perses.rjmc.topology_proposal.TopologyProposal

class perses.rjmc.topology_proposal.TopologyProposal(new_topology=None, new_system=None, old_topology=None, old_system=None, logp_proposal=None, new_to_old_atom_map=None, old_alchemical_atoms=None, old_chemical_state_key=None, new_chemical_state_key=None, metadata=None)[source]

This is a container class with convenience methods to access various objects needed for a topology proposal

Attributes:
logp_proposal
metadata
n_atoms_new
n_atoms_old
new_alchemical_atoms
new_chemical_state_key
new_environment_atoms
new_system
new_to_old_atom_map
new_topology
old_alchemical_atoms
old_chemical_state_key
old_environment_atoms
old_system
old_to_new_atom_map
old_topology
unique_new_atoms
unique_old_atoms
__init__(new_topology=None, new_system=None, old_topology=None, old_system=None, logp_proposal=None, new_to_old_atom_map=None, old_alchemical_atoms=None, old_chemical_state_key=None, new_chemical_state_key=None, metadata=None)[source]

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

Methods

__init__([new_topology, new_system, …]) Initialize self.

Attributes

logp_proposal
metadata
n_atoms_new
n_atoms_old
new_alchemical_atoms
new_chemical_state_key
new_environment_atoms
new_system
new_to_old_atom_map
new_topology
old_alchemical_atoms
old_chemical_state_key
old_environment_atoms
old_system
old_to_new_atom_map
old_topology
unique_new_atoms
unique_old_atoms