perses.rjmc.geometry.ProposalOrderTools

class perses.rjmc.geometry.ProposalOrderTools(topology_proposal, verbose=True)

This is an internal utility class for determining the order of atomic position proposals. It encapsulates funcionality needed by the geometry engine. Atoms can be proposed without torsions or even angles, though this may not be recommended. Default is to require torsions.

Hydrogens are added last in growth order.

Parameters:

topology_proposal : perses.rjmc.topology_proposal.TopologyProposal

The topology proposal containing the relevant move.

Methods

determine_proposal_order([direction])

Determine the proposal order of this system pair.

__init__(topology_proposal, verbose=True)

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

Methods

__init__(topology_proposal[, verbose])	Initialize self.
determine_proposal_order([direction])	Determine the proposal order of this system pair.

determine_proposal_order(direction='forward')

Determine the proposal order of this system pair. This includes the choice of a torsion. As such, a logp is returned.

Parameters:

direction : str, optional

whether to determine the forward or reverse proposal order

Returns:

atoms_torsions : ordereddict

parmed.Atom : parmed.Dihedral

logp_torsion_choice : float

log probability of the chosen torsions