---

name: interactions description: "Choose, parameterize, customize, and troubleshoot ProLIF interaction classes." disable-model-invocation: true metadata: disco-role: operating license: Apache 2.0

ProLIF Interactions

Use this sub-skill when an agent must choose interaction classes, tune interaction parameters, inspect direct residue-level matches, use implicit-hydrogen hydrogen bonds, or configure bridged interactions such as WaterBridge.

Route First

• For molecule conversion, residue labels, water selections, or hydrogen preparation, use ../molecules-and-io/ first.
• For running trajectories, docking poses, single-pair generation, DataFrame export, bitvectors, countvectors, or pickle I/O, use ../fingerprints/ after the interaction setup is chosen.
• For ligand networks, barcode plots, 3D views, or residue display, use ../visualization/ after a fingerprint exists.

Start Here

1. Discover supported names with scripts/list_interactions.py; add --include-bridged when WaterBridge is relevant.
2. Choose interaction names for prolif.Fingerprint(interactions=...); default interactions are documented in references/interaction-catalog.md.
3. Pass constructor overrides through parameters={"InteractionName": {...}}; keep keys case-sensitive and matching the class name.
4. Use count=True when every matching atom combination matters; otherwise ProLIF stores only the first match per residue pair and interaction.
5. Use implicit_hydrogens=True or explicit ImplicitHBAcceptor/ImplicitHBDonor names for heavy-atom-only hydrogen-bond workflows.
6. Use parameters={"WaterBridge": {"water": water_selection_or_molecule, ...}} whenever WaterBridge is included.

Reference Map

• references/api-reference.md: constructor signatures, metadata structure, direct methods, ignore, and bridge APIs.
• references/interaction-catalog.md: available names, defaults, geometric/SMARTS parameter names, and interaction roles.
• references/workflows.md: practical setup patterns for parameter tuning, implicit hydrogen bonds, water bridges, direct residue checks, counts, and custom interactions.
• references/troubleshooting.md: recovery steps for unknown names, implicit/explicit hydrogen mismatches, water bridge errors, VdW radii failures, missing metadata, overbroad searches, and count confusion.