Fix calculateCyclicSymmetryNumber() function

Function was modifying original molecule's bond by changing them
to benzene bonds.  Now we make a copy of the molecule to start with (this uses
up a little extra memory but right now we just need to get it working.)

Also use a try and except block for converting to RDKit Mol, since it can
fail for some nitrogen cases.
Getting rid of fitting warnings in thermo because they clog the log file.
Get rid of warning for overlapping children.

It is clogging up the log file.  Eventually we will want to clean up the
overlapping children in the databases altogether.