Hi Dimitri,
AllChem.EmbedMolecule returns the ID of the conformer that is generated, -1
on failure. In this case you get -1.
In [13]: m = Chem.MolFromMolFile('./tetraoleylcardiolipin.sdf')
In [15]: AllChem.EmbedMolecule(m)
Out[15]: -1
For large molecules like this one, it is often more effective to provide
the useRandomCoords argument to EmbedMolecule:
In [16]: AllChem.EmbedMolecule(m,useRandomCoords=True)
Out[16]: 0
This also works if Hs have been added:
In [17]: m = Chem.MolFromMolFile('./tetraoleylcardiolipin.sdf')
In [18]: mh=Chem.AddHs(m)
In [21]: AllChem.EmbedMolecule(mh,useRandomCoords=True)
Out[21]: 0
Best,
-greg
On Mon, Feb 9, 2015 at 10:49 PM, Dimitri Maziuk <dmaz...@bmrb.wisc.edu>
wrote:
> Hi all,
>
> I'm generating a 3D mol:
>
> assert isinstance( self._mol, rdkit.Chem.rdchem.Mol )
> m = rdkit.Chem.AddHs( self._mol )
> rdkit.Chem.AllChem.EmbedMolecule( m )
> rdkit.Chem.AllChem.UFFOptimizeMolecule( m )
> return rdkit.Chem.MolToMolBlock( m )
>
> and I get
>
> rdkit.Chem.AllChem.UFFOptimizeMolecule( m )
> ValueError: Bad Conformer Id
>
> on the attached molecule. I wonder if it's triggering a bug in RDKit
> somewhere. (I did try RemoveHs() instead of add, it made no difference.)
>
> It's not a nice molecule...
> --
> Dimitri Maziuk
> Programmer/sysadmin
> BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu
>
>
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leadership blogs to news, videos, case studies, tutorials and more. Take a
look and join the conversation now. http://goparallel.sourceforge.net/
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