Comment #4 on issue 3033 by ronan.l...@gmail.com: UndefinedFunction not returned from atoms
http://code.google.com/p/sympy/issues/detail?id=3033
So should eq.atoms(UndefinedFunction) return set([f])?
In that case, eq.atoms(FunctionClass) should be changed return set([f, cos]). But I think we should leave it as it is, because f doesn't appear in the .args of anything, it's only the Python type of f(x) and it's not even an instance of Basic.
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