yes, with "assert" result is the same - output is:
2.43046898916e-316 6 12.0
2.43046898916e-316 6 12.0
2.43046898916e-316 8 15.0
2.43046898916e-316 6 12.0
2.43046898916e-316 16 31.0
C(CO)CS Molecular weight is: 3.15960968591e-315
(problem is only for atomicmass)

while without "app = QtGui.QApplication(sys.argv) and related commands" all
works perfectly.

As about element.txt: 
when I've copied it to project directory and replaced decimal separator to
"," script gives me correct results.

So, problem is in decimal separators in different locales (my is RU). Is it
possible to make workaround in my particular program to not take into
account separator settings?

And, problem is more common - similar bug was in the Avogadro (also based on
openbabel)
http://sourceforge.net/tracker/?func=detail&aid=3057251&group_id=165310&atid=835077
In that thread is mentioned that this bug was fixed... But is it really
fixed? 



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