def add_with_rdkit(self, filename, filetype, strict=False, **kwargs):
"""Add molecule using rdkit"""
with open(filename, "r") as inputfile:
text = inputfile.read()
if filetype == "auto":
filetype = os.path.splitext(filename)[1]
if filetype == "inchi":
rdmol = Chem.MolFromInchi(text)
elif filetype == "mol2":
rdmol = Chem.MolFromMol2File(filename)
elif filetype == "mol":
rdmol = Chem.MolFromMolFile(filename)
elif filetype == "pdb":
rdmol = Chem.MolFromPdbFile(filename)
elif filetype in ["smi", "smiles"]:
rdmol = Chem.MolFromSmiles(text)
elif filetype == "tpl":
rdmol = Chem.MolFromTPLFile(filename)
elif filetype == "smarts":
if strict:
raise IOError("Smarts is pattern, smiles for molecules.")
else:
print "WARNING: Use smiles, ignoring smarts." % filetype
return
else:
if strict:
raise IOError("Filetype (%s) not in rdkit." % filetype)
else:
print "WARNING: Could not filetype %s." % filetype
return
rdmol = Chem.addHs(rdmol)
self.molstr.append(Chem.MolToPDBBlock)
