I have a list of molecules in SMILES format that I am converting to InChIKey format. However, a number of them are generating warnings. I would like to be able to generate a file showing the warnings generated in the process of converting each molecule, so that a team member can review them. Is it possible to capture these messages programmatically, instead of just logging them?
A snippet illustrating what I'd like to be able to do:
import pybel
smiles = pybel.readfile('smi', 'smiles.txt')
converted = []
for mol in smiles:
smiles_str = mol.write('smiles')
inchikey_str = mol.write('inchikey')
warnings = None # Is there something I can do here to capture the warnings?
converted.append((smiles_str, inchikey_str, warnings))