perses.rjmc.topology_proposal.SmallMoleculeAtomMapper

class perses.rjmc.topology_proposal.SmallMoleculeAtomMapper(list_of_smiles: List[str], atom_match_expression: int = None, bond_match_expression: int = None, prohibit_hydrogen_mapping: bool = True)

This is a utility class for generating and retrieving sets of atom maps between molecules using OpenEye. It additionally verifies that all atom maps lead to valid proposals, as well as checking that the graph of proposals is not disconnected.

Attributes:

n_molecules

proposal_matrix

smiles_list

Methods

from_json(json_string)	Restore this class from a saved JSON file.
generate_and_check_proposal_matrix()	Generate a proposal matrix and check it for connectivity.
get_atom_maps(smiles_A, smiles_B)	Given two canonical smiles strings, get the atom maps.
get_oemol_from_smiles(smiles_string)	Get the OEMol corresponding to the smiles string requested.
get_smiles_index(smiles)	Get the index of the smiles in question
map_all_molecules()	Run the atom mapping routines to get all atom maps.
molecule_library_from_string(molecule_string)	Given a library of molecules in a mol2-format string, return a dictionary that maps the respective canonical smiles to the oemol object.
molecule_library_to_string(molecule_library)	Given a list of oechem.OEMol objects, write all of them in mol2 format to a string
to_json()	Write out this class to JSON.

__init__(list_of_smiles: List[str], atom_match_expression: int = None, bond_match_expression: int = None, prohibit_hydrogen_mapping: bool = True)

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

Methods

__init__(list_of_smiles, …)	Initialize self.
from_json(json_string)	Restore this class from a saved JSON file.
generate_and_check_proposal_matrix()	Generate a proposal matrix and check it for connectivity.
get_atom_maps(smiles_A, smiles_B)	Given two canonical smiles strings, get the atom maps.
get_oemol_from_smiles(smiles_string)	Get the OEMol corresponding to the smiles string requested.
get_smiles_index(smiles)	Get the index of the smiles in question
map_all_molecules()	Run the atom mapping routines to get all atom maps.
molecule_library_from_string(molecule_string)	Given a library of molecules in a mol2-format string, return a dictionary that maps the respective canonical smiles to the oemol object.
molecule_library_to_string(molecule_library)	Given a list of oechem.OEMol objects, write all of them in mol2 format to a string
to_json()	Write out this class to JSON.

Attributes

n_molecules
proposal_matrix
smiles_list

classmethod from_json(json_string: str)

Restore this class from a saved JSON file.

Returns:

atom_mapper : SmallMoleculeAtomMapper

An instance of the SmallMoleculeAtomMapper

generate_and_check_proposal_matrix()

Generate a proposal matrix and check it for connectivity. Note that if constraints have not been checked, this may produce a proposal matrix that makes proposals changing constraint lengths.

get_atom_maps(smiles_A: str, smiles_B: str) → List[Dict]

Given two canonical smiles strings, get the atom maps.

Returns:

atom_maps : list of dict

List of map of molecule_A_atom : molecule_B_atom

get_oemol_from_smiles(smiles_string: str) → openeye.oechem.OEMol

Get the OEMol corresponding to the smiles string requested. This method exists to avoid having atom order rearranged by regeneration from smiles.

Returns:

mol : oechem.OEMol

The OEMol corresponding to the requested smiles string.

get_smiles_index(smiles: str) → int

Get the index of the smiles in question

Returns:

mol_index : int

Index of molecule in list

map_all_molecules()

Run the atom mapping routines to get all atom maps. This automatically preserves only maps that contain enough torsions to propose. It does not ensure that constraints do not change–use verify_constraints to check that property. This method is idempotent–running it a second time will have no effect.

static molecule_library_from_string(molecule_string: str) → Dict[str, openeye.oechem.OEMol]

Given a library of molecules in a mol2-format string, return a dictionary that maps the respective canonical smiles to the oemol object.

Parameters:

molecule_string : str

The string containing the molecule data

Returns:

molecule_dictionary : dict of str: oemol

Dictionary mapping smiles strings to OEMols

static molecule_library_to_string(molecule_library: List[openeye.oechem.OEMol]) → str

Given a list of oechem.OEMol objects, write all of them in mol2 format to a string

Parameters:

molecule_library : list of oechem.OEMol

molecules to write to string

Returns:

molecule_string : str

String containing molecules in mol2 format.

to_json() → str

Write out this class to JSON. This saves all information (including built molecules and maps, if present)

Returns:

json_str : str

JSON string representing this class