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
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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
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