perses.rjmc.topology_proposal.PropaneProposalEngine

class perses.rjmc.topology_proposal.PropaneProposalEngine(system_generator, residue_name='MOL', atom_expr=None, bond_expr=None, proposal_metadata=None, storage=None, always_change=True)

Custom ProposalEngine to use with PropaneTestSystem defines two “states” of butane, identified ‘propane-A’ and ‘propane-B’, which are tracked by adding a custom _state_key attribute to the topology

Generates TopologyProposal from propane to propane, only matching one CH3 and the middle C such that geometry must rebuild the other

Can only be used with input topology of propane

Constructor Arguments:

system_generator, SystemGenerator object

SystemGenerator initialized with the appropriate forcefields

residue_name, OPTIONAL, str

Default = “MOL” The name that will be used for small molecule residues in the topology

atom_expr, OPTIONAL, oechem.OEExprOpts

Default is None Currently not implemented – would dictate how match is defined

bond_expr, OPTIONAL, oechem.OEExprOpts

Default is None Currently not implemented – would dictate how match is defined

proposal_metadata, OPTIONAL, dict

Default is None metadata for the proposal engine

storage, OPTIONAL, NetCDFStorageView

Default is None If specified, write statistics to this storage layer

always_change, OPTIONAL, bool

Default is True Currently not implemented – will always behave as True The proposal will always be from the current “state” to the other Self proposals will never be made

Attributes:

chemical_state_list

Methods

canonicalize_smiles(smiles)	Convert a SMILES string into canonical isomeric smiles
clean_molecule_list(smiles_list, atom_opts, …)	A utility function to determine which molecules can be proposed from any other molecule.
compute_state_key(topology)	For this test system, the topologies for the two states are identical; therefore a custom attribute _state_key has been added to the topology itself, to track whether a switch has been accepted
propose(current_system, current_topology[, …])	Custom proposal for NaphthaleneTestSystem will switch from current naphthalene “state” (either ‘naphthalene-A’ or ‘naphthalene-B’) to the other

__init__(system_generator, residue_name='MOL', atom_expr=None, bond_expr=None, proposal_metadata=None, storage=None, always_change=True)

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

Methods

__init__(system_generator[, residue_name, …])	Initialize self.
canonicalize_smiles(smiles)	Convert a SMILES string into canonical isomeric smiles
clean_molecule_list(smiles_list, atom_opts, …)	A utility function to determine which molecules can be proposed from any other molecule.
compute_state_key(topology)	For this test system, the topologies for the two states are identical; therefore a custom attribute _state_key has been added to the topology itself, to track whether a switch has been accepted
propose(current_system, current_topology[, …])	Custom proposal for NaphthaleneTestSystem will switch from current naphthalene “state” (either ‘naphthalene-A’ or ‘naphthalene-B’) to the other

Attributes

chemical_state_list

static canonicalize_smiles(smiles)

Convert a SMILES string into canonical isomeric smiles

Parameters:

smiles : str

Any valid SMILES for a molecule

Returns:

iso_can_smiles : str

OpenEye isomeric canonical smiles corresponding to the input

static clean_molecule_list(smiles_list, atom_opts, bond_opts)

A utility function to determine which molecules can be proposed from any other molecule.

Parameters:

smiles_list

atom_opts

bond_opts

Returns:

safe_smiles

removed_smiles

compute_state_key(topology)

For this test system, the topologies for the two states are identical; therefore a custom attribute _state_key has been added to the topology itself, to track whether a switch has been accepted

compute_state_key will return topology._state_key rather than SMILES, because SMILES are identical in the two states.

propose(current_system, current_topology, current_metadata=None)

Custom proposal for NaphthaleneTestSystem will switch from current naphthalene “state” (either ‘naphthalene-A’ or ‘naphthalene-B’) to the other

This proposal engine can only be used with input topology of naphthalene, and propose() will first confirm naphthalene is residue “MOL” The topology may have water but should not have any other carbon-containing residue.

The “new” system and topology are deep copies of the old, but the atom_map is custom defined to only match one of the two rings.