Source Code for Module Chem.Descriptors

 1  # $Id: Descriptors.py 702 2008-05-30 14:55:22Z glandrum $ 
 2  # 
 3  # Copyright (C) 2001-2006 greg Landrum and Rational Discovery LLC 
 4  # 
 5  #   @@ All Rights Reserved  @@ 
 6  # 
 7  import Chem 
 8  from Chem import rdMolDescriptors 
 9   
10 -def pyMolWt(mol,heavyAtomsOnly=0): 
11    """ The average molecular weight of the molecule 
12   
13    >>> '%.2f'%pyMolWt(Chem.MolFromSmiles('CC')) 
14    '30.07' 
15    >>> '%.2f'%pyMolWt(Chem.MolFromSmiles('CC'),1) 
16    '24.02' 
17    >>> '%.2f'%pyMolWt(Chem.MolFromSmiles('[NH4+].[Cl-]')) 
18    '53.49' 
19    >>> '%.2f'%MolWt(Chem.MolFromSmiles('CC')) 
20    '30.07' 
21    >>> '%.2f'%MolWt(Chem.MolFromSmiles('CC'),1) 
22    '24.02' 
23    >>> '%.2f'%MolWt(Chem.MolFromSmiles('[NH4+].[Cl-]')) 
24    '53.49' 
25    """ 
26    hMass = Chem.GetPeriodicTable().GetAtomicWeight(1) 
27    accum = 0.0 
28    for atom in mol.GetAtoms(): 
29      accum += atom.GetMass() 
30      if not heavyAtomsOnly: 
31        accum += atom.GetTotalNumHs()*hMass 
32    return accum 
33  pyMolWt.version="1.0.0" 
34  MolWt = lambda *x,**y:rdMolDescriptors._CalcMolWt(*x,**y) 
35  MolWt.version=rdMolDescriptors.__CalcMolWt_version__ 
36   
37   
38  HeavyAtomMolWt=lambda x:MolWt(x,1) 
39  HeavyAtomMolWt.__doc__="""The average molecular weight of the molecule ignoring hydrogens 
40   
41    >>> '%.2f'%HeavyAtomMolWt(Chem.MolFromSmiles('CC')) 
42    '24.02' 
43    >>> '%.2f'%HeavyAtomMolWt(Chem.MolFromSmiles('[NH4+].[Cl-]')) 
44    '49.46' 
45   
46  """ 
47  HeavyAtomMolWt.version="1.0.0" 
48   
49 -def NumValenceElectrons(mol): 
50    """ The number of valence electrons the molecule has 
51   
52    >>> NumValenceElectrons(Chem.MolFromSmiles('CC')) 
53    14.0 
54    >>> NumValenceElectrons(Chem.MolFromSmiles('C(=O)O')) 
55    18.0 
56    >>> NumValenceElectrons(Chem.MolFromSmiles('C(=O)[O-]')) 
57    18.0 
58    >>> NumValenceElectrons(Chem.MolFromSmiles('C(=O)')) 
59    12.0 
60     
61   
62    """ 
63    tbl = Chem.GetPeriodicTable() 
64    accum = 0.0 
65    for atom in mol.GetAtoms(): 
66      accum += tbl.GetNOuterElecs(atom.GetAtomicNum()) 
67      accum -= atom.GetFormalCharge() 
68      accum += atom.GetTotalNumHs() 
69   
70    return accum 
71  NumValenceElectrons.version="1.0.0" 
72   
73  #------------------------------------ 
74  # 
75  #  doctest boilerplate 
76  # 
77 -def _test(): 
78    import doctest,sys 
79    return doctest.testmod(sys.modules["__main__"]) 
80   
81  if __name__ == '__main__': 
82    import sys 
83    failed,tried = _test() 
84    sys.exit(failed) 
85