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
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> > <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
>
>
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>
--
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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