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
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