Migrate remaining content of biotite-util repository to biotite

[padix-key]

Most functionalities from https://github.com/biotite-dev/biotite-util have been already integrated in one way or another into this repository. This PR finishes the migration. The analogs of the directories in biotite-util are the following:

biotite-util	biotite
build_gallery	CI job
datasets	Refactored implementation in setup_ccd.py
deploy	CI job
example_trajectories	Needed to be used only once (not migrated)
leontis-westhof-tests	Migration in this PR
python_roles	Needed to be used only once (not migrated)
test_structures	Migration in this PR

As the NDB has been superseded by the NAKB, which uses as different CSV format for describing base pairs (see for example https://www.nakb.org/naparams.html?1GID_1), the script cannot be used anymore to create new test data. However, probably new test data will also not be necessary in the future, so an adaption of the script is not planned.

[padix-key]

@t0mdavid-m As you are the author of the leontis-westhof-tests, do you agree with me that they are not migrated?

[t0mdavid-m]

With minor adjustments, I created a version of the leontis-westhof-tests scripts that work with the NAKB database. Thus, we could create a CI-job to automatically update the test cases.

However, I am not sure if that would actually be useful as the glycosidic bond orientations and interacting edges should not change over time. In my opinion, including the generating scripts into biotite-util was more about providing transparency how the test data was obtained. For this purpose I moved the updated scripts to tests/structure/data/base_pairs.

[padix-key]

Thank you very much! I agree that the bonds will not change anymore, so we can omit a CI job for now. But it is nice to have a way to generate these files, if one would like to add entries to the test dataset in the future.