BioSimSpace.FreeEnergy.Binding

class BioSimSpace.FreeEnergy.Binding(system, protocol=None, box=None, free_leg=True, work_dir=None, engine=None, property_map={})

A class for configuring and running binding free energy simulations.

__init__(system, protocol=None, box=None, free_leg=True, work_dir=None, engine=None, property_map={})

Constructor.

Parameters
  • system (System) – The molecular system.

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

  • box ([Length]) – A list containing the box size in each dimension. This box will be used for the “free” leg of the simulation, which typically can be run with a significantly smaller box than the “bound” leg.

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

  • property_map (dict) – A dictionary that maps system “properties” to their user defined values. This allows the user to refer to properties with their own naming scheme, e.g. { “charge” : “my-charge” }

Methods

__delattr__

Implement delattr(self, name).

__dir__

Default dir() implementation.

__eq__

Return self==value.

__format__

Default object formatter.

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(system[, protocol, box, free_leg, …])

Constructor.

__init_subclass__

This method is called when a class is subclassed.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__

Create and return a new object.

__reduce__

Helper for pickle.

__reduce_ex__

Helper for pickle.

__repr__

Return repr(self).

__setattr__

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 binding free energy data.

run()

Run the simulation.

Attributes

__dict__

__doc__

__module__

__weakref__

list of weak references to the object (if defined)

_analyse_freenrg

_engines

analyse()

Analyse the binding free energy data.

Returns

  • pmf_free ([(float, Energy, Energy)]) – The potential of mean force (PMF) for the free leg of the simulation. The data is a list of tuples, where each tuple contains the lambda value, the PMF, and the standard error.

  • pmf_vacuum ([(float, Energy, Energy)]) – The potential of mean force (PMF) for the vacuum leg of the simulation. The data is a list of tuples, where each tuple contains the lambda value, the PMF, and the standard error.

  • free_energy ((Energy, Energy)) – The binding free energy difference and its associated error.

run()

Run the simulation.