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
ProtocolDAG
ProtocolUnitResult
ProtocolUnitFailure
ProtocolDAGResult
ProtocolDAGResult.name
ProtocolDAGResult.protocol_units
ProtocolDAGResult.protocol_unit_results
ProtocolDAGResult.graph
ProtocolDAGResult.result_graph
ProtocolDAGResult.transformation_key
ProtocolDAGResult.extends_key
ProtocolDAGResult.protocol_unit_failures
ProtocolDAGResult.protocol_unit_successes
ProtocolDAGResult.terminal_protocol_unit_results
ProtocolDAGResult.unit_to_all_results()
ProtocolDAGResult.unit_to_result()
- Specialised classes
- OpenMM Relative Free Energy Protocol
- Protocol Settings
RelativeHybridTopologyProtocolSettings
RelativeHybridTopologyProtocolSettings.alchemical_sampler_settings
RelativeHybridTopologyProtocolSettings.alchemical_settings
RelativeHybridTopologyProtocolSettings.engine_settings
RelativeHybridTopologyProtocolSettings.integrator_settings
RelativeHybridTopologyProtocolSettings.simulation_settings
RelativeHybridTopologyProtocolSettings.solvation_settings
RelativeHybridTopologyProtocolSettings.system_settings
AlchemicalSamplerSettings
AlchemicalSamplerSettings.flatness_criteria
AlchemicalSamplerSettings.gamma0
AlchemicalSamplerSettings.n_repeats
AlchemicalSamplerSettings.n_replicas
AlchemicalSamplerSettings.online_analysis_interval
AlchemicalSamplerSettings.online_analysis_minimum_iterations
AlchemicalSamplerSettings.online_analysis_target_error
AlchemicalSamplerSettings.sampler_method
AlchemicalSettings
AlchemicalSettings.flatten_torsions
AlchemicalSettings.interpolate_old_and_new_14s
AlchemicalSettings.lambda_functions
AlchemicalSettings.lambda_windows
AlchemicalSettings.softcore_LJ_v2
AlchemicalSettings.softcore_alpha
AlchemicalSettings.softcore_electrostatics
AlchemicalSettings.softcore_electrostatics_alpha
AlchemicalSettings.softcore_sigma_Q
AlchemicalSettings.unsampled_endstates
AlchemicalSettings.use_dispersion_correction
OpenMMEngineSettings
IntegratorSettings
SimulationSettings
SolvationSettings
SystemSettings
ThermoSettings
OpenMMSystemGeneratorFFSettings
- Protocol API specification
- Protocol Settings
- CLI Reference