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  • Installation
  • User Guide
  • Tutorials
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  • Reference
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Section Navigation

  • Python API Reference
    • Chemical Systems and Components
      • ChemicalSystem
      • Transformation
      • Component
      • SmallMoleculeComponent
      • ProteinComponent
      • ProteinMembraneComponent
      • SolventComponent
      • SolvatedPDBComponent
      • EasyChemicalSystemGenerator
    • Atom Mappings
      • LigandAtomMapper
      • KartografAtomMapper
      • LomapAtomMapper
      • LigandAtomMapping
      • default_lomap_score()
      • ecr_score()
      • mcsr_score()
      • mncar_score()
      • atomic_number_score()
      • hybridization_score()
      • sulfonamides_score()
      • heterocycles_score()
      • transmuting_methyl_into_ring_score()
      • transmuting_ring_sizes_score()
    • Ligand Network Tools
      • LigandNetwork
      • generate_radial_network()
      • generate_maximal_network()
      • generate_minimal_spanning_network()
      • generate_minimal_redundant_network()
      • generate_lomap_network()
      • generate_network_from_names()
      • generate_network_from_indices()
      • load_orion_network()
      • load_fepplus_network()
    • Simulation Campaign Planning
      • Transformation
      • AlchemicalNetwork
      • RBFEAlchemicalNetworkPlanner
      • RHFEAlchemicalNetworkPlanner
    • Defining and Executing Simulations
      • execute_DAG()
      • setup_task_campaign()
      • Worker
      • TaskStatusDB
      • get_task_df()
      • get_dependency_df()
      • update_max_tries()
      • FileSystemWarehouse
      • ProtocolDAG
      • ProtocolUnitResult
      • ProtocolUnitFailure
      • ProtocolDAGResult
      • Protocol
      • ProtocolUnit
      • ProtocolResult
    • OpenMM Relative Free Energy Protocol
      • RelativeHybridTopologyProtocol
      • HybridTopologySetupUnit
      • HybridTopologyMultiStateSimulationUnit
      • HybridTopologyMultiStateAnalysisUnit
      • RelativeHybridTopologyProtocolResult
    • OpenMM Absolute Solvation Free Energy Protocol
      • AbsoluteSolvationProtocol
      • AHFESolventAnalysisUnit
      • AHFESolventSetupUnit
      • AHFESolventSimUnit
      • AHFEVacuumAnalysisUnit
      • AHFEVacuumSetupUnit
      • AHFEVacuumSimUnit
      • AbsoluteSolvationProtocolResult
    • OpenMM Absolute Binding Free Energy Protocol
      • AbsoluteBindingProtocol
      • ABFEComplexAnalysisUnit
      • ABFEComplexSetupUnit
      • ABFEComplexSimUnit
      • ABFESolventAnalysisUnit
      • ABFESolventSetupUnit
      • ABFESolventSimUnit
      • AbsoluteBindingProtocolResult
    • OpenMM Separated Topologies Protocol
      • SepTopProtocol
      • SepTopComplexSetupUnit
      • SepTopComplexRunUnit
      • SepTopComplexAnalysisUnit
      • SepTopSolventSetupUnit
      • SepTopSolventRunUnit
      • SepTopSolventAnalysisUnit
      • SepTopProtocolResult
    • OpenMM Molecular Dynamics (MD) Protocol
      • PlainMDProtocol
      • PlainMDSetupUnit
      • PlainMDSimulationUnit
      • PlainMDProtocolResult
    • OpenMM Protocol Settings
  • CLI Reference
    • openfe charge-molecules
    • openfe setup-task-campaign
    • openfe plan-rhfe-network
    • openfe plan-rbfe-network
    • openfe view-ligand-network
    • openfe run-task
    • openfe status
    • openfe update-task-db
    • openfe quickrun
    • openfe gather
    • openfe to-legacy-json
    • openfe test
  • Reference
  • CLI Reference

CLI Reference#

Planning & Setup Commands#

  • openfe charge-molecules
  • openfe setup-task-campaign
  • openfe plan-rhfe-network
  • openfe plan-rbfe-network
  • openfe view-ligand-network

Execution Commands#

  • openfe run-task
  • openfe status
  • openfe update-task-db
  • openfe quickrun

Results Gathering Commands#

  • openfe gather
  • openfe to-legacy-json

Miscellaneous Commands#

  • openfe test

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