BioSimSpace.FreeEnergy.Solvation

class BioSimSpace.FreeEnergy.Solvation(system, protocol=None, vacuum_leg=True, work_dir=None, engine=None)

A class for configuring and running solvation free energy simulations.

__init__(system, protocol=None, vacuum_leg=True, work_dir=None, engine=None)

Constructor.

Parameters

• system (System) – The molecular system.

• protocol (Protocol.FreeEnergy) – The simulation protocol.

• vacuum_leg (bool) – Whether to simulation the vacuum leg of the simulation. Set to False if you only wish to run the free leg.

• work_dir (str) – The working directory for the simulation.

• engine (str) – The molecular dynamics engine used to run the simulation. Available options are “GROMACS”, or “SOMD”. If this argument is omitted then BioSimSpace will choose an appropriate engine for you.

Methods

__delattr__(name, /)	Implement delattr(self, name).
__dir__()	Default dir() implementation.
__eq__(value, /)	Return self==value.
__format__(format_spec, /)	Default object formatter.
__ge__(value, /)	Return self>=value.
__getattribute__(name, /)	Return getattr(self, name).
__gt__(value, /)	Return self>value.
__hash__()	Return hash(self).
__init__(system[, protocol, vacuum_leg, …])	Constructor.
__init_subclass__	This method is called when a class is subclassed.
__le__(value, /)	Return self<=value.
__lt__(value, /)	Return self<value.
__ne__(value, /)	Return self!=value.
__new__(**kwargs)	Create and return a new object.
__reduce__()	Helper for pickle.
__reduce_ex__(protocol, /)	Helper for pickle.
__repr__()	Return repr(self).
__setattr__(name, value, /)	Implement setattr(self, name, value).
__sizeof__()	Size of object in memory, in bytes.
__str__()	Return str(self).
__subclasshook__	Abstract classes can override this to customize issubclass().
_analyse_gromacs()	Analyse the GROMACS free energy data.
_analyse_somd()	Analyse the SOMD free energy data.
_initialise_runner(system0, system1)	Internal helper function to initialise the process runner.
_update_run_args(args)	Internal function to update run arguments for all subprocesses.
analyse()	Analyse the solvation free energy data.
run()	Run the simulation.

Attributes

__dict__
__doc__
__module__
__weakref__	list of weak references to the object (if defined)
_analyse_freenrg
_engines