append my results to a file

[Gribouillis]

I am able to obtain the values and I see them on the screen but I don't find the way to append them to the original file

What exactly do you want to append to the original file? Is it the 'smiles', the 'launch' or the output of the calls to subprocess.call()?

In any case, I strongly suggest that you write the desired ouptut to a temporary file first in order to avoid overwriting the initial file.