def __init__(self, selfies=None, selfies_file=None, vocab_file=None):
"""
Can be initiated from either a list of SELFIES, or a line-delimited
SELFIES file.
Args:
selfies (list): the complete set of SELFIES that constitute the
training dataset
selfies_file (string): line-delimited file containing the complete
set of SELFIES that constitute the training dataset
vocab_file (string): line-delimited file containing all tokens to
be used in the vocabulary
"""
if vocab_file is not None:
# read tokens from file, and add to vocabulary
all_chars = read_smiles(vocab_file)
# prevent chain popping open multi-character tokens
self.characters = list(set(chain(*[[char] for char in all_chars])))
else:
# read SMILES
if selfies is not None:
self.selfies = selfies
elif selfies_file is not None:
self.selfies = read_smiles(selfies_file)
else:
raise ValueError("must provide SELFIES list or file to" + \
" instantiate Vocabulary")
# tokenize all SMILES in the input and add all tokens to vocabulary
alphabet = sorted(list(sf.get_alphabet_from_selfies(self.selfies)))
self.characters = alphabet
# add padding token
self.characters.append('<PAD>')
# add SOS/EOS tokens
self.characters.append('SOS')
self.characters.append('EOS')
# create dictionaries
self.dictionary = {key: idx for idx, key in enumerate(self.characters)}
self.reverse_dictionary = {value: key for key, value in \
self.dictionary.items()}
def __init__(self, smiles=None, smiles_file=None, vocab_file=None):
"""
Can be initiated from either a list of SMILES, or a line-delimited
SMILES file, or a file containing only tokens.
Args:
smiles (list): the complete set of SMILES that constitute the
training dataset
smiles_file (string): line-delimited file containing the complete
set of SMILES that constitute the training dataset
vocab_file (string): line-delimited file containing all tokens to
be used in the vocabulary
"""
if vocab_file is not None:
# read tokens from file, and add to vocabulary
self.characters = read_smiles(vocab_file)
else:
# read SMILES
if smiles is not None:
self.smiles = smiles
elif smiles_file is not None:
self.smiles = read_smiles(smiles_file)
else:
raise ValueError("must provide SMILES list or file to" + \
" instantiate Vocabulary")
# tokenize all SMILES in the input and add all tokens to vocabulary
all_chars = [self.tokenize(sm) for sm in self.smiles]
self.characters = list(set(chain(*all_chars)))
# add padding token
if not '<PAD>' in self.characters:
# ... unless reading a padded vocabulary from file
self.characters.append('<PAD>')
# create dictionaries
self.dictionary = {key: idx for idx, key in enumerate(self.characters)}
self.reverse_dictionary = {value: key for key, value in \
self.dictionary.items()}
def __init__(self,
smiles=None,
smiles_file=None,
vocab_file=None,
training_split=0.9):
"""
Can be initiated from either a list of SMILES, or a line-delimited
file.
Args:
smiles (list): the complete set of SMILES that constitute the
training dataset
smiles_file (string): line-delimited file containing the complete
set of SMILES that constitute the training dataset
vocab_file (string): line-delimited file containing all tokens to
be used in the vocabulary
training_split (numeric): proportion of the dataset to withhold for
validation loss calculation
"""
if smiles:
self.smiles = smiles
elif smiles_file:
self.smiles = read_smiles(smiles_file)
else:
raise ValueError("must provide SMILES list or file to" + \
" instantiate SmilesDataset")
# create vocabulary
if vocab_file:
self.vocabulary = Vocabulary(vocab_file=vocab_file)
else:
self.vocabulary = Vocabulary(smiles=self.smiles)
# split into training and validation sets
np.random.seed(0)
n_smiles = len(self.smiles)
split = np.random.choice(range(n_smiles),
size=int(n_smiles * training_split),
replace=False)
self.training = [self.smiles[idx] for idx in \
range(len(self.smiles)) if idx in split]
self.validation = [self.smiles[idx] for idx in \
range(len(self.smiles)) if not idx in split]
### CLI
parser = argparse.ArgumentParser()
parser.add_argument('--input_file', type=str)
parser.add_argument('--output_file', type=str)
parser.add_argument('--enum_factor', type=int,
help='factor to augment the dataset by')
args = parser.parse_args()
# check output directory exists
output_dir = os.path.dirname(args.output_file)
if not os.path.isdir(output_dir):
os.makedirs(output_dir)
# read SMILES
smiles = read_smiles(args.input_file)
# convert to numpy array
smiles = np.asarray(smiles)
# create enumerator
sme = SmilesEnumerator(canonical=False, enum=True)
# also store and write information about enumerated library size
summary = pd.DataFrame()
# enumerate potential SMILES
enum = []
max_tries = 200 ## randomized SMILES to generate for each input structure
for sm_idx, sm in enumerate(tqdm(smiles)):
tries = []
for try_idx in range(max_tries):
help='calculate outcomes for molecules in DeepSMILES format',
action='store_true')
parser.add_argument('--sampled_files',
type=str,
nargs='*',
help='file(s) containing sampled SMILES')
parser.set_defaults(stop_if_exists=False)
args = parser.parse_args()
print(args)
# make output directories
if not os.path.isdir(args.output_dir):
os.makedirs(args.output_dir)
# read the training set SMILES, and convert to moelcules
org_smiles = read_smiles(args.original_file)
org_mols = [
mol for mol in clean_mols(
org_smiles, selfies=args.selfies, deepsmiles=args.deepsmiles) if mol
]
org_canonical = [Chem.MolToSmiles(mol) for mol in org_mols]
# define helper function to get # of rotatable bonds
def pct_rotatable_bonds(mol):
n_bonds = mol.GetNumBonds()
if n_bonds > 0:
rot_bonds = Lipinski.NumRotatableBonds(mol) / n_bonds
else:
rot_bonds = 0
return rot_bonds
if args.output_dir is None:
args.output_dir = os.path.dirname(args.smiles_file)
# optionally stop if output file already exists
filename = os.path.basename(args.smiles_file)
split = os.path.splitext(filename)
output_file = os.path.join(args.output_dir, split[0] + "-outcomes.csv.gz")
if os.path.isfile(output_file) and args.stop_if_exists:
print("output file " + output_file + " exists: stopping early")
sys.exit()
# create results container
res = pd.DataFrame()
# read SMILES and convert to molecules
smiles = read_smiles(args.smiles_file)
mols = [mol for mol in clean_mols(smiles, selfies=args.selfies,
deepsmiles=args.deepsmiles) if mol]
canonical = [Chem.MolToSmiles(mol, isomericSmiles=False) for mol in mols]
# also read the reference file
ref_smiles = read_smiles(args.reference_file)
ref_mols = [mol for mol in clean_mols(ref_smiles) if mol]
ref_canonical = [Chem.MolToSmiles(mol, isomericSmiles=False) for mol in \
ref_mols]
## drop known molecules
canonical = [sm for sm in canonical if sm not in ref_canonical]
# re-parse molecules
mols = [mol for mol in clean_mols(canonical) if mol]
os.chdir(python_dir)
sys.path.append(python_dir)
# import functions
from functions import clean_mols, remove_salts_solvents, read_smiles, \
NeutraliseCharges
# import Vocabulary
from datasets import Vocabulary
# parse arguments
input_file = sys.argv[1]
output_file = sys.argv[2]
# read SMILES
basename = os.path.basename(input_file)
smiles = read_smiles(input_file)
# remove duplicated SMILES
smiles = np.unique(smiles)
# record original count
initial_count = len(smiles)
print("parsing " + str(initial_count) + " unique SMILES")
# convert to molecules
mols = clean_mols(smiles, stereochem=False)
# remove molecules that could not be parsed
mols = [mol for mol in mols if mol]
print("parsed " + str(len(mols)) + " unique, valid canonical SMILES")
# remove salts/solvents
mols = [remove_salts_solvents(mol, hac=3) for mol in tqdm(mols)]