Den 2019-11-26 kl. 13:06, skrev Noel O'Boyle:
Hi David,Can you provide the input file?
Attached, thanks for looking into this.
Regards, - NoelOn Tue, 26 Nov 2019 at 09:50, David van der Spoel <sp...@xray.bmc.uu.se <mailto: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> > <mailto: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> > <mailto: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 BiologyHead 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
2-aminoguanidinium.sdf
Description: chemical/molfile
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