perses.rjmc.topology_proposal.PremappedSmallMoleculeSetProposalEngine

class perses.rjmc.topology_proposal.PremappedSmallMoleculeSetProposalEngine(atom_mapper: perses.rjmc.topology_proposal.SmallMoleculeAtomMapper, system_generator: perses.rjmc.topology_proposal.SystemGenerator, residue_name: str = 'MOL', storage: perses.storage.storage.NetCDFStorageView = None)

This proposal engine uses the SmallMoleculeAtomMapper to have all atoms premapped and the proposal distribution pre-formed and checked. It is intended to be substantially faster, as well as more robust (having excluded mappings that would not lead to a valid geometry proposal)

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)	Given a topology, come up with a state key string.
propose(current_system, current_topology[, …])	Propose the next state, given the current state

__init__(atom_mapper: perses.rjmc.topology_proposal.SmallMoleculeAtomMapper, system_generator: perses.rjmc.topology_proposal.SystemGenerator, residue_name: str = 'MOL', storage: perses.storage.storage.NetCDFStorageView = None)

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

Methods

__init__(atom_mapper, system_generator, …)	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)	Given a topology, come up with a state key string.
propose(current_system, current_topology[, …])	Propose the next state, given the current state

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)

Given a topology, come up with a state key string. For this class, the state key is an isomeric canonical SMILES.

Parameters:

topology : app.Topology object

The topology object in question.

Returns:

chemical_state_key : str

isomeric canonical SMILES

propose(current_system, current_topology, current_smiles=None, proposed_mol=None, map_index=None, current_metadata=None)

Propose the next state, given the current state

Parameters:

current_system : openmm.System object

the system of the current state

current_topology : app.Topology object

the topology of the current state

current_smiles : str, default None

Specify the current SMILES string to avoid perceiving it from the topology. If None, perceive from topology.

proposed_mol : oechem.OEMol, optional

the molecule to propose. If None, choose randomly based on the current molecule

map_index : int, default None

The index of the atom map to use. If None, choose randomly. Otherwise, use map idx of map_index mod n_maps

current_metadata : dict

dict containing current smiles as a key

Returns:

proposal : TopologyProposal object

topology proposal object