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name: interfaces-visualization description: "Use Biotite optional interfaces for PyMOL, RDKit, OpenMM, Matplotlib-backed graphics, and visualization/export-oriented conversions." disable-model-invocation: true metadata: disco-role: operating license: BSD 3-Clause

Biotite Interfaces and Visualization

Use this sub-skill when the task asks a future agent to move Biotite objects into optional visualization, cheminformatics, or simulation packages: biotite.interface.pymol, biotite.interface.rdkit, biotite.interface.openmm, biotite.visualize, biotite.sequence.graphics, or biotite.structure.graphics.

For preparing AtomArray/AtomArrayStack objects, bonds, filters, coordinates, boxes, or trajectories before export, route to ../structure-analysis/. For loading PDB/PDBx/BinaryCIF, MOL/SDF, FASTA/alignment, or trajectory files before plotting/export, route to ../file-io-formats/. For database downloads or external command wrappers, route to ../database-application/.

Start Here

• Read references/api-reference.md to choose PyMOL, RDKit, OpenMM, or Matplotlib-backed graphics APIs and understand conversion boundaries.
• Read references/workflows.md for safe recipes that avoid assuming optional packages, network access, GUI availability, or display backends.
• Read references/troubleshooting.md for missing optional dependencies, PyMOL startup modes, unsupported bond/coordinate conversions, OpenMM unit/template issues, and plotting backend problems.
• Run scripts/check_optional_interfaces.py --help to inspect the bundled diagnostic, or run it directly to report optional interface availability without launching GUI-heavy workflows.

Core Routing Rules

• Treat PyMOL, RDKit, OpenMM, Matplotlib, IPython, ImageMagick, and ffmpeg as optional; check availability before using them.
• Prefer conversion functions over temporary files: PyMOLObject.from_structure(), rdkit.to_mol(), rdkit.from_mol(), openmm.to_topology(), openmm.to_system(), and openmm.from_state()/from_states().
• Keep Matplotlib plotting headless-safe by selecting an appropriate backend before importing matplotlib.pyplot in non-interactive scripts.
• Do not bundle or run gallery, animation, network-fetching, or GUI examples by default; treat them as reference recipes to adapt with local inputs.

Evidence Base

This sub-skill distills the interface tutorials for PyMOL, RDKit, and OpenMM; source modules under src/biotite/interface/; plotting helpers in src/biotite/visualize.py, src/biotite/sequence/graphics/, and src/biotite/structure/graphics/; behavior checks in tests/interface/; and visualization-heavy examples under doc/examples/scripts/ used only as reference recipes.