def rdkit_mmff94_xyz(smiles, **kwargs):
"""
Returns the string of the XYZ file obtained performing the MMFF94 molecular mechanics optimization of the given
SMILES using RDKit.
Writing temporary files in $MM_WORKING_DIR if defined or otherwise in /tmp
:param smiles: input_SMILES
:param max_iterations: max number of iterations (default 500)
:return : XYZ string of optimized geometry, success (whether the MM optimization was successful and the smiles has
stayed identical after optimization)
"""
working_dir = os.environ[
"MM_WORKING_DIR"] if "MM_WORKING_DIR" in os.environ else "/tmp"
# Converting the molecule to RDKit object
mol = MolFromSmiles(smiles)
smi_canon = MolToSmiles(MolFromSmiles(smiles))
# Setting paths
filename_smiles = str(os.getpid()) + "_" + smi_to_filename(smi_canon)
xyz_path = join(working_dir, filename_smiles + '.xyz')
post_MM_smi_path = join(working_dir, filename_smiles + '.smi')
# Computing geometry
try:
# Adding implicit hydrogens
mol = AddHs(mol)
# MM optimization
EmbedMolecule(mol)
value = MMFFOptimizeMolecule(mol, maxIters=kwargs["max_iterations"])
# Success if returned value is null
success_RDKIT_output = value == 0
# Computing XYZ from optimized molecule
xyz_str = MolToXYZBlock(mol)
# Writing optimized XYZ to file
with open(xyz_path, "w") as f:
f.writelines(xyz_str)
# Success if the optimization has converged and the post MM smiles is identical the pre MM smiles
success = success_RDKIT_output and check_identical_geometries(
xyz_path, smi_canon, post_MM_smi_path)
except Exception as e:
success = False
xyz_str = None
finally:
# Removing files
remove_files([post_MM_smi_path, xyz_path])
return xyz_str, success
def get_mol_from_smiles(smiles: str) -> Mol:
mol = MolFromSmiles(smiles)
try:
mol = Chem.AddHs(mol)
AllChem.EmbedMolecule(mol, maxAttempts=5000)
AllChem.UFFOptimizeMolecule(mol)
mol = Chem.RemoveHs(mol)
except ValueError:
mol = MolFromSmiles(smiles)
AllChem.Compute2DCoords(mol)
return mol
def load_pop_from_smiles_list(self, smiles_list, atom_mutability=True):
"""
Loading the population from the given smiles list.
Setting the internal variables to their values
:param smiles_list: list of SMILES
:param atom_mutability: whether the core of the molecules of the starting population can be modified
:return:
"""
if self.shuffle_init_pop:
np.random.shuffle(smiles_list)
# Iterating over all the given smiles
for i, smi in enumerate(smiles_list):
# Loading QuMolGraph object
self.pop[i] = MolGraph(MolFromSmiles(smi), sanitize_mol=True, mutability=atom_mutability)
# Saving smiles in the tabu dictionary and in action history initialization
self.pop_tabu_list[i] = self.pop[i].to_aromatic_smiles()
self.actions_history[i] = self.pop[i].to_aromatic_smiles()
# Evaluation of the population (not recording the count of calls to the objective function)
print("Computing scores at initialization...")
self.evaluation_strategy.set_params(**self.evaluation_strategy_parameters["evaluate_init_pop"])
self.evaluation_strategy.disable_calls_count()
self.evaluation_strategy.compute_record_scores_init_pop(self.pop)
self.evaluation_strategy.enable_calls_count()
self.evaluation_strategy.set_params(**self.evaluation_strategy_parameters["evaluate_new_solution"])
def compute_mol_legend(action_history_k,
smi,
action_history_scores,
legend_scores_keys_strat=None):
legend = ""
last = 0
scores_float = []
if legend_scores_keys_strat is not None:
for i, key_strat in enumerate(legend_scores_keys_strat):
score = None
if isinstance(key_strat, str):
score = action_history_scores[action_history_k][key_strat]
elif isinstance(key_strat, EvaluationStrategy):
score = key_strat.evaluate_individual(
MolGraph(MolFromSmiles(smi), sanitize_mol=True))
scores_float.append(score)
score_str = "{:.2f}".format(score)
if i == 1:
legend += " ["
elif i > 1:
legend += ", "
legend += score_str
last = i
if last >= 1:
legend += "]"
return legend, scores_float
def evaluate_individual(self, individual):
if individual is None:
return None
else:
mol_graph = MolFromSmiles(individual.to_aromatic_smiles())
score = qed(mol_graph)
return score, [score]
def extract_shingles(self, individual):
qry_shingles = set()
radius_constr = self.radius + 1
# Reloading molecule to make it aromatic
mol = MolFromSmiles(individual.to_aromatic_smiles())
for atm_idx in range(individual.mol_graph.GetNumAtoms()):
for N in range(1, radius_constr):
bonds = AllChem.FindAtomEnvironmentOfRadiusN(mol, N, atm_idx)
if not bonds:
break
# the reportedly faster method
atoms = set()
for bond_id in bonds:
bond = mol.GetBondWithIdx(bond_id)
atoms.add(bond.GetBeginAtomIdx())
atoms.add(bond.GetEndAtomIdx())
if self.rooted:
new_shingle = Chem.rdmolfiles.MolFragmentToSmiles(
mol, list(atoms), bonds, 0, 0, False, False, atm_idx,
True, False, False)
else:
new_shingle = Chem.rdmolfiles.MolFragmentToSmiles(
mol, list(atoms), bonds, 0, 0, False, False, -1, True,
False, False)
qry_shingles.add(new_shingle)
return qry_shingles
def compute_mol_attributes(graph,
labels_dict,
actions_history_smi_pop,
actions_history_smi_removed,
actions_history_scores_pop,
actions_history_scores_removed,
legend_scores_keys_strat=None):
images_attributes = {}
scores_attributes = {}
draw_opt = DrawingOptions()
draw_opt.coordScale = 0.9
draw_opt.dotsPerAngstrom = 30
for action_history_k in labels_dict.keys():
if action_history_k in actions_history_smi_pop:
smi = actions_history_smi_pop[action_history_k]
img = MolToImage(MolFromSmiles(smi),
size=(800, 800),
options=draw_opt)
images_attributes[action_history_k] = crop_image_with_transparency(
img)
legend, _ = compute_mol_legend(action_history_k, smi,
actions_history_scores_pop,
legend_scores_keys_strat)
scores_attributes[action_history_k] = legend
else:
smi = actions_history_smi_removed[action_history_k]
img = MolToImage(MolFromSmiles(smi),
size=(800, 800),
options=draw_opt)
images_attributes[action_history_k] = crop_image_with_transparency(
img)
legend, _ = compute_mol_legend(action_history_k, smi,
actions_history_scores_removed,
legend_scores_keys_strat)
scores_attributes[action_history_k] = legend
nx.set_node_attributes(graph, images_attributes, "image")
nx.set_node_attributes(graph, scores_attributes, "score_label")
def test_react(reactant, expected_products):
reactor = Reactor()
reactant_mol = MolFromSmiles(reactant)
AllChem.EmbedMolecule(reactant_mol, AllChem.ETKDG())
products = reactor.react(reactant_mol)
products = mols2smiles(products)
assert products == expected_products
def _transform(self, x):
try:
mol = MolFromInchi(x['standard_inchi'])
except:
mol = MolFromSmiles(x['Compound_SMILES'])
info = {}
AllChem.GetMorganFingerprintAsBitVect(mol, self.radius, self.dim, bitInfo=info)
return list(info.keys())
def get_score_components(smiles):
'''
Get the non-normalized score components
:param smiles: a VALID smiles string
:return: a tuple of floats
'''
this_mol = MolFromSmiles(smiles)
return get_score_components_from_mol(this_mol)
def _set_target_fps(self, pickaxe: Pickaxe):
for smiles in pickaxe.target_smiles:
mol = MolFromSmiles(smiles)
if self.fingerprint_method == "Morgan":
fp = AllChem.GetMorganFingerprintAsBitVect(mol, **self.fingerprint_args)
else:
fp = RDKFingerprint(mol)
self.target_fps.append(fp)
def evaluate_individual(self, individual):
mol_graph = MolFromSmiles(individual.to_aromatic_smiles())
log_p = Descriptors.MolLogP(mol_graph)
sas_score = sascorer.calculateScore(mol_graph)
largest_ring_size = self.get_largest_ring_size(mol_graph)
cycle_score = max(largest_ring_size - 6, 0)
score = log_p - sas_score - cycle_score
return score, [score]
def draw_mol_labels(labels_dict, actions_history_smi_pop, actions_history_smi_removed,
actions_history_scores_pop, actions_history_scores_removed, legend_scores_keys_strat=None,
problem_type="max", mols_per_row=4, draw_n_mols=None):
smi_to_draw = {}
legends_to_draw = {}
scores_float = {}
for action_history_k in labels_dict.keys():
if labels_dict[action_history_k] != "":
if action_history_k in actions_history_smi_pop:
smi = actions_history_smi_pop[action_history_k]
smi_to_draw[labels_dict[action_history_k]] = smi
legend, scores = compute_mol_legend(action_history_k, smi, actions_history_scores_pop,
legend_scores_keys_strat)
legends_to_draw[labels_dict[action_history_k]] = legend
scores_float[labels_dict[action_history_k]] = scores
else:
smi = actions_history_smi_removed[action_history_k]
smi_to_draw[labels_dict[action_history_k]] = smi
legend, scores = compute_mol_legend(action_history_k, smi, actions_history_scores_removed,
legend_scores_keys_strat)
legends_to_draw[labels_dict[action_history_k]] = legend
scores_float[labels_dict[action_history_k]] = scores
mols = []
legends = []
scores_to_sort = []
for k, smi in smi_to_draw.items():
mols.append(MolFromSmiles(smi))
legends.append(legends_to_draw[k])
scores_to_sort.append(scores_float[k][0])
mols = np.array(mols)
legends = np.array(legends)
# Sorting molecules
sorted_order = np.argsort(scores_to_sort)
if problem_type == "max":
sorted_order = sorted_order[::-1]
# Filtering molecules if necessary
if draw_n_mols is not None:
mols = mols[:draw_n_mols]
legends = legends[:draw_n_mols]
legends = list(legends[sorted_order])
mols = list(mols[sorted_order])
img = MolsToGridImage(mols, legends=legends, molsPerRow=mols_per_row, subImgSize=(200, 200))
return img
def get_all_metrics(smiles):
mols = [MolFromSmiles(s) for s in smiles]
scorer = NormalizedScorer()
scores, norm_scores = scorer.get_scores_from_mols(mols)
arom_rings = np.array([Descriptors.NumAromaticRings(m) for m in mols])
metrics = np.concatenate([scores.sum(axis=1)[:, None],
norm_scores.sum(axis=1)[:, None],
scores[:, 1][:, None],
norm_scores[:, 1][:, None],
arom_rings[:, None]],
axis=1)
return (smiles, metrics)
def extract_descriptors(self, individual):
"""
Returning the descriptor(s) extracted from the given individual
:param individual:
:return:
"""
if self.descriptor_key == "gen_scaffolds":
return [
MolToSmiles(
MurckoScaffold.MakeScaffoldGeneric(
MolFromSmiles(individual.to_smiles())))
]
elif self.descriptor_key == "ifg":
curr_ifgs = ifg.identify_functional_groups(
MolFromSmiles(individual.to_smiles()))
return list(set([curr_ifg[2] for curr_ifg in curr_ifgs]))
elif self.descriptor_key == "atoms":
return list(set(individual.get_atom_types()))
elif self.descriptor_key == "shg_1":
return list(extract_shingles(individual, 1))
elif self.descriptor_key == "checkmol":
return list(set(extract_checkmol(individual)))
def obabel_mmff94_xyz(smiles, **kwargs):
"""
Returns the string of the XYZ file obtained performing the MMFF94 molecular mechanics optimization of the given
SMILES using obabel.
Writing temporary files in $MM_WORKING_DIR if defined or otherwise in /tmp
:param smiles : input SMILES
:return : XYZ string of optimized geometry, success (whether the MM optimization was successful and the smiles has
stayed identical after optimization)
"""
working_dir = os.environ[
"MM_WORKING_DIR"] if "MM_WORKING_DIR" in os.environ else "/tmp"
# Computing RDKIT canonical SMILES
smi_canon = MolToSmiles(MolFromSmiles(smiles))
filename_smiles = str(os.getpid()) + "_" + smi_to_filename(smi_canon)
# Computing files paths
smi_path = join(working_dir, filename_smiles + ".smi")
xyz_path = join(working_dir, filename_smiles + ".xyz")
post_MM_smi_path = join(working_dir, filename_smiles + ".post_MM.smi")
try:
# Writing smiles to file
with open(smi_path, "w") as f:
f.write(smi_canon)
# Converting SMILES to XYZ after computing MM (Obabel MMFF94)
command_obabel = join(os.getenv("OPT_LIBS"),
"obabel/openbabel-2.4.1/bin/obabel") + " -ismi " + smi_path \
+ " -oxyz -O " + xyz_path + " --gen3d"
os.system(command_obabel + " > /dev/null 2> /dev/null")
# Reading XYZ string
with open(xyz_path, "r") as f:
xyz_str = f.read()
# Success if the post MM smiles is identical the pre MM smiles
success = check_identical_geometries(xyz_path, smi_canon,
post_MM_smi_path)
except Exception as e:
success = False
xyz_str = None
finally:
# Removing files
remove_files([smi_path, xyz_path, post_MM_smi_path])
return xyz_str, success
def load_obabel_smi(smi_path):
"""
Converting a OpenBabel SMILES into a canonical aromatic RDKit SMILES
:param smi_path:
:return:
"""
# Extracting smiles
with open(smi_path, "r") as f:
new_smi = f.readline()
# Loading converged mol
new_mol = MolFromSmiles(new_smi)
# Removing stereo information
RemoveStereochemistry(new_mol)
# Removing hydrogens
new_mol = RemoveHs(new_mol)
# Converting to SMILES
smi_rdkit = MolToSmiles(MolFromSmiles(MolToSmiles(new_mol)))
return smi_rdkit
def extract_shingles(smiles, level, as_list=False):
"""
Extracting up to the given level from the given smiles
see https://jcheminf.biomedcentral.com/articles/10.1186/s13321-018-0321-8
"""
if as_list:
qry_shingles = list()
else:
qry_shingles = set()
radius_constr = level + 1
# Reloading molecule to make it aromatic
mol = MolFromSmiles(smiles)
for atm_idx in range(mol.GetNumAtoms()):
for N in range(1, radius_constr):
bonds = AllChem.FindAtomEnvironmentOfRadiusN(mol, N, atm_idx)
if not bonds:
break
# the reportedly faster method
atoms = set()
for bond_id in bonds:
bond = mol.GetBondWithIdx(bond_id)
atoms.add(bond.GetBeginAtomIdx())
atoms.add(bond.GetEndAtomIdx())
# Computed rooted shingle
new_shingle = Chem.rdmolfiles.MolFragmentToSmiles(
mol, list(atoms), bonds, 0, 0, False, False, atm_idx, True,
False, False)
if as_list:
qry_shingles.append(new_shingle)
else:
qry_shingles.add(new_shingle)
return qry_shingles
def load_obabel_smi(smi_path, sanitize_mol):
# Extracting smiles
with open(smi_path, "r") as f:
new_smi = f.readline()
print("obabel new smi : " + new_smi)
# Loading converged mol
new_mol = MolFromSmiles(new_smi)
# Removing stereo information
RemoveStereochemistry(new_mol)
# Removing hydrogens
new_mol = RemoveHs(new_mol)
# Converting to SMILES
smi_rdkit = MolGraph(new_mol,
sanitize_mol=sanitize_mol).to_aromatic_smiles()
print("rdkit new smi : " + smi_rdkit)
return smi_rdkit
def load_pop_from_smiles_list(self, smiles_list, atom_mutability=True):
"""
Loading the population from the given smiles list.
Setting the internal variables to their values
:param smiles_list: list of SMILES
:param atom_mutability: whether the core of the molecules of the starting population can be modified
:return:
"""
# Iterating over all the given smiles
for i, smi in enumerate(smiles_list):
# Loading QuMolGraph object
self.pop[i] = MolGraph(MolFromSmiles(smi), sanitize_mol=True, mutability=atom_mutability)
# Saving smiles in the tabu dictionary and in action history initialization
self.pop_tabu_list[i] = self.pop[i].to_aromatic_smiles()
self.actions_history[i] = self.pop[i].to_aromatic_smiles()
# Evaluation of the population
print("Computing descriptors at initialization...")
self.evaluation_strategy.compute_record_scores(self.pop)
def evaluate_individual(self, individual):
"""
from https://github.com/bowenliu16/rl_graph_generation/blob/master/gym-molecule/gym_molecule/envs/molecule.py
"""
# normalization constants, statistics from 250k_rndm_zinc_drugs_clean.smi
logP_mean = 2.4570953396190123
logP_std = 1.434324401111988
SA_mean = -3.0525811293166134
SA_std = 0.8335207024513095
cycle_mean = -0.0485696876403053
cycle_std = 0.2860212110245455
mol_graph = MolFromSmiles(individual.to_aromatic_smiles())
log_p = Descriptors.MolLogP(mol_graph)
SA = -sascorer.calculateScore(mol_graph)
# cycle score
cycle_list = nx.cycle_basis(
nx.Graph(Chem.rdmolops.GetAdjacencyMatrix(mol_graph)))
if len(cycle_list) == 0:
cycle_length = 0
else:
cycle_length = max([len(j) for j in cycle_list])
if cycle_length <= 6:
cycle_length = 0
else:
cycle_length = cycle_length - 6
cycle_score = -cycle_length
normalized_log_p = (log_p - logP_mean) / logP_std
normalized_SA = (SA - SA_mean) / SA_std
normalized_cycle = (cycle_score - cycle_mean) / cycle_std
score = normalized_log_p + normalized_SA + normalized_cycle
return score, [score]
def __init__(self, smiles):
self._mol = MolFromSmiles(smiles)
def get_scores(self, smiles):
mols = [MolFromSmiles(s) for s in smiles]
return self.get_scores_from_mols(mols)
def initialize(self):
"""
Initialization of EvoMol with starting values.
This method MUST BE CALLED BEFORE running the algorithm.
:return:
"""
# Initialization of population
self.pop = list(np.full((self.pop_max_size,), None))
# Initialization of the dictionaries containing the smiles of former and current individuals as keys
self.pop_tabu_list = list(np.full((self.pop_max_size,), None))
# Intialization of the list of all individual ever inserted in the population, the list of their
# corresponding number of calls to the objective function at insertion and the list of the corresponding steps.
# Also recording the values of the objective function
self.all_generated_individuals_smiles = []
self.all_generated_individuals_n_obj_calls = []
self.all_generated_individuals_step = []
self.all_generated_individuals_obj_value = []
self.all_generated_individuals_improver = []
self.all_generated_individuals_success_obj_computation = []
# Insuring the SMILES of the external tabu list are canonical
if self.external_tabu_list is not None:
self.external_tabu_list = [MolGraph(MolFromSmiles(smi)).to_aromatic_smiles() for smi in self.external_tabu_list]
# Initialization of the dictionary containing the traces of steps of the algorithm
self.step_traces = {
'scores': {},
'n_replaced': [],
'additional_values': {},
'timestamps': []
}
# Initialization of keys in the self.step_traces dict declared by the evaluation strategy instance
for k in self.evaluation_strategy.keys() + ["total"]:
for stat in ["mean", "med", "min", "max", "std"]:
self.step_traces["scores"][k + "_" + stat] = []
# Initialization of keys in the self.step_traces dict for additional population scores
for k in self.evaluation_strategy.get_additional_population_scores().keys():
print(k)
self.step_traces['additional_values'][k] = []
# Initialization of the step counter.
self.curr_step_id = 0
# Initialization of errors list
self.errors = []
self.curr_total_scores = None
self.curr_scores = None
self.timestamp_start = None
# Computing idx of kth score to be recorded vector
for i, k in enumerate(self.evaluation_strategy.keys()):
if k == self.kth_score_to_record_key:
self.kth_score_to_record_idx = i
self.kth_score_history = deque(maxlen=500)
self.n_success_mut = np.zeros(self.pop_max_size, dtype=np.int)
self.n_fail_mut = np.zeros(self.pop_max_size, dtype=np.int)
self.actions_history = list(np.full(self.pop_max_size, None))
self.removed_actions_score_smi_tuple = {}
# Computing start timestamp
self.timestamp_start = time.time()
def mol_from_smiles(smiles):
if type(smiles) == 'str':
return MolFromSmiles(smiles)
else: # assume we have a list-like
return [MolFromSmiles(s) for s in smiles]
def edit_smiles(request):
smiles = request.GET.get('SMILES', '')
mol = MolFromSmiles(smiles)
return render(request, 'cspace/chemical-editor.html',
{'molblock': MolToMolBlock(mol)})
if pre_parser(t) is not None]))
print(len(these_smiles))
these_actions = my_model.strings_to_actions(these_smiles)
action_seq_length = my_model.action_seq_length(these_actions)
onehot = my_model.actions_to_one_hot(these_actions)
append_data = {
'smiles': np.array(these_smiles, dtype=dt),
'indices': np.array(these_indices),
'actions': these_actions,
'valid': np.ones((len(these_smiles))),
'seq_len': action_seq_length,
'data': onehot
}
if molecules:
from rdkit.Chem.rdmolfiles import MolFromSmiles
mols = [MolFromSmiles(s) for s in these_smiles]
raw_scores = np.array([get_score_components_from_mol(m) for m in mols])
append_data['raw_scores'] = raw_scores
num_atoms = np.array([len(m.GetAtoms()) for m in mols])
append_data['num_atoms'] = num_atoms
ds.append(append_data)
if molecules:
# also calculate mean and std of the scores, to use in the ultimate objective
raw_scores = np.array(ds.h5f['raw_scores'])
score_std = raw_scores.std(0)
score_mean = raw_scores.mean(0)
ds.append_to_dataset('score_std', score_std)
ds.append_to_dataset('score_mean', score_mean)
def get_mol(self):
return MolFromSmiles(self.smiles)
def main():
# change this to False to produce the equation dataset
molecules = True
# change this to False to get character-based encodings instead of grammar-based
grammar = 'new' #use True for the grammar used by Kusner et al
# can't define model class inside settings as it itself uses settings a lot
_, my_model = get_vae(molecules, grammar)
def pre_parser(x):
try:
return next(my_model._parser.parse(x))
except Exception as e:
return None
settings = get_settings(molecules,grammar)
MAX_LEN = settings['max_seq_length']
#feature_len = settings['feature_len']
dest_file = settings['data_path']
source_file = settings['source_data']
# Read in the strings
f = open(source_file,'r')
L = []
for line in f:
line = line.strip()
L.append(line)
f.close()
# convert to one-hot and save, in small increments to save RAM
#dest_file = dest_file.replace('.h5','_new.h5')
ds = IncrementingHDF5Dataset(dest_file)
step = 100
dt = h5py.special_dtype(vlen=str) # PY3 hdf5 datatype for variable-length Unicode strings
size = min(10000, len(L))
for i in tqdm(range(0, size, step)):#for i in range(0, 1000, 2000):
#print('Processing: i=[' + str(i) + ':' + str(i + step) + ']')
these_indices = list(range(i, min(i + step,len(L))))
these_smiles = L[i:min(i + step,len(L))]
if grammar=='new': # have to weed out non-parseable strings
tokens = [my_model._tokenize(s.replace('-c','c')) for s in these_smiles]
these_smiles, these_indices = list(zip(*[(s,ind) for s,t,ind in zip(these_smiles, tokens, these_indices) if pre_parser(t) is not None]))
#print(len(these_smiles))
these_actions = torch.tensor(my_model.strings_to_actions(these_smiles))
action_seq_length = my_model.action_seq_length(these_actions)
onehot = my_model.actions_to_one_hot(these_actions)
append_data = {'smiles': np.array(these_smiles, dtype=dt),
'indices': np.array(these_indices),
'actions': these_actions,
'valid': np.ones((len(these_smiles))),
'seq_len': action_seq_length,
'data': onehot}
if molecules:
from rdkit.Chem.rdmolfiles import MolFromSmiles
mols = [MolFromSmiles(s) for s in these_smiles]
raw_scores = np.array([get_score_components_from_mol(m) for m in mols])
append_data['raw_scores'] = raw_scores
num_atoms = np.array([len(m.GetAtoms()) for m in mols])
append_data['num_atoms'] = num_atoms
ds.append(append_data)
if molecules:
# also calculate mean and std of the scores, to use in the ultimate objective
raw_scores = np.array(ds.h5f['raw_scores'])
score_std = raw_scores.std(0)
score_mean = raw_scores.mean(0)
ds.append_to_dataset('score_std',score_std)
ds.append_to_dataset('score_mean', score_mean)
print('success!')
def _is_radical(self, mol):
return NumRadicalElectrons(MolFromSmiles(
mol.to_aromatic_smiles())) != 0