Biotite is a comprehensive Python library (current version 1.6.0) for computational molecular biology, offering a broad set of tools for sequence analysis, structural bioinformatics, and accessing data from biological databases. It leverages NumPy arrays for efficient, high-performance operations and provides seamless interfaces to integrate with external bioinformatics software, allowing users to streamline their analyses from basic scripting to developing full software packages. The library maintains an active development and release schedule, with significant updates in recent years.
pip install biotiteVerified import paths — ran on the pinned version, not inferred.
Downloads two protein sequences (avidin and streptavidin) from the NCBI Entrez database, parses them from a FASTA file, and performs a pairwise optimal sequence alignment using the BLOSUM62 matrix with affine gap penalties.
Ensure `biotraj` is installed (`pip install biotraj`) and update import paths if directly using `mdtraj` features that were previously proxied by Biotite.
Familiarize yourself with NumPy array operations and indexing. Biotite's documentation provides examples of how to interact with its NumPy-based data structures.
Always refer to the official documentation or example gallery to find the correct import paths for the specific classes or functions you intend to use.
Explicitly set `color_scheme='rainbow'` if you wish to retain the old default, or adapt to the new `flower` default. Consider if your visualization interpretations are affected by the color scheme change.
Update both NumPy and Biotite to their latest compatible versions: `pip install --upgrade numpy biotite` or `conda update numpy biotite`.
Ensure `biotite` is properly installed and updated: `pip install --upgrade biotite`. If the problem persists, downgrading to a specific working version (e.g., `pip install biotite==0.41.2` as seen in some contexts) might resolve it for certain environments.
Pre-process the PDB file to ensure charge fields adhere to the 'X+' format, or if possible, update Biotite to a version that might include a more robust parser for such non-standard formats. Manually editing the problematic charge entries in the PDB file is a direct solution.
Provide a `template` parameter to the `load_structure` function, typically by first loading a single frame or a reference structure from the trajectory or a separate PDB file. Example: `template_structure = biotite.structure.io.load_structure('reference.pdb'); trajectory = biotite.structure.io.load_structure('trajectory.xtc', template=template_structure)`.