Just to follow up with the details - here is the line in the script to
change:
conformers = AllChem.EmbedMultipleConfs
(molecule,numConfs,pruneRmsThresh=0.5, numThreads =3)
to
conformers = AllChem.EmbedMultipleConfs
(molecule,numConfs,pruneRmsThresh=0.5, numThreads =3, randomSeed=737 )
(where 737 is an integer constant of your choice, but not -1).
Richard
On Tue, Aug 28, 2018 at 12:55 PM Richard Cooper <
richardiancooper+rdkitdisc...@gmail.com> wrote:
>
> Hi Ali,
>
> Sorry I missed your email.
>
> The behaviour you describe is correct, due to a random seed in the
conformer generation step. The descriptor value usually doesn't vary by too
much.
>
> I think you can give the conformer generation a constant random seed if
you need a reproducible number for nConf20.
>
> Regards, Richard
>
>
> On Tue, 28 Aug 2018, 00:25 Ali Eftekhari, <a.b.eftekh...@gmail.com> wrote:
>>
>> Hello all,
>>
>> I am trying to calculate 3D Descriptors following this publication:
>> "Beyond Rotatable Bond Counts: Capturing 3D Conformational Flexibility
in a Single Descriptor", Jerome G. P. Wicker and Richard I. Cooper. J.
Chem. Inf. Model. 2016, 56, 2347−2352
>>
>> I am essentially using the same script as they have in the supporting
information and i have attached it here as well. In Table 2 from the above
calculation, the value of the descriptor (nConf20) for ZINC000290539224
molecule is listed as 10. However, when I run the exact code as the one
they used, I get different value at each run.
>>
>> I have already contacted the authors but got no response. I am
wondering if the code they have in the supporting information is not right
or the value they listed in the table is wrong?
>>
>> The SMILES string for this particular molecule is:
>> 'CC(C)N2CC(NCc1cnc(C(C)O)s1)CC2=O'
>>
>> Thanks in advance for your help!
>>
>
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