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Dihedral Backbone Does Not Account for Gaps, Returns Incorrect Values

3

I didn't see anything in the docs that says `biotite.structure.dihedral_backbone()` will return an incorrect value if there's a gap the protein backbone, i.e. it fails `biotite.structure.check_res_id_continuity()`. For example in the...

cing

Refactor test parametrization

2

Many tests in the `tests/` directory are parametrized. However, there are some aspects of these parametrizations that be made cleaner: - [ ] Replace `itertools.product` by multiple `@pytest.mark.parametrize` decorators -...

padix-key

Support for A2M/A3M files

1

Reading/writing MSAs from/to A3M files might be a useful addition to Biotite. A2M/A3M files are quite commonly accepted as input/produced by alignment programs or protein structure prediction pipelines (e.g. MMseqs2,...

JHKru

Python Binding for ViennaRNA

2

Python bindings for ViennaRNA are now available (and have been for a couple of years): https://www.tbi.univie.ac.at/RNA/ViennaRNA/refman/api_python.html We could think about replacing the call to the `RNAPlot` binary in `biotite.structure.graphics.plot_nucleotide_secondary_structure()` with...

t0mdavid-m

Currently the only way to ensure reproducible results of the `EValueEstimator` is calling `np.random.seed()` before creating it. However, this `np.random.xxx` API is deprecated and superseded by using an explicit [`Generator`](https://numpy.org/doc/2.0/reference/random/generator.html)....

padix-key

padix-key

Bonds cannot be found for alternative atom names

1

Following up #668, `chem_comp_atom.alt_atom_id` is part of the internal CCD, but is not used to determine bonds yet. However some (especially older) PDB entries contain those alternative atom names. For...

padix-key

This example should demonstrate the pairwise alignment of a protein sequence against a sequence profile. The profile can for example be compiled from a SCOP family. Ideally this example should...

padix-key

This example should comprise the following tasks: - [ ] Detect transmembrane parts of a protein structure - [ ] Plot the transmembrane region using - [ ] a [Protter-like](https://wlab.ethz.ch/protter/start/)...

padix-key

Analogous to https://www.biotite-python.org/latest/examples/gallery/structure/protein/peptide_assembly.html an idealized DNA double helix could be created from a sequence.

padix-key