perses.rjmc.geometry.FFAllAngleGeometryEngine

class perses.rjmc.geometry.FFAllAngleGeometryEngine(metadata=None, use_sterics=False, n_torsion_divisions=180, verbose=True, storage=None, bond_softening_constant=1.0, angle_softening_constant=1.0)

This is an implementation of GeometryEngine which uses all valence terms and OpenMM

Parameters:

use_sterics : bool, optional, default=False

If True, sterics will be used in proposals to minimize clashes. This may significantly slow down the simulation, however.

Methods

logp_reverse(top_proposal, new_coordinates, …)	Calculate the logp for the given geometry proposal
propose(top_proposal, current_positions, beta)	Make a geometry proposal for the appropriate atoms.

__init__(metadata=None, use_sterics=False, n_torsion_divisions=180, verbose=True, storage=None, bond_softening_constant=1.0, angle_softening_constant=1.0)

Initialize self. See help(type(self)) for accurate signature.

Methods

__init__([metadata, use_sterics, …])	Initialize self.
logp_reverse(top_proposal, new_coordinates, …)	Calculate the logp for the given geometry proposal
propose(top_proposal, current_positions, beta)	Make a geometry proposal for the appropriate atoms.

logp_reverse(top_proposal, new_coordinates, old_coordinates, beta)

Calculate the logp for the given geometry proposal

Returns:

logp : float

The log probability of the proposal for the given transformation

propose(top_proposal, current_positions, beta)

Make a geometry proposal for the appropriate atoms.

Returns:

new_positions : [n, 3] ndarray

The new positions of the system

logp_proposal : float

The log probability of the forward-only proposal