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
Or, if you are feeling adventurous, I think it would be great if we
had a plain text file of obabel commands that are run with the
expected outputs following some standard naming convention. For
example, maybe each line is of the form:
<CMD> <ARGUMENTS> # files/correct_output
and the test function compares the standard out of running the command
to the correct_output file.
This would make it much easier to add tests if it is appropriate to
compare file outputs exactly.
We have a script that reads a Gaussian file and a reference sdf file and
compares whether the double bonds are in the same place and whether
generated atom types for the GAFF force field are the same. It uses the
openbabel python interface such as to keep everything in memory and not
create a ton of temporary files or tedious parsing of stdout. Would that
be an option? The crux is then that we need to add largish Gaussian
output files to the repository.
Thanks,
David Koes
Associate Professor
Computational & Systems Biology
University of Pittsburgh
On 6/8/21 11:22 AM, David van der Spoel wrote:
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 framework? Or should we just add a new python
script there with in and output data?
FYI, we have made quite a few fixes already that likely are of interest
to others:
% git diff master:data/bondtyp.txt data/bondtyp.txt | wc
128 784 4532
--
David van der Spoel, Ph.D.,
Professor of Computational Molecular Biophysics
Uppsala University.
http://virtualchemistry.org
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