Added the "-r" option for the choice of atom/bond type prediction

[Mishakolok]

Mentioned in issue #26

Added new variable predIndex (for prediction Index) which transfers "-r" command line option to the Antechamber "-j" option for determining the type of bond/atom type prediction. The acpype "-j" option was already taken by the "chiral" option, so I took the free "-r" option.

[alanwilter]

I need some time to check this PR and thanks a lot for doing this.