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A comprehensive library for computational molecular biology
When parsing some small molecules as `.pdb` files, extra incorrect bonds are being found by biotite. See [this issue](https://github.com/BradyAJohnston/MolecularNodes/issues/548) for more details for Molecular Nodes.  I've had a poke...
`numpydoc` now comes with a command line utility that validates docstrings: https://numpydoc.readthedocs.io/en/latest/validation.html This can be used by us to ensure correct docstrings. - Add CI step for `numpydoc validate` -...
Yasara Petworld model are written in a custom cif file, that put space in front of the catergories name. download models from http://download.yasara.org/petworld/index.html
Metal coordination within a molecule is currently recognized by Biotite as the the CCD describes it as single bond. However inter-residue metal coordinations are not recognized. For example, the heme...
As discussed in #607 `DsspApp` is not usable with more recent `mkdssp` version, limiting its usability. Hence, it should be compatible with version `3.0` (as currently) and later version. If...
Structural alphabets are a fusion of structure and sequence methods and can greatly benefit from the already implemented functionality in Biotite. In summary they tokenize each residue into some symbol...
This PR adds support for the *Protein Blocks* structural alphabet. Furthermore, it makes `dihedral_backbone()` more robust against missing backbone atoms, but it can only be used for a single protein...
This PR adds support for the CLePAPS structural alphabet (https://doi.org/10.1142/s0219720008003461). This PR is currently on hold as the obtained sequences do not fit the sequences from the reference implementation (taken...
Although the [Dynamic Request Throttling](https://pubchem.ncbi.nlm.nih.gov/docs/dynamic-request-throttling) is implemented in `biotite.database.pubchem`, it does not work properly, especially in the CI. Hence, the PubChem tests are relaxed in this PR: A `RequestError` due...
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A comprehensive library for computational molecular biology