Patrick Kunzmann
Patrick Kunzmann
The *UniProt KB* has revamped its REST API, with a new URL and changed parameter names (https://www.uniprot.org/help/api). While fetching entries still works (for now), the doctests and tests involving `search()`...
When a `Tree` is created from a large number of sequences, the following error occurs: ``` src/biotite/sequence/phylo/tree.pyx:323: in biotite.sequence.phylo.tree.Tree.from_newick root, distance = TreeNode.from_newick(newick, labels) src/biotite/sequence/phylo/tree.pyx:921: in biotite.sequence.phylo.tree.TreeNode.from_newick child, dist =...
Currently, *Biotite* uses the classical `setuptools` with a `setup.py` for building the package. However, with the changes introduced by PEP517, we can now use more modern and cleaner tools, like...
Both `mmtf.get_structure()` and `connect_via_residue_names()` assign too many bonds, if two adjacent residues share the same residue ID. An example is `LEU/ILE 25` in `1JXT`. In this case all terminal hydrogen...
This PR aims to improve the performance of `biotite.structure.rdf()` (issue #307): Although a `CellList` scales well for a large number of centers, the *brute-force* approach, i.e. the pairwise distance measurement...
### Bug Description Hi, I have a project (https://github.com/biotite-dev/fastpdb) built with `maturin` that uses mixed Rust/Python code. However, the wheels built from this project do only include the `.so` file,...
- [x] I have searched the [issues](https://github.com/python-poetry/poetry/issues) of this repo and believe that this is not a duplicate. - [x] I have searched the [documentation](https://python-poetry.org/docs/) and believe that my question...
With the deprecation of `MMTF` (#525), this PR implements `BinaryCIF` as the new standard binary structure file format for Biotite. - [ ] Adds `biotite.structure.io.pdbx.BinaryCIFFile` which is completely compatible with...
The Biotite example gallery extensively uses structure files in MMTF format. However, MMTF will stop to be served soon (#525) and hence a lot of examples will also stop working...
As MMTF is now deprecated (#525) another method is desired to parse the secondary structure from PDB. PDBx files contain annotations of helices and sheets in the `struct_conf` and `struct_sheet_range`...