At least for the MCS calculation, there is an R package
for chemistry:

https://bioconductor.org/packages/release/bioc/vignettes/fmcsR/inst/doc/fmcsR.html

On 02/19/2017 07:33 PM, Thomas Evangelidis wrote:
> Dear all,
>
> I want to align 250 compounds that binding to the same pocket to one of
> the 9 available crystal ligands. I chose the reference ligand based on
> the Morgan2 similarity to the probe molecule. Then I align the 2
> compounds using:
>
> pyO3A = rdMolAlign.GetO3A(qmol, refmol, prbCid=qconfID, refCid=0,
> reflect=True)
> RMSD = pyO3A.Align()
>
> ​and keep only the conformer of the probe with the lowest RMSD to the
> reference compound. However, the alignment looks terrible when I
> visualize it, so I would like to ask if there is any way to align the
> maximum common substructure only. I tried to align only the core of both
> molecules as defined by MurckoScaffold.GetScaffoldForMol(mol)​, but
> still the alignment looks bad. I have seen in the documentation how to
> find the maximum common substructure with rdFMCS.FindMCS but before I
> engage into programming it I would like to know if there is any
> automatic way to find it on the fly while aligning the 2 molecules.
>
>
>
> --
>
> ======================================================================
>
> Thomas Evangelidis
>
> Research Specialist
>
> CEITEC - Central European Institute of Technology
> Masaryk University
> Kamenice 5/A35/1S081,
> 62500 Brno, Czech Republic
>
> email: tev...@pharm.uoa.gr <mailto:tev...@pharm.uoa.gr>
>
>           teva...@gmail.com <mailto:teva...@gmail.com>
>
>
> website: https://sites.google.com/site/thomasevangelidishomepage/
> <https://sites.google.com/site/thomasevangelidishomepage/>
>
>

------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, SlashDot.org! http://sdm.link/slashdot
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Reply via email to