def find(smile, smart_torsion="[*]~[!$(*#*)&!D1]-&!@[!$(*#*)&!D1]~[*]",
filter_smart_torsion=None, positions=None):
if positions is None:
mol = Chem.MolFromSmiles(smile)
if mol is None:
raise ValueError("The smile is invalid")
pattern_tor = Chem.MolFromSmarts(smart_torsion)
torsion = list(mol.GetSubstructMatches(pattern_tor))
if filter_smart_torsion:
pattern_custom = Chem.MolFromSmarts(filter_smart_torsion)
custom = list(mol.GetSubstructMatches(pattern_custom))
to_del_bef_custom = []
for x in reversed(range(len(torsion))):
for y in reversed(range(len(custom))):
ix1, ix2 = ig(1)(torsion[x]), ig(2)(torsion[x])
iy1, iy2 = ig(1)(custom[y]), ig(2)(custom[y])
if (ix1 == iy1 and ix2 == iy2) or (ix1 == iy2 and
ix2 == iy1):
to_del_bef_custom.append(x)
custom_torsion = copy(torsion)
custom_torsion = [v for i, v in enumerate(custom_torsion)
if i not in set(to_del_bef_custom)]
torsion = custom_torsion
positions = cleaner(torsion)
return positions
def find(smiles, smarts_cistrans=None, positions=None):
if positions is None:
mol = Chem.MolFromSmiles(smiles)
if mol is None:
raise ValueError("The smiles is invalid")
pattern_cistrans = Chem.MolFromSmarts(smarts_cistrans)
cistrans = list(mol.GetSubstructMatches(pattern_cistrans))
positions = cleaner(cistrans)
return positions
def find(smiles, smarts_cistrans=None, positions=None):
if positions is None:
mol = Chem.MolFromSmiles(smiles)
if mol is None:
raise ValueError("The smiles is invalid")
pattern_cistrans = Chem.MolFromSmarts(smarts_cistrans)
cistrans = list(mol.GetSubstructMatches(pattern_cistrans))
positions = cleaner(cistrans)
return positions
def find(smiles,
smarts_torsion="[*]~[!$(*#*)&!D1]-&!@[!$(*#*)&!D1]~[*]",
filter_smarts_torsion=None,
positions=None):
"""Find the positions of rotatable bonds in the molecule.
Args(required):
smiles (str)
Arge(optional)
smarts_torion (str) : pattern defintion for the torsions, if not
defined, a default pattern "[*]~[!$(*#*)&!D1]-&!@[!$(*#*)&!D1]~[*]"
will be used
filter_smarts_torsion (str): pattern defition for the torsion to be
ignored
positions (list of tuples) : if the positions (in terms of atom
indicies) of the torsions is known, they can be passed directly
"""
if positions is None:
mol = Chem.MolFromSmiles(smiles)
if mol is None:
raise ValueError("The smiles is invalid")
pattern_tor = Chem.MolFromSmarts(smarts_torsion)
torsion = list(mol.GetSubstructMatches(pattern_tor))
if filter_smarts_torsion:
pattern_custom = Chem.MolFromSmarts(filter_smarts_torsion)
custom = list(mol.GetSubstructMatches(pattern_custom))
to_del_bef_custom = []
for x in reversed(range(len(torsion))):
for y in reversed(range(len(custom))):
ix1, ix2 = ig(1)(torsion[x]), ig(2)(torsion[x])
iy1, iy2 = ig(1)(custom[y]), ig(2)(custom[y])
if (ix1 == iy1 and ix2 == iy2) or (ix1 == iy2
and ix2 == iy1):
to_del_bef_custom.append(x)
custom_torsion = copy(torsion)
custom_torsion = [
v for i, v in enumerate(custom_torsion)
if i not in set(to_del_bef_custom)
]
torsion = custom_torsion
positions = cleaner(torsion)
return positions
def find(smiles, smarts_torsion="[*]~[!$(*#*)&!D1]-&!@[!$(*#*)&!D1]~[*]",
filter_smarts_torsion=None, positions=None):
"""Find the positions of rotatable bonds in the molecule.
Args(required):
smiles (str)
Arge(optional)
smarts_torion (str) : pattern defintion for the torsions, if not
defined, a default pattern "[*]~[!$(*#*)&!D1]-&!@[!$(*#*)&!D1]~[*]"
will be used
filter_smarts_torsion (str): pattern defition for the torsion to be
ignored
positions (list of tuples) : if the positions (in terms of atom
indicies) of the torsions is known, they can be passed directly
"""
if positions is None:
mol = Chem.MolFromSmiles(smiles)
if mol is None:
raise ValueError("The smiles is invalid")
pattern_tor = Chem.MolFromSmarts(smarts_torsion)
torsion = list(mol.GetSubstructMatches(pattern_tor))
if filter_smarts_torsion:
pattern_custom = Chem.MolFromSmarts(filter_smarts_torsion)
custom = list(mol.GetSubstructMatches(pattern_custom))
to_del_bef_custom = []
for x in reversed(range(len(torsion))):
for y in reversed(range(len(custom))):
ix1, ix2 = ig(1)(torsion[x]), ig(2)(torsion[x])
iy1, iy2 = ig(1)(custom[y]), ig(2)(custom[y])
if (ix1 == iy1 and ix2 == iy2) or (ix1 == iy2 and
ix2 == iy1):
to_del_bef_custom.append(x)
custom_torsion = copy(torsion)
custom_torsion = [v for i, v in enumerate(custom_torsion)
if i not in set(to_del_bef_custom)]
torsion = custom_torsion
positions = cleaner(torsion)
return positions
from utilities import cleaner
"""
Train Modification
"""
k = 1
with open("./data/given/train_tweets.txt", "r") as rf:
ct = rf.readlines()
ct_user = [c.split()[0] for c in ct]
ct_tweet = [" ".join(c.split()[1:]) for c in ct]
df = pd.DataFrame({"User": ct_user, "Tweets": ct_tweet})
clean_tweets = []
for i in range(len(df)):
clean_tweets.append(cleaner(df['Tweets'][i]))
pd.DataFrame({
"User": ct_user,
"Tweets": ct_tweet,
"Clean Tweets": clean_tweets
}).to_csv("./data/train_tweets_mod2.csv", index=False)
"""
Test Modification
"""
k = 1
with open("./data/given/test_tweets_unlabeled.txt", "r") as rf:
ct = rf.readlines()
test_df = pd.DataFrame({"Tweets": ct})
