remove using namespace std in .cpp file
adding qulified name prefix std
Molecule, Atom, DirectionalAtom, RigidBody and StuntDouble classes get compiled
This commit was manufactured by cvs2svn to create branch 'new_design'.
Chris doesn't know about the OOPSE-2.0 directory structure yet
made the file reading in restraints more intelligent - no longer gives uninformative seg faults
change the #include in source files
Import of OOPSE v. 2.0
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