openmmtools.mcmc.MCRotationMove¶

class openmmtools.mcmc.MCRotationMove(**kwargs)[source]¶

A metropolized move that randomly rotate a subset of atoms.

Parameters:	atom_subset : slice or list of int, optional If specified, the move is applied only to those atoms specified by these indices. If None, the move is applied to all atoms (default is None). context_cache : openmmtools.cache.ContextCache, optional The ContextCache to use for Context creation. If None, the global cache openmmtools.cache.global_context_cache is used (default is None).

See also

Attributes:	n_accepted : int The number of proposals accepted. n_proposed : int The total number of attempted moves. atom_subset context_cache

Methods

`apply`(thermodynamic_state, sampler_state)	Apply a metropolized move to the sampler state.
`generate_random_rotation_matrix`()	Return a random 3x3 rotation matrix.
`rotate_positions`(positions)	Return the positions after applying a random rotation to them.

__init__(**kwargs)[source]¶: x.__init__(…) initializes x; see help(type(x)) for signature

Methods

`__init__`(**kwargs)	x.__init__(…) initializes x; see help(type(x)) for signature
`apply`(thermodynamic_state, sampler_state)	Apply a metropolized move to the sampler state.
`generate_random_rotation_matrix`()	Return a random 3x3 rotation matrix.
`rotate_positions`(positions)	Return the positions after applying a random rotation to them.

Attributes

statistics The acceptance statistics as a dictionary.

apply(thermodynamic_state, sampler_state)¶

Apply a metropolized move to the sampler state.

Total number of acceptances and proposed move are updated.

Parameters:	thermodynamic_state : openmmtools.states.ThermodynamicState The thermodynamic state to use to apply the move. sampler_state : openmmtools.states.SamplerState The initial sampler state to apply the move to. This is modified.

classmethod generate_random_rotation_matrix()[source]¶

Return a random 3x3 rotation matrix.

Returns:	Rq : 3x3 numpy.ndarray The random rotation matrix.

classmethod rotate_positions(positions)[source]¶

Return the positions after applying a random rotation to them.

Parameters:	positions : nx3 numpy.ndarray simtk.unit.Quantity The positions to rotate.
Returns:	rotated_positions : nx3 numpy.ndarray simtk.unit.Quantity The rotated positions.

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