Hey guys, Thanks for the responses!
So I now got the answer for my Q #2: No symmetry taken into account for AlignMolConformers(). Thanks Paolo for the example link. You guys are all very welcome to give me any suggestions on all three questions I asked. I appreciate it. Best, Leon On Mon, Nov 18, 2019 at 11:02 AM Paolo Tosco <paolo.tosco.m...@gmail.com> wrote: > Hi Omar, > > you may have a look at this thread for an explanation and an example: > > https://sourceforge.net/p/rdkit/mailman/message/36787480/ > > Cheers, > p. > On 18/11/2019 15:28, Omar H94 wrote: > > 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 >>>> >>> _______________________________________________ >> Rdkit-discuss mailing list >> Rdkit-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> > > > _______________________________________________ > Rdkit-discuss mailing > listRdkit-discuss@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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