def template_sdf(smiles, distance_cutoff_1, distance_cutoff_2):
"""Create a template sdf string and writes it to file.
Args(required):
smiles (str): one-line representation of the molecule
Args(optional):
distance_cutoff_1 (float): min distance between non-bonded atoms [A]
distance_cutoff_2 (float): max distance between bonded atoms [A]
Returns:
sdf string
"""
cnt = 0
sdf_check = True
while sdf_check:
mol = Chem.MolFromSmiles(smiles)
mol = Chem.AddHs(mol)
AllChem.EmbedMolecule(mol)
AllChem.UFFOptimizeMolecule(mol)
Chem.SDWriter('mol.sdf').write(mol)
sdf_string = Chem.MolToMolBlock(mol)
check = check_geo_sdf(sdf_string, distance_cutoff_1, distance_cutoff_2)
if check:
sdf_check = False
Chem.SDWriter('mol.sdf').write(mol)
else:
cnt += 1
return sdf_string
def template_sdf(smiles, distance_cutoff_1, distance_cutoff_2):
"""Create a template sdf string and writes it to file.
Args(required):
smiles (str): one-line representation of the molecule
Args(optional):
distance_cutoff_1 (float): min distance between non-bonded atoms [A]
distance_cutoff_2 (float): max distance between bonded atoms [A]
Returns:
sdf string
"""
cnt = 0
sdf_check = True
while sdf_check:
mol = Chem.MolFromSmiles(smiles)
mol = Chem.AddHs(mol)
AllChem.EmbedMolecule(mol)
AllChem.UFFOptimizeMolecule(mol)
Chem.SDWriter('mol.sdf').write(mol)
sdf_string = Chem.MolToMolBlock(mol)
check = check_geo_sdf(sdf_string, distance_cutoff_1, distance_cutoff_2)
if check:
sdf_check = False
Chem.SDWriter('mol.sdf').write(mol)
else:
cnt += 1
return sdf_string
def is_geometry_valid(self):
"""Return True if the geometry is valid."""
check = check_geo_sdf(self.sdf_string, self.mol_info.distance_cutoff_1,
self.mol_info.distance_cutoff_2)
return check
def is_geometry_valid(self):
"""Return True if the geometry is valid."""
check = check_geo_sdf(self.sdf_string, self.mol_info.distance_cutoff_1,
self.mol_info.distance_cutoff_2)
return check