On 2021-05-11 21:00, David Koes wrote:
Hi David,
The data file _should_ be being used as long as openbabel can find
it. The hardcoded values in the C++ source code are there as a
fallback when the data files can't be found.
I recently had a pull request merged that updates the C++ versions to
match the data files (previously they were very out of date resulting
in bad behavior when the data files couldn't be found due to, for
example, openbabel being installed in strange place):
https://github.com/openbabel/openbabel/pull/2328
If you want to improve the bond typing, change the data files, not the
source code. If the problem is the source code has bad bond typing,
update to a version with the pull request and rebuild.
Thanks for your reply. The problem was that charged ring systems are not
detected in all cases. In order to fix this, we could add this
information to bondtyp.txt (including code to parse it), or make an
additional data file. The advantage of adding it to bondtyp.txt is that
(in this case) the smarts defining the ring are in one place only. A
separate file would have the advantage that bondtyp.txt does not have to
change its format.
Preferences? Or are there other ways to make OB detect charge localization?
Cheers, David.
Thanks,
David Koes
Associate Professor
Computational & Systems Biology
University of Pittsburgh
On 5/11/21 2:51 PM, David van der Spoel wrote:
Hi,
is anyone working on bondtyper.cpp? Apparently, the data file
bondtyp.txt is not used at all and the information about bonding is
hardcoded in the C++ source code. I would be happy to help, but before
spending considerable effort it would be good to know if there is a plan
for this part of the code.
Cheers,
--
David van der Spoel, Ph.D.,
Professor of Computational Molecular Biophysics
Uppsala University.
https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fvirtualchemistry.org%2F&data=04%7C01%7Cdkoes%40pitt.edu%7C7c0df21efdda4474888708d914addb90%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C1%7C637563559213381322%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=lffer4K7HY%2BExwngNb%2F3r0JFz1yQYRiWrYXz7Pd7ZGY%3D&reserved=0
--
David van der Spoel, Ph.D.,
Professor of Computational Molecular Biophysics
Uppsala University.
http://virtualchemistry.org
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