biotite
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biotite-dev
A comprehensive library for computational molecular biology
Currently `MolFile` only supports `V2000` CTAB formats. However, there are also many V3000 MOL/SDF files out there. The authoring company [even recommends using V3000](https://discover.3ds.com/sites/default/files/2020-08/biovia_ctfileformats_2020.pdf).
Currently, `write_alignment_to_cigar()` omits terminal gaps in the segment sequence. However, there are use cases where it is practical to keep terminal gaps as deletions (`D` code). An optional parameter would...
This PR implements `ruff` as code formatter and linter and reformats the entire code base (except Cython https://github.com/astral-sh/ruff/issues/10250).
fix #570 use 3 regex patterns to match fields in one line for handle embed quote in mmcif file: ``` single_quote_pattern = r"('(?:'(?! )|[^'])*')(?:\s|$)" double_quote_pattern = r'("(?:"(?! )|[^"])*")(?:\s|$)' unquoted_pattern =...
after adding two bond list, `merged_bond_list` has wrong `_max_bonds_per_atom`. ``` import numpy as np import biotite.structure as struc bond_list1 = struc.BondList(2, np.array([(0,1)])) # max_bond_per_atom=1 bond_list2 = struc.BondList(3, np.array([(0,1),(0,2)])) # max_bond_per_atom=2...
Currently Biotite requires *MDTraj* as additional dependency only for reading coordinates from trajectory files. However, *MDTraj* does not support NumPy 2.0, yet, but Biotite 1.0 will require NumPy 2.0. Therefore...
The new documentation #552 contains also a revamped tutorial. However, some important sets of functionalities miss a tutorial: - [ ] `tantan` application interface: `tutorial/application/tantan` - [ ] `sra-tools` application...
Currently the default color scheme for protein sequence alignment and logo plots is `"rainbow"`. However `"flower"` is visually more appealing and depicts amino acid similarities better: https://doi.org/10.1186/s12859-020-3526-6
As the Biotite code base has become quite stable and well tested in recent years, a `1.0` release is reasonable. However, before all necessary backwards incompatible changes should be implemented...
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A comprehensive library for computational molecular biology