Patrick Kunzmann comments

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                                            Patrick Kunzmann

Incorrect bonds during parsing form `connect_via_residue_names()`

If I am not wrong, the problem is not that these PDB files use other alternative atom naming, but the wrong residue names, i.e. they use the name `XYZ` for...

Incorrect bonds during parsing form `connect_via_residue_names()`

One could set `custom_bond_dict` in [`connect_via_residue_names()`](https://www.biotite-python.org/latest/apidoc/biotite.structure.connect_via_residue_names.html) and restrict them to amino acid and nucleotides. However, I did some further research and did not find a trustful source which other residues...

`DsspApp` is not usable with more recent `mkdssp` versions

DSSP 4 is now available on Conda https://github.com/conda-forge/staged-recipes/pull/27330

Install rust toolchain on building source distribution

Thanks for the discussion. For me both options, an explicit extra dependency in `build-system` or an implicit installation in an environment by `maturin` would work.

Install rust toolchain on building source distribution

Thanks a lot!

Add function to filter hydrogen atoms

Good to know there is a special residue name for deuterated water. This can be added to `filter_solvent()` then.

Introducing Rust code into Biotite

> Do you plan to still accept Cython in new contributions in the long-term? Yes, at least for the foreseeable future. However, I think @JacobAnter and me were the only...

Add function to parse secondary structure elements from PDBx

I think a dictionary mapping the chain ID to the secondary structure elements (SSE) would be good. I think the SSE should be an ndarray - either using letters like...

Add function to parse secondary structure elements from PDBx

Thanks by the way for tackling this feature! I assigned the issue to you.

Add function to parse secondary structure elements from PDBx

Hi, are you still planning to implement this feature? If not, this is also fine, but I would free the issue up again.