Is there a way to generate an InChI if I have a connection table, but not in CML, Mol or SDF form?
There is, though as you may know the InChI generation program will currently only accept CML, Mol or SDF files. We have set up an Open Babel Server at our WWMM Portal which can be used to convert to CML, Mol or SDF form from file types as listed here. Help on how to use the Server is provided on the page.