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. 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 ;) -- Dimitri Maziuk Programmer/sysadmin BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu
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