Source Code for Package rdkit.Chem

  1  ## Automatically adapted for numpy.oldnumeric Jun 27, 2008 by -c 
  2   
  3  # $Id: __init__.py 1773 2011-06-29 05:20:47Z glandrum $ 
  4  # 
  5  #  Copyright (C) 2000-2008  greg Landrum and Rational Discovery LLC 
  6  # 
  7  #   @@ All Rights Reserved @@ 
  8  #  This file is part of the RDKit. 
  9  #  The contents are covered by the terms of the BSD license 
 10  #  which is included in the file license.txt, found at the root 
 11  #  of the RDKit source tree. 
 12  # 
 13  """ A module for molecules and stuff 
 14   
 15   see Chem/index.html in the doc tree for documentation 
 16    
 17  """ 
 18  from rdkit import rdBase 
 19  from rdkit import RDConfig 
 20   
 21  from rdkit import DataStructs 
 22  from rdkit.Geometry import rdGeometry 
 23  import PeriodicTable as pyPeriodicTable 
 24  import rdchem 
 25  _HasSubstructMatchStr=rdchem._HasSubstructMatchStr 
 26  from rdchem import * 
 27  from rdmolfiles import * 
 28  from rdmolops import * 
 29  from inchi import * 
 30   
 31 -def QuickSmartsMatch(smi,sma,unique=True,display=False): 
 32    m = MolFromSmiles(smi) 
 33    p = MolFromSmarts(sma) 
 34    res = m.GetSubstructMatches(p,unique) 
 35    if display: 
 36      pass 
 37    return res   
 38   
 39 -def CanonSmiles(smi,useChiral=1): 
 40    m = MolFromSmiles(smi) 
 41    return MolToSmiles(m,useChiral) 
 42   
 43 -def SupplierFromFilename(fileN,delim='',**kwargs): 
 44    ext = fileN.split('.')[-1].lower() 
 45    if ext=='sdf': 
 46      suppl = SDMolSupplier(fileN,**kwargs) 
 47    elif ext=='csv': 
 48      if not delim: 
 49        delim = ',' 
 50      suppl = SmilesMolSupplier(fileN,delimiter=delim,**kwargs) 
 51    elif ext=='txt': 
 52      if not delim: 
 53        delim='\t' 
 54      suppl = SmilesMolSupplier(fileN,delimiter=delim,**kwargs) 
 55    elif ext=='tdt': 
 56      suppl = TDTMolSupplier(fileN,delimiter=delim,**kwargs) 
 57    else: 
 58      raise ValueError,"unrecognized extension: %s"%ext 
 59       
 60    return suppl 
 61   
 62 -def FindMolChiralCenters(mol,force=True,includeUnassigned=False): 
 63    """ 
 64      >>> from rdkit import Chem 
 65      >>> mol = Chem.MolFromSmiles('[C@H](Cl)(F)Br') 
 66      >>> FindMolChiralCenters(mol) 
 67      [(0, 'R')] 
 68      >>> mol = Chem.MolFromSmiles('[C@@H](Cl)(F)Br') 
 69      >>> FindMolChiralCenters(mol) 
 70      [(0, 'S')] 
 71     
 72      >>> FindMolChiralCenters(Chem.MolFromSmiles('CCC')) 
 73      [] 
 74   
 75      By default unassigned stereo centers are not reported: 
 76      >>> mol = Chem.MolFromSmiles('C[C@H](F)C(F)(Cl)Br') 
 77      >>> FindMolChiralCenters(mol) 
 78      [(1, 'S')] 
 79   
 80      but this can be changed: 
 81      >>> FindMolChiralCenters(mol,includeUnassigned=True) 
 82      [(1, 'S'), (3, '?')] 
 83   
 84      The handling of dependent stereochemistry is not correct: 
 85      >>> Chem.FindMolChiralCenters(Chem.MolFromSmiles('C1CC(C)C(C)C(C)C1'),includeUnassigned=True) 
 86      [(2, '?'), (6, '?')] 
 87      >>> Chem.FindMolChiralCenters(Chem.MolFromSmiles('C1C[C@H](C)C(C)[C@H](C)C1'),includeUnassigned=True) 
 88      [(2, 'S'), (6, 'R')] 
 89       
 90    """ 
 91    AssignStereochemistry(mol,force=force, flagPossibleStereoCenters=includeUnassigned) 
 92    centers = [] 
 93    for atom in mol.GetAtoms(): 
 94      if atom.HasProp('_CIPCode'): 
 95        centers.append((atom.GetIdx(),atom.GetProp('_CIPCode'))) 
 96      elif includeUnassigned and atom.HasProp('_ChiralityPossible'): 
 97        centers.append((atom.GetIdx(),'?')) 
 98    return centers 
 99   
100  #------------------------------------ 
101  # 
102  #  doctest boilerplate 
103  # 
104 -def _test(): 
105    import doctest,sys 
106    return doctest.testmod(sys.modules["__main__"]) 
107   
108   
109  if __name__ == '__main__': 
110    import sys 
111    failed,tried = _test() 
112    sys.exit(failed) 
113