Source Code for Module Chem.TemplateAlign

 1  # $Id: TemplateAlign.py 2 2006-05-06 22:54:39Z glandrum $
 
 2  #
 
 3  #  Copyright (C) 2005-2006 Rational Discovery LLC
 
 4  #
 
 5  #   @@ All Rights Reserved  @@
 
 6  #
 
 7  import Chem 
 8  from Chem import rdDepictor 
 9  import Geometry 
10  
 
11 -def AlignMolToTemplate2D(mol,template,match=None,clearConfs=False,
 
12                           templateConfId=-1,): 
13    """
 
14     Arguments:
 
15  
 
16       - mol:      the molecule to be aligned
 
17       - template: the template to align to
 
18       - match:    If provided, this should be a sequence of integers
 
19                   containing the indices of the atoms in mol that match
 
20                   those in template. This is the result of calling:
 
21                     mol.GetSubstructMatch(template)
 
22       - clearConfs: toggles removing any existing conformers on mol
 
23  
 
24      Returns the confId of the conformer containing the depiction
 
25  
 
26      >>> patt = Chem.MolFromSmiles('C1CC1')
 
27      >>> rdDepictor.Compute2DCoords(patt)
 
28      0
 
29      >>> mol = Chem.MolFromSmiles('OC1CC1CC1CCC1')
 
30      >>> rdDepictor.Compute2DCoords(mol)
 
31      0
 
32      >>> pc = patt.GetConformer(0)
 
33      >>> mc = mol.GetConformer(0)
 
34  
 
35      We start out with the molecules not aligned:
 
36      >>> vs = [abs(pc.GetAtomPosition(i).x-mc.GetAtomPosition(i+1).x) for i in range(pc.GetNumAtoms())]
 
37      >>> [x<1e-4 for x in vs]
 
38      [False, False, False]
 
39  
 
40      But then we can replace the conformer of mol:
 
41      >>> AlignMolToTemplate2D(mol,patt,clearConfs=True)
 
42      0
 
43      >>> mol.GetNumConformers()
 
44      1
 
45      >>> pc = patt.GetConformer(0)
 
46      >>> mc = mol.GetConformer(0)
 
47      >>> vs = [abs(pc.GetAtomPosition(i).x-mc.GetAtomPosition(i+1).x) for i in range(pc.GetNumAtoms())]
 
48      >>> [x<1e-4 for x in vs]
 
49      [True, True, True]
 
50  
 
51      If we like, we can specify the atom map explicitly in order to align to the second
 
52      matching ring in the probe molecule:
 
53      >>> match = (5,6,7)
 
54      >>> AlignMolToTemplate2D(mol,patt,clearConfs=True,match=match)
 
55      0
 
56      >>> mol.GetNumConformers()
 
57      1
 
58      >>> pc = patt.GetConformer(0)
 
59      >>> mc = mol.GetConformer(0)
 
60      >>> vs = [abs(pc.GetAtomPosition(i).x-mc.GetAtomPosition(i+1).x) for i in range(pc.GetNumAtoms())]
 
61      >>> [x<1e-4 for x in vs]
 
62      [False, False, False]
 
63      >>> vs = [abs(pc.GetAtomPosition(i).x-mc.GetAtomPosition(i+5).x) for i in range(pc.GetNumAtoms())]
 
64      >>> [x<1e-4 for x in vs]
 
65      [True, True, True]
 
66  
 
67  
 
68      
 
69    """ 
70    if not match: 
71      match = mol.GetSubstructMatch(template) 
72    if not match: 
73      raise ValueError,'no match between mol and template' 
74    
 
75    atomMap = {} 
76    templateConf = template.GetConformer(templateConfId) 
77    for i,idx in enumerate(match): 
78      p = templateConf.GetAtomPosition(i) 
79      atomMap[idx] = Geometry.Point2D(p.x,p.y) 
80    molConfId = rdDepictor.Compute2DCoords(mol,clearConfs=clearConfs,coordMap=atomMap) 
81    return molConfId 
82  
 
83  
 
84  #------------------------------------
 
85  #
 
86  #  doctest boilerplate
 
87  #
 
88 -def _test(): 
89    import doctest,sys 
90    return doctest.testmod(sys.modules["__main__"]) 
91  
 
92  
 
93  if __name__ == '__main__': 
94    import sys 
95    failed,tried = _test() 
96    sys.exit(failed) 
97