Hi -
I've found that while Indigo can correctly parse ctfile strings containing many small molecules, and will correctly generate SMILES strings for them, when canonical smiles is retrieved using the molecule.canonicalSmiles() method of the Python API then the library aoppears to hang indefinitely, with 100% of one core CPU usage. It never seems to complete or throw an error.
Unfortunately I cannot share the exact chemical structures, as they're protected by an NDA, but the complete atom count is C835 H946 Cl19 F5 N108 O111 S37 over 30 small molecules. I run canonicalization, which completes fine, before attempting to get the canonical SMILES:
molecule.aromatize()
molecule_smiles = molecule.canonicalSmiles()
I can reproduce this on Indigo 1.2.3 and Indigo 4.0 Beta, on both Windows and Linux. This is using the Python wrappers to call the pre-built Indigo libraries.
All the best,
Jonathan Ayling