Source Code for Module rdkit.Chem.ChemUtils.AlignDepict

 1  # $Id: AlignDepict.py 736 2008-02-14 14:09:36Z landrgr1 $ 
 2  # 
 3  #  Copyright (C) 2006 Greg Landrum 
 4  #  This file is part of RDKit and covered by $RDBASE/license.txt 
 5  # 
 6  from rdkit import Chem 
 7  from rdkit.Chem import rdDepictor 
 8  from rdkit import Geometry 
 9   
10 -def AlignDepict(mol,core,corePattern=None,acceptFailure=False): 
11    """ 
12   
13    Arguments: 
14      - mol:          the molecule to be aligned, this will come back 
15                      with a single conformer. 
16      - core:         a molecule with the core atoms to align to; 
17                      this should have a depiction. 
18      - corePattern:  (optional) an optional molecule to be used to  
19                      generate the atom mapping between the molecule 
20                      and the core. 
21    """ 
22    if core and corePattern: 
23      if not core.GetNumAtoms(onlyHeavy=True)==corePattern.GetNumAtoms(onlyHeavy=True): 
24        raise ValueError,'When a pattern is provided, it must have the same number of atoms as the core' 
25      coreMatch = core.GetSubstructMatch(corePattern) 
26      if not coreMatch: 
27        raise ValueError,"Core does not map to itself" 
28    else: 
29      coreMatch = range(core.GetNumAtoms(onlyHeavy=True)) 
30    if corePattern: 
31      match = mol.GetSubstructMatch(corePattern) 
32    else: 
33      match = mol.GetSubstructMatch(core) 
34   
35    if not match: 
36      if not acceptFailure: 
37        raise ValueError,'Substructure match with core not found.' 
38      else: 
39        coordMap={} 
40    else: 
41      conf = core.GetConformer() 
42      coordMap={} 
43      for i,idx in enumerate(match): 
44        pt3 = conf.GetAtomPosition(coreMatch[i]) 
45        pt2 = Geometry.Point2D(pt3.x,pt3.y) 
46        coordMap[idx] = pt2 
47    rdDepictor.Compute2DCoords(mol,clearConfs=True,coordMap=coordMap) 
48   
49  if __name__=='__main__': 
50    import sys,getopt 
51   
52 -  def Usage(): 
53      pass 
54     
55    args,extras = getopt.getopt(sys.argv[1:],'p:ho:',['smiles','pattern=']) 
56    if len(extras)!=2: 
57      print >>sys.stderr,'ERROR: Not enough arguments' 
58      Usage() 
59      sys.exit(1) 
60    patt = None 
61    useSmiles = False 
62    outF=None 
63    for arg,val in args: 
64      if arg=='-h': 
65        Usage() 
66        sys.exit(0) 
67      elif arg=='-p' or arg=='--pattern': 
68        patt = Chem.MolFromSmarts(val) 
69      elif arg=='--smiles': 
70        useSmiles = True 
71      elif arg=='-o': 
72        outF = val 
73     
74    if not useSmiles: 
75      core = Chem.MolFromMolFile(extras[0]) 
76    else: 
77      core = Chem.MolFromSmiles(extras[0]) 
78      rdDepictor.Compute2DCoords(core) 
79   
80    if not useSmiles: 
81      mol = Chem.MolFromMolFile(extras[1]) 
82    else: 
83      mol = Chem.MolFromSmiles(extras[1]) 
84   
85    AlignDepict(mol,core,patt) 
86     
87    if outF: 
88      outF = open(outF,'w+') 
89    else: 
90      outF = sys.stdout 
91   
92    print >>outF,Chem.MolToMolBlock(mol) 
93