You might want to take a look at this older thread for some additional
hints:
http://www.mail-archive.com/rdkit-discuss%40lists.sourceforge.net/msg00484.html
-greg
On Tue, Feb 10, 2015 at 5:13 PM, Dmitri Maziuk <dmaz...@bmrb.wisc.edu>
wrote:
> 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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