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name: structure-analysis description: "Use Biotite structure analysis APIs for AtomArray construction, filtering, bonds, geometry, superposition, contacts, trajectories, and structural alphabets." disable-model-invocation: true metadata: disco-role: operating license: BSD 3-Clause

Biotite Structure Analysis

Use this sub-skill when the task centers on in-memory molecular structures with biotite.structure: constructing or editing Atom, AtomArray, or AtomArrayStack objects; filtering atoms/residues/chains; managing bonds/connectivity; measuring geometry; superimposing structures; computing RMSD/RMSF, SASA, hydrogen bonds, base pairs, pseudoknots, secondary structure, periodic boxes, or trajectory summaries.

For file parser classes, PDB/PDBx/BinaryCIF conversion, or trajectory file reading/writing, route to ../file-io-formats/. For RCSB/Entrez/AlphaFold fetching or external applications such as DSSP, route to ../database-application/. For PyMOL/RDKit/OpenMM or plotting/export-oriented tasks, route to ../interfaces-visualization/.

Start Here

• Read references/api-reference.md for the main classes, annotations, filters, geometry, connectivity, and structure-info helpers.
• Read references/workflows.md for task recipes covering construction, filtering, bonds, superposition, trajectories, nucleic acids, and structural alphabets.
• Read references/troubleshooting.md when coordinates, annotations, bonds, altlocs, periodic boxes, secondary structure, or residue names behave unexpectedly.
• Run scripts/structure_geometry_smoke.py --help to inspect the bundled smoke helper, or run it directly for a tiny local AtomArray geometry check.

Core Routing Rules

• Prefer import biotite.structure as struc and import biotite.structure.info as info for structure work.
• Treat coordinates, distances, surface areas, boxes, and trajectory lengths as Å-based unless a caller explicitly converted units.
• Keep parser decisions out of this sub-skill: load structures with the file-IO sub-skill, then return here for in-memory analysis.
• Keep database and visualization side effects out of structure recipes unless another sub-skill owns that step.

Evidence Base

This sub-skill distills the Biotite structure tutorial pages for atoms, filtering, bonds, editing, measurement, trajectories, and structural alphabets; source modules under src/biotite/structure/; structure examples under doc/examples/scripts/structure/; and behavior checks from tests/structure/test_atoms.py, test_filter.py, test_geometry.py, test_superimpose.py, test_hbond.py, test_sasa.py, test_connect.py, and test_basepairs.py.