> I am trying to evaluate whether this software can help me compare two 
> chemical structures and find out whether they are same or similar.

Well, I'm not exactly sure what you want, but yes there are ways to detect 
identical molecules or compute similarity:
http://openbabel.org/docs/current/Command-line_tools/babel.html#substructure-and-similarity-searching

(Among other pages in the documentation.)

Hope that helps,
-Geoff
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