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