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_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
