Dear James,
On Fri, May 20, 2011 at 4:54 PM, James Davidson <[email protected]> wrote:
> 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
>
Yep, there's a bug here. Something changed and apparently this bit of
code isn't being tested.
I'll check in a real fix and some tests, but the quick fix is to
modify the area around line 294 of AllChem.py from:
# rotate the embedded conformation onto the core:
rms = AlignMol(mol,core,atomMap=algMap)
to:
# rotate the embedded conformation onto the core:
algMap = [(y,x) for (x,y) in algMap]
rms = AlignMol(mol,core,atomMap=algMap)
Thanks for reporting this,
-greg
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