On Wed, Oct 25, 2017 at 6:52 PM, Sereina <sereina.rini...@gmail.com> wrote:
> Hi Paul,
>
> Regarding your second question:
>
> On 25 Oct 2017, at 18:36, Paul Hawkins <phawk...@eyesopen.com> wrote:
>
> Also, once I generate the conformers what is best way to cluster them by
> RMSD so that each conformer has a minimum RMSD to all the others in the set?
>
>
> I think the function AllChem.GetConformerRMSMatrix() might do (parts of)
> what you want.
>
And since we're doing the "each reply refines the answer" thing, here's a
bit of code that does Butina clustering to group the conformers:
In [71]: m = Chem.AddHs(Chem.MolFromSmiles('OCCc1ncccc1CCCC'))
In [72]: AllChem.EmbedMultipleConfs(m,50,AllChem.ETKDG())
Out[72]: <rdkit.rdBase._vecti at 0x11630ac90>
In [73]: dm = AllChem.GetConformerRMSMatrix(m)
In [76]: cs =
Butina.ClusterData(dm,m.GetNumConformers(),1.5,isDistData=True,reordering=True)
In [77]: len(cs)
Out[77]: 9
In [78]: for c in cs:
...: print(c)
...:
(36, 2, 3, 4, 7, 8, 9, 11, 14, 15, 16, 17, 21, 29, 30, 33, 34, 40, 43, 44,
46, 47)
(10, 0, 32, 35, 38, 45, 49, 18, 19, 22, 23, 25, 27)
(48, 6, 39, 42, 12, 24, 26)
(5, 41, 31)
(37,)
(28,)
(20,)
(13,)
(1,)
The 1.5 argument in the call to Butina.ClusterData is the distance
threshold for things to be considered neighbors.
-greg
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