How about "explicit", rather than "physical", hydrogens?
-P. Sent from a cell phone. Please forgive brvty and m1St@kes. On Sep 9, 2016 1:57 AM, "Greg Landrum" <greg.land...@gmail.com> wrote: > > > On Thu, Sep 8, 2016 at 10:35 PM, Dimitri Maziuk <dmaz...@bmrb.wisc.edu> > wrote: > >> On 09/08/2016 02:26 PM, Brian Kelley wrote: >> > Dimitri, Hs are removed. >> > >> > Their is a removeHs argument in MolFromMolBlock (python) that defaults >> to >> > true. >> > >> > There is a corollary in SDMolSupplier if you are using that. >> > >> > supplier = SDMolSupplier(filename, removeHs=false) >> > >> > if this helps. >> >> Thank you, it does: >> rdkit.Chem.SupplierFromFilename(sys.argv[1], removeHs = False ).next() >> returns a molecule with -- presumably "physical" -- hydrogens. >> > > "Physical hydrogens" (I'm not sure that I like that term, but since I > don't have a ready alternative other than "hydrogens that are in the graph" > I will use it for now) are actually present in the graph, if you do > mol.Debug(), Chem.MolToMolBlock() for Chem.MolToSmiles() you will see them. > > >> The reason I ask is if they're removed and re-added, I'd worry about >> their indexes matching what's in the source file. Which might matter in >> the case of e.g. stereospecifically assigned methylene protons. (Or so >> they tell me ;) > > > This is absolutely correct: if you remove the Hs and then later re-add > them it is extremely unlikely that you will end up with the same H indices > before and after the change. It makes much more sense to just use > removeHs=False > > -greg > > > ------------------------------------------------------------ > ------------------ > > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > >
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