Ring Systems

class RingSystemFinder[source]

A class to identify ring systems

Initialize susbstructure search objects to identify key functionality

tag_bonds_to_preserve(mol)[source]: Assign the property “protected” to all ring carbonyls, etc. :type mol: :param mol: input molecule :return: None

static cleave_linker_bonds(mol)[source]: Cleave bonds that are not in rings and not protected :type mol: :param mol: input molecule :return: None

cleanup_fragments(mol, keep_dummy=False)[source]: Split a molecule containing multiple ring systems into individual ring systems :type keep_dummy: :param keep_dummy: retain dummy atoms :type mol: :param mol: input molecule :return: a list of SMILES corresponding to individual ring systems

static fix_bond_stereo(mol)[source]: Loop over double bonds and change stereo specification for double bonds that don’t have stereo :type mol: :param mol: input RDKit molecule :return: output RDKit molecule

find_ring_systems(mol, keep_dummy=False, as_mols=False)[source]: Find the ring systems for an RDKit molecule :type as_mols: :param as_mols: return results a molecules (otherwise return SMILES) :type keep_dummy: :param keep_dummy: retain dummy atoms :type mol: :param mol: input molecule :return: a list of SMILES corresponding to individual ring systems

test_ring_system_finder()[source]: A quick test for the RingSystemFinder class :return: None

create_ring_dictionary(input_chemreps, output_csv)[source]: Read the ChEMBL chemreps.txt file, extract ring systems, write out ring systems and frequency :type input_chemreps: :param input_chemreps: ChEMBL chemreps file :type output_csv: :param output_csv: output csv file :return: None

build_ring_systems_dataframe(res)[source]

Build a DataFrame with ring system information and minimum frequency.

Parameters:: res (list) – List of ring system results for each molecule.
Return type:: DataFrame
Returns:: DataFrame with columns for ring systems, min ring, and min frequency.

class RingSystemLookup(ring_file=None, ignore_stereo=False)[source]

Lookup ring systems from a dictionary of rings and frequencies

process_mol(mol_in)[source]: find ring systems in an RDKit molecule :type mol_in: :param mol_in: input molecule :return: list of SMILES for ring systems

process_smiles(smi)[source]: find ring systems from a SMILES :type smi: :param smi: input SMILES :return: list of SMILES for ring systems

pandas_smiles(smiles_list)[source]: find ring systems from a list of SMILES :type smiles_list: :param smiles_list: list of SMILES :return: dataframe with ring information

pandas_mols(mol_list)[source]: find ring systems from a list of SMILES :param smiles_list: list of SMILES :return: dataframe with ring information

test_ring_system_lookup(input_filename, output_filename)[source]: Test for RingSystemLookup :type input_filename: :param input_filename: input smiles file :type output_filename: :param output_filename: output csv file :return: None

get_min_ring_frequency(ring_list)[source]

Get minimum frequency from RingSystemLookup.process_smiles

Parameters:: ring_list – output from RingSystemLookup.process_smiles
Returns:: [ring_with minimum frequency, minimum frequency], acyclic molecules return [“”,-1]

get_spiro_atoms(mol)[source]

Get atoms that are part of a spiro fusion

Parameters:: mol – input RDKit molecule
Returns:: a list of atom numbers for atoms that are the centers of spiro fusions

max_ring_size(mol)[source]

Get the size of the largest ring in a molecule

ring_stats(mol)[source]

Get some simple statistics for rings