Thank you very much.

You understand me exactly! Its perfect!

Now im just wondering how i could make the command line prompt for
openbabel:

obabel -ismi - testfile.smi -omol -m O output.mol

into a pyhton script. That would make everything much much faster and
easier.

import pybel
mymol = list(pybel.readfile("smi","testfile.smi")).next # and heres my
problem
mymol.write('mol','output1.mol')


#my problem: How do i can call the other molecules in the file besides the
first one?

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