Chem.TemplateAlign

Package Chem :: Module TemplateAlign |
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# Source Code for Module Chem.TemplateAlign

     1  # $Id: TemplateAlign.py 746 2008-07-07 13:21:24Z 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