API Documentation

a3fe.configuration	Pydantic configuration classes for the a3fe package.
a3fe.configuration.slurm_config	Configuration classes for SLURM configuration.
a3fe.configuration.engine_config	Configuration classes for SOMD engine configuration.
a3fe.configuration.system_prep_config	Configuration classes for system preparation.
a3fe.run
a3fe.run._simulation_runner	Abstract base class for simulation runners.
a3fe.run.CalcSet([calc_paths, calc_args, ...])	Class to set up, run, and analyse sets of ABFE calculations (each represented by Calculation objects).
a3fe.run.Calculation([equil_detection, ...])	Class to set up and run an entire ABFE calculation, consisting of two legs (bound and unbound) and multiple stages.
a3fe.run.Leg(leg_type[, equil_detection, ...])	Class set up and run the stages of a leg of the calculation.
a3fe.run.Stage(stage_type[, ...])	Class to hold and manipulate an ensemble of SOMD simulations for a single stage of a calculation.
a3fe.run.LamWindow(lam, virtual_queue[, ...])	A class to hold and manipulate a set of SOMD simulations at a given lambda value.
a3fe.run.Simulation(lam, run_no, virtual_queue)	Class to store information about a single SOMD simulation.
a3fe.run.system_prep	Functionality for running preparation simulations.
a3fe.run._virtual_queue	Utilities for the Ensemble, Window, and Simulation Classes
a3fe.run._utils	"Utilities for SimulationRunners.
a3fe.analyse
a3fe.analyse.analyse_set	Functionality to analyse a set of calculations and compare the result with experiment
a3fe.analyse.compare	Functionality for comparing two or more simulation runners.
a3fe.analyse.detect_equil	Functions for detecting equilibration based on an ensemble of simulations.
a3fe.analyse.mbar	Functionality for running mbar on SOMD output files.
a3fe.analyse.plot	Plotting functions
a3fe.analyse.rmsd	Functionality to compute RMSDs
a3fe.analyse.waters	Functions to analyse binding site waters.