What does it mean to take symmetry into account ?
On Mon, Nov 18, 2019 at 6:07 PM topgunhaides . <sunzhi....@gmail.com> wrote:
> Hi Greg,
>
> Thanks a lot! This is very helpful. Further questions:
>
> 1. If I need RMSD matrix for clustering, I guess I will have to figure out
> a way to loop over all conformers to get the matrix first, if I choose to
> use GetBestRMS()?
>
> 2. Does the AlignMolConformers() handle symmetry and align all
> permutations to get the best "RMSlist"?
>
> 3. So I guess the EmbedMultipleConfs() also uses "standard" (no symmetry
> consideration) method to compute RMS for pruning?
>
> I appreciate your help!
>
> Best,
> Leon
>
>
> On Thu, Nov 14, 2019 at 2:45 AM Greg Landrum <greg.land...@gmail.com>
> wrote:
>
>> Hi Leon,
>>
>> There's not really a "right" answer to your question - it depends on what
>> you want to calculate.
>> I personally think it makes more sense to use the heavy atom RMSD (which
>> is what you get if you remove Hs before calculating the RMSD), particularly
>> if you are comparing to experiment.
>>
>> Note that AllChem.GetConformerRMSMatrix() does not take symmetry into
>> account, so you may not get the correct results.
>> I just opened a ticket to fix this, but in the meantime if you have
>> molecules with symmetry-equivalent atoms you are probably better off
>> generating the conformer RMS matrix manually using GetBestRMS().
>>
>> Best,
>> -greg
>>
>> On Wed, Nov 13, 2019 at 5:17 PM topgunhaides . <sunzhi....@gmail.com>
>> wrote:
>>
>>> Hi guys,
>>>
>>> I am new to RDKit, and have a question about adding and removing Hs.
>>>
>>> As recommended in the documentation, hydrogen atoms should be added for
>>> generating conformers, optimization, etc.
>>>
>>> However, for clustering, should the Hs be removed first, before
>>> generating the conformer RMS matrix? For instance:
>>>
>>>
>>> from rdkit import Chem
>>> from rdkit.Chem import AllChem, TorsionFingerprints
>>>
>>> suppl = Chem.SDMolSupplier('molecule.sdf')
>>>
>>> for mol in suppl:
>>> mh = Chem.AddHs(mol)
>>> cids = AllChem.EmbedMultipleConfs(mh, numConfs=5, maxAttempts=1000,
>>> pruneRmsThresh=0.5, numThreads=0,
>>> randomSeed=1)
>>> m = Chem.RemoveHs(mh)
>>> # RMS matrix
>>> rmsmat = AllChem.GetConformerRMSMatrix(m, prealigned=False)
>>> # TFD matrix
>>> tfdmat = TorsionFingerprints.GetTFDMatrix(m)
>>> print(rmsmat)
>>> print(tfdmat)
>>>
>>>
>>> Note I remove the Hs before getting RMS and TFD matrices. Both resulting
>>> matrices are different if I do not remove Hs. The RMS without Hs, in
>>> general, tend to be smaller than the RMS with Hs. This will in turn affect
>>> the subsequent clustering result.
>>>
>>> Could you guys give me some suggestions? Thank you!
>>>
>>> Best,
>>> Leon
>>> _______________________________________________
>>> Rdkit-discuss mailing list
>>> Rdkit-discuss@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>>
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