def convert_babel_to_system(mol):
"""
Convert a BigDFT fragment to an open babel molecule.
Args:
mol (openbabel.OBMol): the molecule to convert.
Returns:
(BigDFT.Systems.System): bigdft system.
"""
from BigDFT.IO import read_mol2
from openbabel.openbabel import OBConversion
# py2 workaround
from sys import version_info
if version_info[0] < 3:
from io import BytesIO as StringIO
else:
try:
from io import StringIO
except ImportError:
from StringIO import StringIO
conv = OBConversion()
conv.SetOutFormat("mol2")
sval = StringIO(conv.WriteString(mol))
return read_mol2(sval)
def compute_smiles(sys):
"""
Computes the SMILES representation of a given system.
Args:
sys (BigDFT.System.Systems): the system to compute the
representation of.
Return:
(str): the smiles representation of this molecule.
"""
from openbabel.openbabel import OBConversion
conv = OBConversion()
mol = convert_system_to_babel(sys)
conv.SetOutFormat("SMI")
retstr = conv.WriteString(mol)
retstr = retstr.replace("\n", "")
retstr = retstr.replace("\t", "")
return retstr