Changes for implementing Amber force field: Added Inversions and worked on BaseAtomTypes so that they'd function with the fortran side.
A few formatting changes to prettify the code
Adding single precision capabilities to c++ side
xemacs has been drafted to perform our indentation services
Fixing a bug in BitSet.cpp
Fix for compilation on the Sun
merging new_design branch into OOPSE-2.0
change the #include in source files
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