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
>> Oxford
>> OX1 1BP
>> UK
>> (+44 / 0) 1865 262 034
>>
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>
>
> --
>
> Jean-Paul Ebejer
> Early Stage Researcher
> InhibOx Ltd
> Pembroke House
> 36-37 Pembroke Street
> Oxford
> OX1 1BP
> UK
> (+44 / 0) 1865 262 034
>
>
> This email and any files transmitted with it are confidential and intended
> solely for the use of the individual or entity to whom they are addressed.
> Any unauthorised dissemination or copying of this email or its attachments,
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