Hi David, Can you provide the input file?
Regards, - Noel On Tue, 26 Nov 2019 at 09:50, David van der Spoel <sp...@xray.bmc.uu.se> wrote: > Den 2019-11-26 kl. 10:12, skrev Noel O'Boyle: > > 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. > Unfortunately, no. The structure below has 7 hydrogens and one charge > but obprop adds one H and 4 (!) charges. > > % obprop 2-aminoguanidinium.sdf > name 2-aminoguanidinium.sdf 1 > formula CH8N4+++++ > > > > > > OpenBabel11261907103D > > 12 11 0 0 0 0 0 0 0 0999 V2000 > -1.5988 -0.6139 0.0135 N 0 0 0 0 0 0 0 0 0 0 0 0 > -0.4655 1.3957 -0.0077 N 0 0 0 0 0 0 0 0 0 0 0 0 > 0.7405 -0.6123 0.0118 N 0 0 0 0 0 0 0 0 0 0 0 0 > 1.9392 0.1153 0.0724 N 0 0 0 0 0 0 0 0 0 0 0 0 > -0.4481 0.0607 0.0074 C 0 0 0 0 0 0 0 0 0 0 0 0 > -1.6144 -1.6250 0.0385 H 0 0 0 0 0 0 0 0 0 0 0 0 > -2.4894 -0.1345 0.0041 H 0 0 0 0 0 0 0 0 0 0 0 0 > -1.3186 1.9349 -0.0175 H 0 0 0 0 0 0 0 0 0 0 0 0 > 0.4173 1.8753 -0.1389 H 0 0 0 0 0 0 0 0 0 0 0 0 > 1.9696 0.6569 0.9451 H 0 0 0 0 0 0 0 0 0 0 0 0 > 2.7365 -0.5322 0.1048 H 0 0 0 0 0 0 0 0 0 0 0 0 > 0.8109 -1.6139 -0.1611 H 0 0 0 0 0 0 0 0 0 0 0 0 > 1 6 1 0 0 0 0 > 2 8 1 0 0 0 0 > 4 3 1 0 0 0 0 > 4 11 1 0 0 0 0 > 4 10 1 0 0 0 0 > 5 1 1 0 0 0 0 > 5 2 1 0 0 0 0 > 5 3 1 0 0 0 0 > 7 1 1 0 0 0 0 > 9 2 1 0 0 0 0 > 12 3 1 0 0 0 0 > M CHG 1 1 5 > M END > > > > > Regards, > > - Noel > > > > On Tue, 26 Nov 2019 at 06:50, David van der Spoel <sp...@xray.bmc.uu.se > > <mailto: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 > > <mailto:OpenBabel-Devel@lists.sourceforge.net> > > https://lists.sourceforge.net/lists/listinfo/openbabel-devel > > > > > -- > 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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