That sounds great. I for one will never complain about inconveniences induced by adding additional testing. You should
be able to gzip the files and read the gz version directly with obabel to save on space.
David Koes
Associate Professor
Computational & Systems Biology
University of
On 2021-06-08 17:37, David Koes wrote:
If all the issues manifest themselves with calls to obabel, I would
add functions to test/testbabel.py (the filename is a throwback to
when obabel was babel). You can see an example in this pull request:
https://github.com/openbabel/openbabel/pull/2379
If all the issues manifest themselves with calls to obabel, I would add functions to test/testbabel.py (the filename is
a throwback to when obabel was babel). You can see an example in this pull request:
https://github.com/openbabel/openbabel/pull/2379
Or, if you are feeling adventurous, I
On 2021-06-08 15:42, David Koes wrote:
Hi Madeleine,
It sounds like you have a really excellent set of test structures. It
would be fantastic if you could contribute these to the testing
framework.
We would be happy to do that, but maybe you can give a suggestion on
where in the testing
Hi Madeleine,
It sounds like you have a really excellent set of test structures. It would be fantastic if you could contribute these
to the testing framework.
David Koes
Associate Professor
Computational & Systems Biology
University of Pittsburgh
On 6/8/21 8:15 AM, Marie-Madeleine Walz
Hi Madeleine,
There is also a data file for ring types. That might help you fix the problem
with small rings.
openbabel/data/ringtyp.txt
Best,
Mohammad
> On Jun 8, 2021, at 8:15 AM, Marie-Madeleine Walz
> wrote:
>
> Hi David,
>
> thank you for your advice regarding using
Hi Mohammad,
thank you for your advice! I will have a look at that file.
With kind regards,
Madeleine
On 8 Jun 2021, at 14:34, Ghahremanpour, Mohammad
mailto:mohammad.ghahremanp...@yale.edu>> wrote:
Hi Madeleine,
There is also a data file for ring types. That might help you fix the problem
Hi David,
thank you for your advice regarding using AssignTotalChargeToAtoms. Adding it
resulted in less errors in the bond order assignment.
Unfortunately, it did not remove e.g. the error with sulfite (SO3^2-) that is
still getting three double bonds.
Another issue is that some of the small
