Dear All,
I am currently having some problems using the AllChem.ConstrainedEmbed() -
which I have previously used successfully in version 2010_09_1 (Windows py26
binary). The following example demonstrates the issue:
>>> from rdkit import Chem
>>> from rdkit.Chem import AllChem
>>> template = Chem.MolFromSmiles("c1cnn(Cc2ccccc2)c1")
>>> mol = Chem.MolFromSmiles("c1ccc(Cn2ncc(-c3ccccc3)c2)cc1")
Now I give the template some 3D coordinates:
>>> AllChem.EmbedMolecule(template)
>>> AllChem.UFFOptimizeMolecule(template)
and finally, try to force an overlay of 'mol' onto 'template'
>>> AllChem.ConstrainedEmbed(mol, template, True)
Traceback (most recent call last):
File "<pyshell#7>", line 1, in <module>
AllChem.ConstrainedEmbed(mol, template, True)
File "C:\RDKit_2010_12_1\rdkit\Chem\AllChem.py", line 294, in
ConstrainedEmbed
rms = AlignMol(mol,core,atomMap=algMap)
RuntimeError: Range Error
I am not getting a ValueError - so I think this shows the substructure match
is ok, but wasn't sure where to go to dig into the AlignMol() function...
As the error message above shows, this is running 2010_12_1. I have just
tried with 2011_03_1beta1 and 2011_03_2 and get the same thing. In
2010_09_1 the ConstrainedEmbed() passes back an RDKit molecule fine.
Kind regards
James
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