Biotite

Use this repo skill when a task involves Biotite, biotite.sequence, biotite.structure, biological sequence/structure files, RCSB/Entrez/UniProt/PubChem/AlphaFold DB access, external bioinformatics application wrappers, or optional PyMOL/RDKit/OpenMM/Matplotlib integration.

Biotite is a Python package for computational molecular biology. It represents sequences and molecular structures with NumPy-backed objects and exposes APIs for file parsing, local analysis, database queries, visualization, and external tool orchestration.

Start Here

1. Confirm Biotite is installed in the active Python environment with the safe root check below.
2. Route to the focused sub-skill that owns the task; avoid using source-repo examples, tests, or docs at runtime.
3. Use sibling cross-links when a workflow spans fetch → parse → analyze → visualize.
4. Treat database calls, external executables, GUI rendering, and optional interfaces as opt-in side effects.
5. Read references/troubleshooting.md for install/import, build, optional dependency, and routing failures.

Install And Import Check

For normal package use, prefer wheel installs:

python -m pip install biotite
python - <<'PY'
import biotite
import biotite.sequence as seq
import biotite.structure as struc
print(biotite.__version__)
print(seq.ProteinSequence("ACDE"))
print(struc.AtomArray(1).array_length())
PY

For source checkouts, Biotite may need Python 3.12+, NumPy, Cython/build tooling, Rust build support, and compiled extension wheels. Prefer wheel installs for use-only tasks and source installs only for development or unreleased APIs.

Run the bundled diagnostic when routing a user problem:

python scripts/check_biotite_environment.py

It performs import/version checks and can also call the sub-skill optional diagnostics without contacting networks or running analyses.

Sub-skill Routes

• sequence-analysis: sequence objects, alphabets, annotations, translation/codons, pairwise and multiple alignment, substitution matrices, k-mer searches, profiles, phylogenetic trees, and sequence graphics decisions.
• structure-analysis: Atom, AtomArray, AtomArrayStack, filters, bonds, geometry, superposition, RMSD/RMSF, SASA, hydrogen bonds, base pairs, pseudoknots, periodic boxes, secondary structure, and trajectory analysis.
• file-io-formats: FASTA, FASTQ, GenBank, GFF, Clustal, PDB, PDBx/mmCIF, BinaryCIF, GRO, PDBQT, MOL/SDF, trajectory IO, and conversions into Biotite objects.
• database-application: RCSB, AlphaFold DB, Entrez, UniProt, PubChem, BLAST, Clustal Omega, MAFFT, MUSCLE, DSSP, AutoDock Vina, SRA, Tantan, and ViennaRNA wrappers.
• interfaces-visualization: PyMOL, RDKit, OpenMM, Matplotlib-backed graphics, sequence/structure visualization, and optional dependency diagnostics.

Common Workflow Routing

• Remote sequence alignment: use database-application for Entrez/UniProt/RCSB retrieval, file-io-formats for FASTA/GenBank parsing, then sequence-analysis for alignment/profile/phylogeny.
• Protein structure measurement: use database-application for RCSB/AFDB fetch if needed, file-io-formats for PDBx/BinaryCIF parsing, then structure-analysis for filtering, bonds, geometry, SASA, contacts, or superposition.
• Molecular interoperability: use file-io-formats for MOL/SDF/PDBx loading, structure-analysis to prepare coordinates/bonds, then interfaces-visualization for RDKit/OpenMM/PyMOL/plotting.
• External bioinformatics tools: use database-application first to check binaries and wrapper lifecycle; route outputs to file-io-formats, sequence-analysis, or structure-analysis.

Shared References And Scripts

• Repository snapshot and refresh baseline: references/repo-provenance.md.
• Router import metadata: references/repo-routing-metadata.json.
• Cross-cutting failure recovery: references/troubleshooting.md.
• Root environment diagnostic: scripts/check_biotite_environment.py.