Changes for implementing Amber force field: Added Inversions and worked on BaseAtomTypes so that they'd function with the fortran side.
Changes required for Inversions and Base Atom types. This will break OOPSE badly for a few days or so...
End of the Link --> List Return of the Oject-Oriented replace yacc/lex parser with antlr parser
moved Package variable into subdirectory makefiles to speed up the building process
merging new_design branch into OOPSE-2.0
Making ShapeType into a ShapeAtomType, fixing some isXXX
More on AtomType and DirectionalAtomType
Working on getting Shapes into OOPSE
define DEV_ROOT as relative path
change Makefile to relative path
Import of OOPSE v. 2.0
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