perses.rjmc.topology_proposal.SmallMoleculeSetProposalEngine

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

This class proposes new small molecules from a prespecified set. It uses uniform proposal probabilities, but can be extended. The user is responsible for providing a list of smiles that can be interconverted! The class includes extra functionality to assist with that (it is slow).

Parameters:

list_of_smiles : list of string

list of smiles that will be sampled

system_generator : SystemGenerator object

SystemGenerator initialized with the appropriate forcefields

residue_name : str

The name that will be used for small molecule residues in the topology

proposal_metadata : dict

metadata for the proposal engine

storage : NetCDFStorageView, optional, default=None

If specified, write statistics to this storage

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__(list_of_smiles, system_generator, residue_name='MOL', atom_expr=None, bond_expr=None, proposal_metadata=None, storage=None, always_change=True, atom_map=None)

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

Methods

__init__(list_of_smiles, 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_mol=None, proposed_mol=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_metadata : dict

dict containing current smiles as a key

current_mol : OEMol, optional, default=None

If specified, use this OEMol instead of converting from topology

proposed_mol : OEMol, optional, default=None

If specified, use this OEMol instead of converting from topology

Returns:

proposal : TopologyProposal object

topology proposal object