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) ASFESolventUnit (class in pontibus.protocols.solvation) ASFEVacuumUnit (class in pontibus.protocols.solvation) assign_solvent_charges (pontibus.utils.settings.BasePontibusSolvationSettings attribute) (pontibus.utils.settings.InterchangeOpenMMSolvationSettings attribute) (pontibus.utils.settings.PackmolSolvationSettings attribute) B 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.HybridTopProtocolUnit property) (pontibus.protocols.solvation.ASFESolventUnit property) (pontibus.protocols.solvation.ASFEVacuumUnit property) E engine_settings (pontibus.protocols.relative.HybridTopProtocolSettings attribute) (pontibus.protocols.relative.settings.HybridTopProtocolSettings attribute) equilibration_iterations() (pontibus.protocols.relative.HybridTopProtocolResult method) (pontibus.protocols.solvation.ASFEProtocolResult method) execute() (pontibus.protocols.relative.HybridTopProtocolUnit method) (pontibus.protocols.solvation.ASFESolventUnit method) (pontibus.protocols.solvation.ASFEVacuumUnit 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) (pontibus.protocols.solvation.ASFEProtocolResult method) get_individual_estimates() (pontibus.protocols.relative.HybridTopProtocolResult method) (pontibus.protocols.solvation.ASFEProtocolResult method) get_overlap_matrices() (pontibus.protocols.relative.HybridTopProtocolResult method) (pontibus.protocols.solvation.ASFEProtocolResult method) get_replica_states() (pontibus.protocols.relative.HybridTopProtocolResult method) (pontibus.protocols.solvation.ASFEProtocolResult method) get_replica_transition_statistics() (pontibus.protocols.relative.HybridTopProtocolResult method) (pontibus.protocols.solvation.ASFEProtocolResult 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) HybridTopProtocolUnit (class in pontibus.protocols.relative) hydrogen_mass (pontibus.utils.settings.InterchangeFFSettings attribute) I inputs (pontibus.protocols.relative.HybridTopProtocolUnit property) (pontibus.protocols.solvation.ASFESolventUnit property) (pontibus.protocols.solvation.ASFEVacuumUnit 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.HybridTopProtocolUnit property) (pontibus.protocols.solvation.ASFESolventUnit property) (pontibus.protocols.solvation.ASFEVacuumUnit 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) (pontibus.protocols.solvation.ASFEProtocolResult 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.HybridTopProtocolUnit method) (pontibus.protocols.solvation.ASFESolventUnit method) (pontibus.protocols.solvation.ASFEVacuumUnit method) S settings (pontibus.protocols.relative.HybridTopProtocol property) (pontibus.protocols.solvation.ASFEProtocol property) simtype (pontibus.protocols.solvation.ASFESolventUnit attribute) (pontibus.protocols.solvation.ASFEVacuumUnit 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) structural_analysis() (pontibus.protocols.relative.HybridTopProtocolUnit static method) 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 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)
