Hi Dr. Cooper,
Thanks for your response and the suggestions. I added randomSeed=737 and I
now get value of 14 for descriptor nConf20 for ZINC000290539224 molecule
(although it is different than your paper [the value is 10] it does not
change on each run). My concern now is on the general usage of nConf20
descriptor. For instance, is there a limitation on what molecules can be
used for estimating their nConf20? Since the conformers are generated
randomly, how reliable is this descriptor to use it as a replacement for
Rotatable Bond Count (RBC) in all machine learning models.
In my application, the calculated values of RBC for 350 molecules range
from 0 to 7 with (80% between 0-4 and 20% between 5-7). The calculated
values of nconf20 is between 0-40 but with 95% between 0-3. Since nConf20
for majority of molecules is between 0-3, I am concerned on the usage of
nconf20 as the main descriptor. Could you please comment on that?
Thanks,
Ali
On Wed, Aug 29, 2018 at 6:32 AM Richard Cooper <
richardiancooper+rdkitdisc...@gmail.com> wrote:
>
> 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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