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name: network-planning description: "Plan OpenFE components, atom mappings, ligand networks, and RBFE/RHFE alchemical networks before execution." disable-model-invocation: true metadata: disco-role: operating license: MIT

Network Planning

Use this sub-skill when a task is about building OpenFE inputs before simulation: components, atom mappings, ligand networks, RBFE/RHFE alchemical networks, or deciding whether to use API planning, CLI planning, or manual network construction.

Start Here

1. Validate ligand/protein inputs with validate_ligand_inputs.py before planning or diagnosing mapper failures.
2. Use API Reference for constructors, mapper/scorer choices, ligand network functions, and RBFE/RHFE planner data flow.
3. Use Workflows for end-to-end planning recipes, difficult diagnostics, and protocol handoff decisions.
4. Use Data Formats for SDF/MOL2/PDB/PDBx, GraphML ligand networks, alchemical-network JSON, and transformation JSON expectations.
5. Use Troubleshooting for missing optional dependencies, invalid ligand names, unmapped edges, disconnected networks, charged transformations, malformed files, and immutable objects.

Scope

This sub-skill covers:

• SmallMoleculeComponent, ProteinComponent, ProteinMembraneComponent, SolventComponent, ChemicalSystem, LigandAtomMapping, and LigandNetwork construction concepts.
• LomapAtomMapper, KartografAtomMapper, PersesAtomMapper, lomap_scorers, perses_scorers, and openfe.setup.ligand_network_planning functions.
• RBFEAlchemicalNetworkPlanner, RHFEAlchemicalNetworkPlanner, and the RelativeAlchemicalNetworkPlanner data flow from ligands to AlchemicalNetwork, including the difference between Python planner defaults and CLI planning defaults.
• Pre-execution route decisions: API vs CLI planning, topology choice, mapper/scorer tradeoffs, and when to hand a plan to protocol or CLI execution guidance.

Route elsewhere:

• Protocol settings, OpenMM backend choices, adaptive settings details, and simulation configuration -> protocols.
• CLI flag syntax, openfe plan-*, openfe quickrun, repeat job construction, and gather* command use -> cli-workflows.
• Post-run estimates, uncertainties, failed edge summaries, and result aggregation -> results-analysis.

Safe Default Pattern

• Do input checks first; do not run OpenMM while diagnosing planning failures.
• Prefer unique, explicit ligand names before creating networks; duplicate or empty names can create ambiguous radial centers and duplicate transformation labels.
• Start with a maximal network to debug mapper coverage, then choose minimal spanning, redundant minimal spanning, radial, or explicit edges based on campaign needs.
• Treat OpenFE components, mappings, and networks as immutable; rebuild them from corrected inputs rather than mutating them in place.
• For charged transformations, identify the affected ligand pairs during planning and hand protocol-setting decisions to protocols.