On 2/9/2015 11:12 PM, Greg Landrum wrote:
> 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:
Thanks, but I'm trying to run an unattended pipeline. Is there a
downside of calling useRandomCoords on molecules that don't have this
problem? Would this be the way to go:
x = AllChem.EmbedMolecule(m)
if x < 0 :
x = AllChem.EmbedMolecule(m,useRandomCoords=True)
# if x is still < 0 -- then what?
try :
AllChem.UFFOptimizeMolecule( m )
except :
pass
MolToMolBlock( m )
Thanks again,
Dima
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