Inversion fixes and amber mostly working

Changes for implementing Amber force field:  Added Inversions and
worked on BaseAtomTypes so that they'd function with the fortran side.

Checking in changes for Hefland moment calculations

Removed older version of openbabel from our code.  We now have a
configure check to see if openbabel is installed and then we link to
the stuff we need.  Conversion to OOPSE's md format is handled by only
one application (atom2md), so most of the work went on there.
ElementsTable still needs some work to function in parallel.

Changes to add thetacorr to dynamic props and fixes to radial rcorr.

Adding single precision capabilities to c++ side

using setFrc in RigidBody::calcForcesAndTorques will discard if there are force and torque applied in rigid body itself. use addFrc instead.

End of the Link --> List
Return of the Oject-Oriented
replace yacc/lex parser with antlr parser

streamlined reaction field for dipoles (now a good bit faster) and added reaction field for charges - still need to do charge-dipole RF

Don't remember what we did

erase output of inertia tensor. There is still something wrong with current implementation.

fix a bug in projecting the inertia tensor of
directional atom in rigibody into rigidbody's body frame (previous commit is wrong)

Rotation matrix multiplication order error

xemacs has been drafted to perform our indentation services

more memory leak are fixed

Fixing a bug in BitSet.cpp

Fix for compilation on the Sun

adding dynamicProps

adding missing implementation

(1)Cast wrong atom to DirectionalAtom in GhostTorsion
(2)get the wrong column of electroframe

moved Package variable into subdirectory makefiles to speed up
the building process

port to SGI platform

isLinear and linearAxis are virtual in StuntDouble,
but are implemented by DirectionalAtom and RigidBody
In StuntDouble, they should return false and "-1" but
there should be logic to figure them out in the other
two classes

replace old GebericData with  new GenericData

define DEV_ROOT as relative path

change the #include in source files