Index A | B | C | D | E | F | G | H | I | L | M | N | O | P | R | S | T | U | V A alchemical_settings (pontibus.protocols.relative.HybridTopProtocolSettings attribute) (pontibus.protocols.relative.settings.HybridTopProtocolSettings attribute) (pontibus.protocols.solvation.ASFESettings attribute) (pontibus.protocols.solvation.settings.ASFESettings attribute) ASFEProtocol (class in pontibus.protocols.solvation) ASFEProtocolResult (class in pontibus.protocols.solvation) ASFESolventAnalysisUnit (class in pontibus.protocols.solvation) ASFESolventSetupUnit (class in pontibus.protocols.solvation) ASFESolventSimUnit (class in pontibus.protocols.solvation) ASFEVacuumAnalysisUnit (class in pontibus.protocols.solvation) ASFEVacuumSetupUnit (class in pontibus.protocols.solvation) ASFEVacuumSimUnit (class in pontibus.protocols.solvation) assign_solvent_charges (pontibus.utils.settings.BasePontibusSolvationSettings attribute) (pontibus.utils.settings.InterchangeOpenMMSolvationSettings attribute) (pontibus.utils.settings.PackmolSolvationSettings attribute) B bound_state (pontibus.protocols.solvation.ASFEProtocolResult attribute) box_shape (pontibus.utils.settings.BasePontibusSolvationSettings attribute) (pontibus.utils.settings.InterchangeOpenMMSolvationSettings attribute) (pontibus.utils.settings.PackmolSolvationSettings attribute) box_vectors (pontibus.utils.settings.BasePontibusSolvationSettings attribute) (pontibus.utils.settings.InterchangeOpenMMSolvationSettings attribute) (pontibus.utils.settings.PackmolSolvationSettings attribute) C compute_mean_estimate() (pontibus.protocols.relative.HybridTopProtocolResult static method) compute_uncertainty() (pontibus.protocols.relative.HybridTopProtocolResult static method) create() (pontibus.protocols.relative.HybridTopProtocol method) (pontibus.protocols.solvation.ASFEProtocol method) D data (pontibus.protocols.relative.HybridTopProtocolResult property) (pontibus.protocols.solvation.ASFEProtocolResult property) default_settings() (pontibus.protocols.relative.HybridTopProtocol class method) (pontibus.protocols.solvation.ASFEProtocol class method) dependencies (pontibus.protocols.relative.HybridTopProtocolSetupUnit property) (pontibus.protocols.solvation.ASFESolventAnalysisUnit property) (pontibus.protocols.solvation.ASFESolventSetupUnit property) (pontibus.protocols.solvation.ASFESolventSimUnit property) (pontibus.protocols.solvation.ASFEVacuumAnalysisUnit property) (pontibus.protocols.solvation.ASFEVacuumSetupUnit property) (pontibus.protocols.solvation.ASFEVacuumSimUnit property) E engine_settings (pontibus.protocols.relative.HybridTopProtocolSettings attribute) (pontibus.protocols.relative.settings.HybridTopProtocolSettings attribute) equilibration_iterations() (pontibus.protocols.relative.HybridTopProtocolResult method) execute() (pontibus.protocols.relative.HybridTopProtocolSetupUnit method) (pontibus.protocols.solvation.ASFESolventAnalysisUnit method) (pontibus.protocols.solvation.ASFESolventSetupUnit method) (pontibus.protocols.solvation.ASFESolventSimUnit method) (pontibus.protocols.solvation.ASFEVacuumAnalysisUnit method) (pontibus.protocols.solvation.ASFEVacuumSetupUnit method) (pontibus.protocols.solvation.ASFEVacuumSimUnit method) F forcefield_settings (pontibus.protocols.relative.HybridTopProtocolSettings attribute) (pontibus.protocols.relative.settings.HybridTopProtocolSettings attribute) forcefields (pontibus.utils.settings.InterchangeFFSettings attribute) frozen_copy() (pontibus.protocols.relative.HybridTopProtocolSettings method) (pontibus.protocols.solvation.ASFESettings method) G gather() (pontibus.protocols.relative.HybridTopProtocol method) (pontibus.protocols.solvation.ASFEProtocol method) get_defaults() (pontibus.protocols.relative.HybridTopProtocolSettings class method) get_estimate() (pontibus.protocols.relative.HybridTopProtocolResult method) (pontibus.protocols.solvation.ASFEProtocolResult method) get_forward_and_reverse_energy_analysis() (pontibus.protocols.relative.HybridTopProtocolResult method) get_individual_estimates() (pontibus.protocols.relative.HybridTopProtocolResult method) (pontibus.protocols.solvation.ASFEProtocolResult method) get_overlap_matrices() (pontibus.protocols.relative.HybridTopProtocolResult method) get_replica_states() (pontibus.protocols.relative.HybridTopProtocolResult method) get_replica_transition_statistics() (pontibus.protocols.relative.HybridTopProtocolResult method) get_uncertainty() (pontibus.protocols.relative.HybridTopProtocolResult method) (pontibus.protocols.solvation.ASFEProtocolResult method) H HybridTopProtocol (class in pontibus.protocols.relative) HybridTopProtocolResult (class in pontibus.protocols.relative) HybridTopProtocolSetupUnit (class in pontibus.protocols.relative) hydrogen_mass (pontibus.utils.settings.InterchangeFFSettings attribute) I inputs (pontibus.protocols.relative.HybridTopProtocolSetupUnit property) (pontibus.protocols.solvation.ASFESolventAnalysisUnit property) (pontibus.protocols.solvation.ASFESolventSetupUnit property) (pontibus.protocols.solvation.ASFESolventSimUnit property) (pontibus.protocols.solvation.ASFEVacuumAnalysisUnit property) (pontibus.protocols.solvation.ASFEVacuumSetupUnit property) (pontibus.protocols.solvation.ASFEVacuumSimUnit property) integrator_settings (pontibus.protocols.relative.HybridTopProtocolSettings attribute) (pontibus.protocols.relative.settings.HybridTopProtocolSettings attribute) (pontibus.protocols.solvation.ASFESettings attribute) (pontibus.protocols.solvation.settings.ASFESettings attribute) interchange_system_creation() (in module pontibus.utils.system_creation) is_frozen (pontibus.protocols.relative.HybridTopProtocolSettings property) (pontibus.protocols.solvation.ASFESettings property) L lambda_settings (pontibus.protocols.relative.HybridTopProtocolSettings attribute) (pontibus.protocols.relative.settings.HybridTopProtocolSettings attribute) (pontibus.protocols.solvation.ASFESettings attribute) (pontibus.protocols.solvation.settings.ASFESettings attribute) M module pontibus pontibus.protocols.relative pontibus.protocols.relative.settings pontibus.protocols.solvation pontibus.protocols.solvation.settings pontibus.utils.settings pontibus.utils.system_creation pontibus.utils.system_solvation must_be_positive() (pontibus.protocols.relative.HybridTopProtocolSettings class method) (pontibus.protocols.solvation.ASFESettings class method) N n_protocol_dag_results (pontibus.protocols.relative.HybridTopProtocolResult property) (pontibus.protocols.solvation.ASFEProtocolResult property) name (pontibus.protocols.relative.HybridTopProtocolSetupUnit property) (pontibus.protocols.solvation.ASFESolventAnalysisUnit property) (pontibus.protocols.solvation.ASFESolventSetupUnit property) (pontibus.protocols.solvation.ASFESolventSimUnit property) (pontibus.protocols.solvation.ASFEVacuumAnalysisUnit property) (pontibus.protocols.solvation.ASFEVacuumSetupUnit property) (pontibus.protocols.solvation.ASFEVacuumSimUnit property) nonbonded_cutoff (pontibus.utils.settings.InterchangeFFSettings attribute) nonbonded_method (pontibus.utils.settings.InterchangeFFSettings attribute) number_of_solvent_molecules (pontibus.utils.settings.BasePontibusSolvationSettings attribute) (pontibus.utils.settings.InterchangeOpenMMSolvationSettings attribute) (pontibus.utils.settings.PackmolSolvationSettings attribute) O openmm_solvation() (in module pontibus.utils.system_solvation) output_settings (pontibus.protocols.relative.HybridTopProtocolSettings attribute) (pontibus.protocols.relative.settings.HybridTopProtocolSettings attribute) P packing_tolerance (pontibus.utils.settings.BasePontibusSolvationSettings attribute) (pontibus.utils.settings.InterchangeOpenMMSolvationSettings attribute) (pontibus.utils.settings.PackmolSolvationSettings attribute) packmol_solvation() (in module pontibus.utils.system_solvation) partial_charge_settings (pontibus.protocols.relative.HybridTopProtocolSettings attribute) (pontibus.protocols.relative.settings.HybridTopProtocolSettings attribute) (pontibus.protocols.solvation.ASFESettings attribute) (pontibus.protocols.solvation.settings.ASFESettings attribute) pontibus module pontibus.protocols.relative module pontibus.protocols.relative.settings module pontibus.protocols.solvation module pontibus.protocols.solvation.settings module pontibus.utils.settings module pontibus.utils.system_creation module pontibus.utils.system_solvation module production_iterations() (pontibus.protocols.relative.HybridTopProtocolResult method) protocol_repeats (pontibus.protocols.relative.HybridTopProtocolSettings attribute) (pontibus.protocols.relative.settings.HybridTopProtocolSettings attribute) (pontibus.protocols.solvation.ASFESettings attribute) (pontibus.protocols.solvation.settings.ASFESettings attribute) R result_cls (pontibus.protocols.relative.HybridTopProtocol attribute) (pontibus.protocols.solvation.ASFEProtocol attribute) run() (pontibus.protocols.relative.HybridTopProtocolSetupUnit method) (pontibus.protocols.solvation.ASFESolventAnalysisUnit method) (pontibus.protocols.solvation.ASFESolventSetupUnit method) (pontibus.protocols.solvation.ASFESolventSimUnit method) (pontibus.protocols.solvation.ASFEVacuumAnalysisUnit method) (pontibus.protocols.solvation.ASFEVacuumSetupUnit method) (pontibus.protocols.solvation.ASFEVacuumSimUnit method) S settings (pontibus.protocols.relative.HybridTopProtocol property) (pontibus.protocols.solvation.ASFEProtocol property) simtype (pontibus.protocols.solvation.ASFESolventAnalysisUnit attribute) (pontibus.protocols.solvation.ASFESolventSetupUnit attribute) (pontibus.protocols.solvation.ASFESolventSimUnit attribute) (pontibus.protocols.solvation.ASFEVacuumAnalysisUnit attribute) (pontibus.protocols.solvation.ASFEVacuumSetupUnit attribute) (pontibus.protocols.solvation.ASFEVacuumSimUnit attribute) simulation_settings (pontibus.protocols.relative.HybridTopProtocolSettings attribute) (pontibus.protocols.relative.settings.HybridTopProtocolSettings attribute) solvation_settings (pontibus.protocols.relative.HybridTopProtocolSettings attribute) (pontibus.protocols.relative.settings.HybridTopProtocolSettings attribute) (pontibus.protocols.solvation.ASFESettings attribute) (pontibus.protocols.solvation.settings.ASFESettings attribute) solvent_engine_settings (pontibus.protocols.solvation.ASFESettings attribute) (pontibus.protocols.solvation.settings.ASFESettings attribute) solvent_equil_output_settings (pontibus.protocols.solvation.ASFESettings attribute) (pontibus.protocols.solvation.settings.ASFESettings attribute) solvent_equil_simulation_settings (pontibus.protocols.solvation.ASFESettings attribute) (pontibus.protocols.solvation.settings.ASFESettings attribute) solvent_forcefield_settings (pontibus.protocols.solvation.ASFESettings attribute) (pontibus.protocols.solvation.settings.ASFESettings attribute) solvent_output_settings (pontibus.protocols.solvation.ASFESettings attribute) (pontibus.protocols.solvation.settings.ASFESettings attribute) solvent_padding (pontibus.utils.settings.BasePontibusSolvationSettings attribute) (pontibus.utils.settings.InterchangeOpenMMSolvationSettings attribute) (pontibus.utils.settings.PackmolSolvationSettings attribute) solvent_simulation_settings (pontibus.protocols.solvation.ASFESettings attribute) (pontibus.protocols.solvation.settings.ASFESettings attribute) switch_width (pontibus.utils.settings.InterchangeFFSettings attribute) T target_density (pontibus.utils.settings.BasePontibusSolvationSettings attribute) (pontibus.utils.settings.InterchangeOpenMMSolvationSettings attribute) (pontibus.utils.settings.PackmolSolvationSettings attribute) thermo_settings (pontibus.protocols.relative.HybridTopProtocolSettings attribute) (pontibus.protocols.relative.settings.HybridTopProtocolSettings attribute) (pontibus.protocols.solvation.ASFESettings attribute) (pontibus.protocols.solvation.settings.ASFESettings attribute) U unbound_state (pontibus.protocols.solvation.ASFEProtocolResult attribute) unfrozen_copy() (pontibus.protocols.relative.HybridTopProtocolSettings method) (pontibus.protocols.solvation.ASFESettings method) V vacuum_engine_settings (pontibus.protocols.solvation.ASFESettings attribute) (pontibus.protocols.solvation.settings.ASFESettings attribute) vacuum_equil_output_settings (pontibus.protocols.solvation.ASFESettings attribute) (pontibus.protocols.solvation.settings.ASFESettings attribute) vacuum_equil_simulation_settings (pontibus.protocols.solvation.ASFESettings attribute) (pontibus.protocols.solvation.settings.ASFESettings attribute) vacuum_forcefield_settings (pontibus.protocols.solvation.ASFESettings attribute) (pontibus.protocols.solvation.settings.ASFESettings attribute) vacuum_output_settings (pontibus.protocols.solvation.ASFESettings attribute) (pontibus.protocols.solvation.settings.ASFESettings attribute) vacuum_simulation_settings (pontibus.protocols.solvation.ASFESettings attribute) (pontibus.protocols.solvation.settings.ASFESettings attribute) validate() (pontibus.protocols.relative.HybridTopProtocol method) (pontibus.protocols.solvation.ASFEProtocol method)
