Patrick Kunzmann

No, unfortunately this information is currently only obtainable from PDB files via [`PDBFile.get_symmetry_mates()`](https://www.biotite-python.org/latest/apidoc/biotite.structure.io.pdb.PDBFile.html#biotite.structure.io.pdb.PDBFile.get_symmetry_mates). The reason is that it is much simpler to compute them from PDB files as the necessary...

Great! I think the aim would be to have a function `get_symmetry_mates()` in https://github.com/biotite-dev/biotite/blob/main/src/biotite/structure/io/pdbx/convert.py, analogous to the function in `structure.io.pdb` (https://www.biotite-python.org/latest/apidoc/biotite.structure.io.pdb.get_symmetry_mates.html). But for the start some private function that takes...

Hi, do you still work on this feature? Otherwise, I would try to tackle this issue soon.

Thanks for the fix. I checked the [CIF specification](https://www.iucr.org/resources/cif/spec/version1.1/cifsyntax) again (bottom of the document) and it seems that leading whitespaces in category names are not allowed. > DataItems ::= Tag...

@corredD If you do not have objections, I would simply apply my suggestions and merge this PR

Thanks for providing your great code and the initial refactoring! As indicated a will further refactor it.

I pushed some intermediate refactored code. No worries, I am not finished yet 😉 .

Did you create the reference sequence in `test_3di.py` with `foldssek`? And if so, how did you tell `foldseek` just to create the 3Di sequences without aligning anything? I am asking,...

Todo-list as reminder to myself: - [x] Add doctests - [x] Add substitution matrix - [x] Fill missing unit tests - [x] Add `foldseek` citation - [x] Add to `doc/apidoc.json`

From my side the code is ready, have a look if you like. Thanks again for providing the code from your package! Of course you can also add yourself to...