def convert_str(str_data, in_format, out_format):
mol = OBMol()
conv = OBConversion()
conv.SetInFormat(in_format)
conv.SetOutFormat(out_format)
conv.ReadString(mol, str_data)
return (conv.WriteString(mol), conv.GetOutFormat().GetMIMEType())
def convert_str(str_data,
in_format,
out_format,
gen3d=False,
add_hydrogens=False,
perceive_bonds=False,
out_options=None):
# Make sure that the start of InChI is valid before passing it to
# Open Babel, or Open Babel will crash the server.
if in_format.lower() == 'inchi':
validate_start_of_inchi(str_data)
if out_options is None:
out_options = {}
obMol = OBMol()
conv = OBConversion()
conv.SetInFormat(in_format)
conv.SetOutFormat(out_format)
conv.ReadString(obMol, str_data)
if add_hydrogens:
obMol.AddHydrogens()
if gen3d:
# Generate 3D coordinates for the input
mol = pybel.Molecule(obMol)
mol.make3D()
if perceive_bonds:
obMol.ConnectTheDots()
obMol.PerceiveBondOrders()
for option, value in out_options.items():
conv.AddOption(option, conv.OUTOPTIONS, value)
return (conv.WriteString(obMol), conv.GetOutFormat().GetMIMEType())