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name: cli-workflows description: "Use OpenFE console commands for planning networks, running quickrun jobs, gathering outputs, generating charges, fetching examples, viewing ligand networks, and testing installations." disable-model-invocation: true metadata: disco-role: operating license: MIT

OpenFE CLI Workflows

Use this sub-skill when the task is about the openfe command line interface: choosing a subcommand, ordering planning/execution/gathering steps, constructing quickrun commands, preparing repeat-safe job scripts, or troubleshooting CLI misuse.

Route Tasks

• Plan RBFE/RHFE campaign files with openfe plan-rbfe-network or openfe plan-rhfe-network; see planning and quickrun.
• Execute one transformation JSON with openfe quickrun, resume interrupted work, or generate shell/Slurm command plans; see planning and quickrun and the repeat command helper.
• Gather completed result JSONs with openfe gather, openfe gather-abfe, or openfe gather-septop; use this sub-skill for command selection only, then route detailed TSV schemas and result interpretation to ../results-analysis/SKILL.md.
• Generate charged ligand SDFs with openfe charge-molecules, view GraphML ligand networks with openfe view-ligand-network, fetch tutorial resources with openfe fetch, or run the OpenFE test suite with openfe test; see CLI reference.
• Debug CLI symptoms such as misplaced global options, missing transformation JSONs, duplicate repeat outputs, malformed YAML, or quickrun cache issues; see troubleshooting.

Safe Operating Rules

• Prefer help and inspection commands first: openfe --help, openfe <command> --help, and the bundled command generator with --help are safe.
• Treat openfe quickrun, planning commands, charge generation, fetch, and openfe test as potentially expensive or mutating; openfe test --long is especially slow. Do not run them unless the user explicitly wants execution.
• Put global options before the subcommand, for example openfe --log logging.conf quickrun transformation.json -d work -o result.json.
• Keep planning, execution, and gathering separate: planners write network files and transformation JSONs, quickrun runs exactly one transformation JSON, and gather commands summarize completed result JSONs.
• Use unique -o result paths and -d work directories for repeated quickrun jobs; never reuse the same output path for parallel repeats.

Boundary Handoffs

• Python object construction, molecule/protein component concepts, atom mapper tradeoffs, and ligand-network topology decisions belong in ../network-planning/SKILL.md.
• Protocol class settings, OpenMM backend details, protocol repeat semantics beyond CLI flags, and execution internals belong in ../protocols/SKILL.md.
• Result JSON contents, TSV columns, error propagation, and estimate/uncertainty interpretation belong in ../results-analysis/SKILL.md.