Reference#
This contains details of the Python API as well as a reference to the command line interface.
- OpenFE API Reference
- Alchemical Data Objects
- Ligand Network Tools
- Alchemical Network Planning
- Defining and Executing Simulations
- Executing Simulations
- General classes
ProtocolDAGProtocolUnitResultProtocolUnitFailureProtocolDAGResultProtocolDAGResult.nameProtocolDAGResult.protocol_unitsProtocolDAGResult.protocol_unit_resultsProtocolDAGResult.graphProtocolDAGResult.result_graphProtocolDAGResult.transformation_keyProtocolDAGResult.extends_keyProtocolDAGResult.protocol_unit_failuresProtocolDAGResult.protocol_unit_successesProtocolDAGResult.terminal_protocol_unit_resultsProtocolDAGResult.unit_to_all_results()ProtocolDAGResult.unit_to_result()
- Specialised classes
- OpenMM Relative Free Energy Protocol
- Protocol Settings
RelativeHybridTopologyProtocolSettingsRelativeHybridTopologyProtocolSettings.alchemical_sampler_settingsRelativeHybridTopologyProtocolSettings.alchemical_settingsRelativeHybridTopologyProtocolSettings.engine_settingsRelativeHybridTopologyProtocolSettings.integrator_settingsRelativeHybridTopologyProtocolSettings.simulation_settingsRelativeHybridTopologyProtocolSettings.solvation_settingsRelativeHybridTopologyProtocolSettings.system_settings
AlchemicalSamplerSettingsAlchemicalSamplerSettings.flatness_criteriaAlchemicalSamplerSettings.gamma0AlchemicalSamplerSettings.n_repeatsAlchemicalSamplerSettings.n_replicasAlchemicalSamplerSettings.online_analysis_intervalAlchemicalSamplerSettings.online_analysis_minimum_iterationsAlchemicalSamplerSettings.online_analysis_target_errorAlchemicalSamplerSettings.sampler_method
AlchemicalSettingsAlchemicalSettings.flatten_torsionsAlchemicalSettings.interpolate_old_and_new_14sAlchemicalSettings.lambda_functionsAlchemicalSettings.lambda_windowsAlchemicalSettings.softcore_LJ_v2AlchemicalSettings.softcore_alphaAlchemicalSettings.softcore_electrostaticsAlchemicalSettings.softcore_electrostatics_alphaAlchemicalSettings.softcore_sigma_QAlchemicalSettings.unsampled_endstatesAlchemicalSettings.use_dispersion_correction
OpenMMEngineSettingsIntegratorSettingsSimulationSettingsSimulationSettings.checkpoint_intervalSimulationSettings.checkpoint_storageSimulationSettings.equilibration_lengthSimulationSettings.forcefield_cacheSimulationSettings.minimization_stepsSimulationSettings.output_filenameSimulationSettings.output_indicesSimulationSettings.output_structureSimulationSettings.production_length
SolvationSettingsSystemSettingsThermoSettingsOpenMMSystemGeneratorFFSettings
- Protocol API specification
- Protocol Settings
- CLI Reference