Should have used vim. :-) On Tue, 26 Nov 2019 at 13:12, David van der Spoel <sp...@xray.bmc.uu.se> wrote:
> Den 2019-11-26 kl. 13:58, skrev Noel O'Boyle: > > The "M CHG" line looks dubious. It states that there is a single > > charge, a +5 charge on atom 1. What is the source of this SDF file? > > Emacs :( > > > > > Regards, > > - Noe > > > > On Tue, 26 Nov 2019 at 12:12, David van der Spoel <sp...@xray.bmc.uu.se > > <mailto:sp...@xray.bmc.uu.se>> wrote: > > > > 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, > > > - Noel > > > > > > On Tue, 26 Nov 2019 at 09:50, 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: > > > > > > 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>> > > > > <mailto: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>> > > > > <mailto: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 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 Biology > > Head of Department, Cell & Molecular Biology, Uppsala University. > > Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. > > http://www.icm.uu.se > > > > > -- > 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 >
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