perses.rjmc.geometry.OmegaGeometryEngine

class perses.rjmc.geometry.OmegaGeometryEngine(n_omega_references=1, proposal_sigma=1.0, metadata=None)

This class proposes new small molecule geometries based on a set of precomputed omega geometries.

Methods

logp_reverse(top_proposal, new_coordinates, …)	Parameters:
propose(top_proposal, current_positions, beta)	Propose positions of new atoms according to a selected omega geometry.

__init__(n_omega_references=1, proposal_sigma=1.0, metadata=None)

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

Methods

__init__([n_omega_references, …])	Initialize self.
logp_reverse(top_proposal, new_coordinates, …)	Parameters:
propose(top_proposal, current_positions, beta)	Propose positions of new atoms according to a selected omega geometry.

logp_reverse(top_proposal, new_coordinates, old_coordinates, beta)

Parameters:

top_proposal

new_coordinates

old_coordinates

beta

propose(top_proposal, current_positions, beta)

Propose positions of new atoms according to a selected omega geometry.

Parameters:

top_proposal : TopologyProposal object

TopologyProposal object generated by the proposal engine

current_positions : [n, 3] np.array of float

Positions of the current system

beta : float

inverse temperature

Returns:

new_positions : [m, 3] np.array of float

The positions of the new system

logp_propose : float

The log-probability of the proposal