added draft runMM4 function along with other changes
added draft runMM4 function along with other changes

other changes include error message fix for MOPAC and making variable initialization placement in successfulMM4ResultExistsQ consistent with that in runMM4

KEHANG/RMG-Java,connie/RMG-Java,KEHANG/RMG-Java,rwest/RMG-Java,jwallen/RMG-Java,rwest/RMG-Java,ReactionMechanismGenerator/RMG-Java,nyee/RMG-Java,jwallen/RMG-Java,keceli/RMG-Java,faribas/RMG-Java,enochd/RMG-Java,faribas/RMG-Java,connie/RMG-Java,keceli/RMG-Java,faribas/RMG-Java,connie/RMG-Java,nyee/RMG-Java,ReactionMechanismGenerator/RMG-Java,ReactionMechanismGenerator/RMG-Java,ReactionMechanismGenerator/RMG-Java,nyee/RMG-Java,connie/RMG-Java,keceli/RMG-Java,KEHANG/RMG-Java,rwest/RMG-Java,jwallen/RMG-Java,rwest/RMG-Java,KEHANG/RMG-Java,KEHANG/RMG-Java,ReactionMechanismGenerator/RMG-Java,nyee/RMG-Java,enochd/RMG-Java,keceli/RMG-Java,faribas/RMG-Java,nyee/RMG-Java,KEHANG/RMG-Java,enochd/RMG-Java,keceli/RMG-Java,rwest/RMG-Java,enochd/RMG-Java,jwallen/RMG-Java,nyee/RMG-Java,connie/RMG-Java,jwallen/RMG-Java,jwallen/RMG-Java,enochd/RMG-Java,enochd/RMG-Java,keceli/RMG-Java