Source Code for Module rdkit.Chem.Descriptors

  1  # $Id: Descriptors.py 1911 2012-01-07 06:06:58Z glandrum $ 
  2  # 
  3  # Copyright (C) 2001-2010 greg Landrum and 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 Chem 
 12  import collections 
 13   
 14 -def _isCallable(thing): 
 15    return (hasattr(collections,'Callable') and isinstance(thing,collections.Callable)) or \ 
 16                hasattr(thing,'__call__')    
 17   
 18  _descList=[] 
 19 -def _setupDescriptors(namespace): 
 20    global _descList,descList 
 21    from rdkit.Chem import GraphDescriptors,MolSurf,Lipinski,Fragments,Crippen 
 22    from rdkit.Chem.EState import EState_VSA 
 23    mods = [GraphDescriptors,MolSurf,EState_VSA,Lipinski,Crippen,Fragments] 
 24   
 25    otherMods = [Chem] 
 26   
 27    for nm,thing in namespace.iteritems(): 
 28      if nm[0]!='_' and _isCallable(thing): 
 29        _descList.append((nm,thing)) 
 30     
 31    others = [] 
 32    for mod in otherMods: 
 33      tmp = dir(mod) 
 34      for name in tmp: 
 35        if name[0] != '_': 
 36          thing = getattr(mod,name) 
 37          if _isCallable(thing): 
 38            others.append(name) 
 39   
 40    for mod in mods: 
 41      tmp = dir(mod) 
 42   
 43      for name in tmp: 
 44        if name[0] != '_' and name[-1] != '_' and name not in others: 
 45          # filter out python reference implementations: 
 46          if name[:2]=='py' and name[2:] in tmp: 
 47            continue 
 48          thing = getattr(mod,name) 
 49          if _isCallable(thing): 
 50            namespace[name]=thing 
 51            _descList.append((name,thing)) 
 52    descList=_descList 
 53   
 54  from rdkit.Chem import rdMolDescriptors as _rdMolDescriptors 
 55  MolWt = lambda *x,**y:_rdMolDescriptors._CalcMolWt(*x,**y) 
 56  MolWt.version=_rdMolDescriptors._CalcMolWt_version 
 57  MolWt.__doc__="""The average molecular weight of the molecule ignoring hydrogens 
 58   
 59    >>> MolWt(Chem.MolFromSmiles('CC')) 
 60    30.07... 
 61    >>> MolWt(Chem.MolFromSmiles('[NH4+].[Cl-]')) 
 62    53.49... 
 63   
 64  """ 
 65   
 66  HeavyAtomMolWt=lambda x:MolWt(x,True) 
 67  HeavyAtomMolWt.__doc__="""The average molecular weight of the molecule ignoring hydrogens 
 68   
 69    >>> HeavyAtomMolWt(Chem.MolFromSmiles('CC')) 
 70    24.02... 
 71    >>> HeavyAtomMolWt(Chem.MolFromSmiles('[NH4+].[Cl-]')) 
 72    49.46... 
 73   
 74  """ 
 75  HeavyAtomMolWt.version="1.0.0" 
 76   
 77 -def NumValenceElectrons(mol): 
 78    """ The number of valence electrons the molecule has 
 79   
 80    >>> NumValenceElectrons(Chem.MolFromSmiles('CC')) 
 81    14.0 
 82    >>> NumValenceElectrons(Chem.MolFromSmiles('C(=O)O')) 
 83    18.0 
 84    >>> NumValenceElectrons(Chem.MolFromSmiles('C(=O)[O-]')) 
 85    18.0 
 86    >>> NumValenceElectrons(Chem.MolFromSmiles('C(=O)')) 
 87    12.0 
 88     
 89   
 90    """ 
 91    tbl = Chem.GetPeriodicTable() 
 92    accum = 0.0 
 93    for atom in mol.GetAtoms(): 
 94      accum += tbl.GetNOuterElecs(atom.GetAtomicNum()) 
 95      accum -= atom.GetFormalCharge() 
 96      accum += atom.GetTotalNumHs() 
 97   
 98    return accum 
 99  NumValenceElectrons.version="1.0.0" 
100   
101 -def _pyMolecularFormula(mol): 
102     """ DEPRECATED: this is now implemented in C++ 
103     Return the molecular formula 
104   
105     contribution from Andrew Dalke 
106      
107     """ 
108     import collections 
109   
110     # Count the different atom types 
111     counts = collections.defaultdict(int) 
112     charge = 0 
113     for atom in mol.GetAtoms(): 
114         symb = atom.GetSymbol() 
115         counts[symb]+=1 
116         # Also track the implicit hydrogen counts and total charge 
117         num_hydrogens = atom.GetTotalNumHs() 
118         # A counts key should only exist if an element is present. 
119         # Do this test to prevent the creation of an "H": 0 for 
120         # things like [C], which have no implicit hydrogens. 
121         if num_hydrogens: 
122             counts['H'] += num_hydrogens 
123         charge += atom.GetFormalCharge() 
124   
125     # Alphabetize elements by name 
126     elements = sorted(counts) 
127   
128     # Put into Hill system order: 
129     # If there are carbons then they go first, followed by hydrogens, 
130     # then followed alphabetically by the other elements. 
131     # If there are no carbons then the elements are in alphabetical 
132     # order (including hydrogens) 
133     if "C" in elements: 
134         elements.remove("C") 
135         elements.insert(0, "C") 
136         if "H" in elements: 
137             elements.remove("H") 
138             elements.insert(1, "H") 
139   
140     # Include the count, so {"C": 1, "H": 4} becomes ["C", "H4"] 
141     formula_terms = [] 
142     for element in elements: 
143         formula_terms.append(element) 
144         if counts[element] > 1: 
145             formula_terms.append(str(counts[element])) 
146   
147     # Handle the total charge. The result will be NH4+, Ca+2, etc. 
148     if charge == 0: 
149         pass 
150     elif charge == 1: 
151         formula_terms.append("+") 
152     elif charge == -1: 
153         formula_terms.append("-") 
154     else: 
155         formula_terms.append("%+d" % charge) 
156   
157     return "".join(formula_terms) 
158  MolecularFormula=lambda x:_rdMolDescriptors.CalcMolFormula(x) 
159  MolecularFormula.version=_rdMolDescriptors._CalcMolFormula_version 
160   
161  _setupDescriptors(locals()) 
162   
163   
164   
165  #------------------------------------ 
166  # 
167  #  doctest boilerplate 
168  # 
169 -def _test(): 
170    import doctest,sys 
171    return doctest.testmod(sys.modules["__main__"],optionflags=doctest.ELLIPSIS) 
172   
173  if __name__ == '__main__': 
174    import sys 
175    failed,tried = _test() 
176    sys.exit(failed) 
177