doc__="""The average molecular weight of the molecule ignoring hydrogens 
30   
31    >>> '%.2f'%HeavyAtomMolWt(Chem.MolFromSmiles('CC')) 
32    '24.02' 
33    >>> '%.2f'%HeavyAtomMolWt(Chem.MolFromSmiles('[NH4+].[Cl-]')) 
34    '49.46' 
35   
36  """ 
37  HeavyAtomMolWt.version="1.0.0" 
38   
39 -def NumValenceElectrons(mol): 
40    """ The number of valence electrons the molecule has 
41   
42    >>> NumValenceElectrons(Chem.MolFromSmiles('CC')) 
43    14.0 
44    >>> NumValenceElectrons(Chem.MolFromSmiles('C(=O)O')) 
45    18.0 
46    >>> NumValenceElectrons(Chem.MolFromSmiles('C(=O)[O-]')) 
47    18.0 
48    >>> NumValenceElectrons(Chem.MolFromSmiles('C(=O)')) 
49    12.0 
50     
51   
52    """ 
53    tbl = Chem.GetPeriodicTable() 
54    accum = 0.0 
55    for atom in mol.GetAtoms(): 
56      accum += tbl.GetNOuterElecs(atom.GetAtomicNum()) 
57      accum -= atom.GetFormalCharge() 
58      accum += atom.GetTotalNumHs() 
59   
60    return accum 
61  NumValenceElectrons.version="1.0.0" 
62   
63  #------------------------------------ 
64  # 
65  #  doctest boilerplate 
66  # 
67 -def _test(): 
68    import doctest,sys 
69    return doctest.testmod(sys.modules["__main__"]) 
70   
71  if __name__ == '__main__': 
72    import sys 
73    failed,tried = _test() 
74    sys.exit(failed) 
75