You are right about SMILES. We trained on the canonical SMILES output by the RDKit, so as far as our AE is concerned, there is only one way to write SMILES for

You are right about SMILES. We trained on the canonical SMILES output by the RDKit, so as far as our AE is concerned, there is only one way to write SMILES for a given molecule (http://www.rdkit.org/docs/GettingStartedInPython.html#writing-molecules http://www.rdkit.org/docs/GettingStartedInPython.html#writin...). Of course, the choice of what the canonical SMILES is is somewhat arbitrary.