Source Code for Module rdkit.Chem.TemplateAlign

 1  # $Id: TemplateAlign.py 997 2009-02-25 06:12:43Z glandrum $ 
 2  # 
 3  #  Copyright (C) 2005-2006 Rational Discovery LLC 
 4  # 
 5  #   @@ All Rights Reserved  @@ 
 6  # 
 7  from rdkit import Chem 
 8  from rdkit.Chem import rdDepictor 
 9  from rdkit 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