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Site Navigation

  • Installation
  • Tutorials
  • User Guide
  • Cookbook
  • Reference
    • Changelog
  • GitHub

Section Navigation

  • OpenFE API Reference
    • Chemical Systems and Components
      • SmallMoleculeComponent
      • ProteinComponent
      • SolventComponent
      • ChemicalSystem
      • EasyChemicalSystemGenerator
    • Atom Mappings
      • LigandAtomMapper
      • LomapAtomMapper
      • PersesAtomMapper
      • 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()
      • default_perses_scorer()
    • 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()
      • ProtocolDAG
      • ProtocolUnitResult
      • ProtocolUnitFailure
      • ProtocolDAGResult
      • Protocol
      • ProtocolUnit
      • ProtocolResult
    • OpenMM Relative Free Energy Protocol
      • RelativeHybridTopologyProtocol
      • RelativeHybridTopologyProtocolUnit
      • RelativeHybridTopologyProtocolResult
    • OpenMM Absolute Solvation Free Energy Protocol
      • AbsoluteSolvationProtocol
      • AbsoluteSolvationVacuumUnit
      • AbsoluteSolvationSolventUnit
      • AbsoluteSolvationProtocolResult
    • OpenMM Molecular Dynamics (MD) Protocol
      • PlainMDProtocol
      • PlainMDProtocolUnit
      • PlainMDProtocolResult
    • OpenMM Protocol Settings
  • CLI Reference
    • plan-rhfe-network command
    • plan-rbfe-network command
    • quickrun command
    • gather command
    • charge-molecules command
  • Reference
  • CLI Reference

CLI Reference#

  • plan-rhfe-network command
  • plan-rbfe-network command
  • quickrun command
  • gather command
  • charge-molecules command

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OpenMM Protocol Settings

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plan-rhfe-network command
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