An SDF file describes the number of hydrogens on each atom. Open Babel is neither adding nor removing them. AddHydrogens() is just making them explicit.
Regards, - Noel On Tue, 26 Nov 2019 at 06:50, David van der Spoel <sp...@xray.bmc.uu.se> wrote: > Hi, > > I was trying to use obprop on an SDF file, but found out that it adds > one hydrogen to my compound that should not be there. I then went to > look at the code and removed these two lines > if (!mol.HasHydrogensAdded()) > mol.AddHydrogens(); > recompiled and installed. > Lo and behold, the bug is still there! That is, upon reading an SDF file > the library already adds a hydrogen that shouldn't be there. > > What to do about this? > Replace > conv.Read(&mol, &ifs); > by a new call > conv.ReadAndDoNotModifyMyCompound(&mol, &ifs); > > Other suggestions? > > -- > David van der Spoel, Ph.D., Professor of Biology > Head of Department, Cell & Molecular Biology, Uppsala University. > Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. > http://www.icm.uu.se > > > _______________________________________________ > OpenBabel-Devel mailing list > OpenBabel-Devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-devel >
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