With my luck factor, I'd probably randomly get the same seed twice.
I'd rather do it the Java way - something akin to using
getCurrentTimeInMillis() as seed.
Yes, in utils.cpp, it always looks like it is initialized to static rng_type
generator(42u);
Some Hitch-hikers Guide to the Galaxy fan there...
Thanks Greg
On 12 April 2011 11:28, Greg Landrum <greg.land...@gmail.com> wrote:
> Hi JP,
>
> On Tue, Apr 12, 2011 at 6:19 AM, JP <jeanpaul.ebe...@inhibox.com> wrote:
> >
> > A further discovery -- if you change the random seed
> > in .EmbedMultipleConfs(m, numConfs=10) you do get different conformers
> > randomSeed=1000
> > randomSeed=100
> > randomSeed=10
> > But randomSeed=-1 should do that by default! (no ?)
>
> There's an error in the documentation. If you don't provide a seed to
> EmbedMultipleConfs(), it uses -1 as the seed. If you want truly random
> conformations, use something like randomSeed=random.randint(0,1e6).
>
> Best,
> -greg
>
> >
> > On 12 April 2011 11:08, JP <jeanpaul.ebe...@inhibox.com> wrote:
> >>
> >> I cannot understand this. Using distance geometry, you should get
> >> different molecules each time you run the following program right
> (because
> >> of the random distance matrix) ?
> >> Why does this produce identical conformers on every run?
> >> from rdkit import Chem
> >> from rdkit.Chem import AllChem
> >> from rdkit.Chem import Descriptors
> >> def generateconformations(m):
> >> m = Chem.AddHs(m)
> >> ids=AllChem.EmbedMultipleConfs(m, numConfs=10)
> >> for id in ids:
> >> AllChem.UFFOptimizeMolecule(m, confId=id)
> >> return m
> >> mol = Chem.MolFromSmiles('C1CCC1OC')
> >> m = generateconformations(mol)
> >> confIds = [x.GetId() for x in m.GetConformers()]
> >> for id in confIds:
> >> print Chem.MolToMolBlock(m, confId=id)
> >>
> >>
> >> Is this the intended behaviour? A common use case is to generate
> >> conformers for a molecule and save them in a database -- but if you run
> this
> >> code 10 times, you will get the same 10 conformers, 10 times...
> >> Why is this?
> >>
> >>
> >>
> >>
> >>
> >> --
> >>
> >> Jean-Paul Ebejer
> >> Early Stage Researcher
> >> InhibOx Ltd
> >> Pembroke House
> >> 36-37 Pembroke Street
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> >> UK
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> > Jean-Paul Ebejer
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InhibOx Ltd
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UK
(+44 / 0) 1865 262 034
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