BioSimSpace.Protocol.FreeEnergy

class BioSimSpace.Protocol.FreeEnergy(lam=0.0, lam_vals=None, min_lam=0.0, max_lam=1.0, num_lam=11, timestep=2.0000 fs, runtime=1.0000 ns, temperature=300.0000 K, pressure=1.0000 atm, frames=20)

A class for storing free energy protocols.

__init__(lam=0.0, lam_vals=None, min_lam=0.0, max_lam=1.0, num_lam=11, timestep=2.0000 fs, runtime=1.0000 ns, temperature=300.0000 K, pressure=1.0000 atm, frames=20)

Constructor.

Parameters

  • lam (float) – The perturbation parameter: [0.0, 1.0]

  • lam_vals ([float]) – The list of lambda parameters.

  • min_lam (float) – The minimum lambda value.

  • max_lam (float) – The maximum lambda value.

  • num_lam (int) – The number of lambda values.

  • timestep (Time) – The integration timestep.

  • runtime (Time) – The running time.

  • temperature (Temperature) – The temperature.

  • pressure (Pressure) – The pressure. Pass pressure=None to use the NVT ensemble.

  • frames (int) – The number of trajectory frames to record.

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__([lam, lam_vals, min_lam, max_lam, …])

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 a string showing how to instantiate the object.

__setattr__(name, value, /)

Implement setattr(self, name, value).

__sizeof__()

Size of object in memory, in bytes.

__str__()

Return a human readable string representation of the object.

__subclasshook__

Abstract classes can override this to customize issubclass().

_setCustomised(is_customised)

Internal function to flag whether a protocol has been customised.

getFrames()

Return the number of frames.

getLambda()

Get the value of the perturbation parameter.

getLambdaValues()

Get the list of lambda values.

getPressure()

Return the pressure.

getRunTime()

Return the running time.

getTemperature()

Return temperature.

getTimeStep()

Return the time step.

setFrames(frames)

Set the number of frames.

setLambdaValues(lam[, lam_vals, min_lam, …])

Set the list of lambda values.

setPressure(pressure)

Set the pressure.

setRunTime(runtime)

Set the running time.

setTemperature(temperature)

Set the temperature.

setTimeStep(timestep)

Set the time step.

Attributes

__dict__

__doc__

__module__

__weakref__

list of weak references to the object (if defined)