Is there anyway to prepend the smiles string to the output of fingerprints to generfp tool? If not could you add that as an option in future releases.
sorry, butn o direct support for such output format.
Two workarounds come into my mind.
1. This works on linux/unix only: try the paste command it can merge two (or more) files line-by-line.
2. Generate and SDfile output by generatemd c infile.smiles -k CF -o outfile.sdf -S and then ocnvert it to smiles keeping the <CF> tag from the SDF:
molconvert smiles outfile.sdf -T CF > outfile.smiles
Hope this helps.