TIES_MD.openmmtools package

Submodules

TIES_MD.openmmtools.alchemy module

exception TIES_MD.openmmtools.alchemy.AlchemicalStateError

Bases: GlobalParameterError

Error raised by an AlchemicalState.

class TIES_MD.openmmtools.alchemy.ModifiedAbsoluteAlchemicalFactory(consistent_exceptions=False, switch_width=Quantity(value=1.0, unit=angstrom), alchemical_pme_treatment='exact', alchemical_rf_treatment='switched', disable_alchemical_dispersion_correction=False, split_alchemical_forces=True)

Bases: AbsoluteAlchemicalFactory

Super from AbsoluteAlchemicalFactory in Openmmtools

class TIES_MD.openmmtools.alchemy.ModifiedAlchemicalState(parameters_name_suffix=None, **kwargs)

Bases: GlobalParameterState

Super from GlobalParameterState in openmmtools

apply_to_context(context)

Put the Context into this AlchemicalState. Parameters β€”β€”β€”- context : openmm.Context

The context to set.

AlchemicalStateError

If the context does not have the required lambda global variables.

apply_to_system(system)

Set the alchemical state of the system to this. Parameters β€”β€”β€”- system : openmm.System

The system to modify.

AlchemicalStateError

If the system does not have the required lambda global variables.

check_system_consistency(system)

Check if the system is in this alchemical state. It raises a AlchemicalStateError if the system is not consistent with the alchemical state. Parameters β€”β€”β€”- system : openmm.System

The system to test.

AlchemicalStateError

If the system is not consistent with this state.

classmethod from_system(system, *args, **kwargs)

Constructor reading the state from an alchemical system. Parameters β€”β€”β€”- system : openmm.System

An alchemically modified system in a defined alchemical state.

parameters_name_suffixstr, optional

If specified, the state will search for a modified version of the alchemical parameters with the name parameter_name + '_' + parameters_name_suffix.

The AlchemicalState object representing the alchemical state of the system. Raises β€”β€” AlchemicalStateError

If the same parameter has different values in the system, or if the system has no lambda parameters.

get_alchemical_variable(variable_name)

Return the value of the alchemical parameter. .. warning:

This is deprecated. Use get_function_variable instead.

variable_namestr

The name of the alchemical variable.

variable_valuefloat

The value of the alchemical variable.

get_function_variable(variable_name)

Return the value of the function variable. Function variables are variables entering mathematical expressions specified with AlchemicalFunction, which can be use to enslave a lambda parameter to arbitrary variables. Parameters β€”β€”β€”- variable_name : str

The name of the function variable.

variable_valuefloat

The value of the function variable.

lambda_angles

A global parameter in the interval [0, 1] with standard value 1.

lambda_bonds

A global parameter in the interval [0, 1] with standard value 1.

lambda_electrostatics

A global parameter in the interval [0, 1] with standard value 1.

lambda_sterics

A global parameter in the interval [0, 1] with standard value 1.

lambda_torsions

A global parameter in the interval [0, 1] with standard value 1.

set_alchemical_parameters(new_value)

Set all defined lambda parameters to the given value. The undefined parameters (i.e. those being set to None) remain undefined. Parameters β€”β€”β€”- new_value : float

The new value for all defined parameters.

set_alchemical_variable(variable_name, new_value)

Set the value of the alchemical variable. .. warning:

This is deprecated. Use set_function_variable instead.

variable_namestr

The name of the alchemical variable.

new_valuefloat

The new value for the variable.

set_function_variable(variable_name, new_value)

Set the value of the function variable. Function variables are variables entering mathematical expressions specified with AlchemicalFunction, which can be use to enslave a lambda parameter to arbitrary variables. Parameters β€”β€”β€”- variable_name : str

The name of the function variable.

new_valuefloat

The new value for the variable.

Module contents