OpenFE API Reference

• Alchemical Data Objects
  • Chemical Systems
    • SmallMoleculeComponent
    • ProteinComponent
    • SolventComponent
    • ChemicalSystem
      • ChemicalSystem.components
      • ChemicalSystem.name
  • Atom Mappings
    • LigandAtomMapping
  • Alchemical Simulations
    • Transformation
      • Transformation.stateA
      • Transformation.stateB
      • Transformation.protocol
      • Transformation.mapping
      • Transformation.name
    • AlchemicalNetwork
      • AlchemicalNetwork.edges
      • AlchemicalNetwork.nodes
      • AlchemicalNetwork.name
• Ligand Network Tools
  • Atom Mappers
    • LomapAtomMapper
    • PersesAtomMapper
  • Scorers
    • LOMAP Scorers
      • default_lomap_score()
      • ecr_score()
      • mcsr_score()
      • mncar_score()
      • tmcsr_score()
      • atomic_number_score()
      • hybridization_score()
      • sulfonamides_score()
      • heterocycles_score()
      • transmuting_methyl_into_ring_score()
      • transmuting_ring_sizes_score()
    • PersesScorers
      • default_perses_scorer()
  • Network Planners
    • generate_radial_network()
    • generate_maximal_network()
    • generate_minimal_spanning_network()
• Alchemical Network Planning
  • Alchemical Network Planners
    • RBFEAlchemicalNetworkPlanner
    • RHFEAlchemicalNetworkPlanner
  • Chemical System Generators
    • EasyChemicalSystemGenerator