ToDo

• CharmmParameterReader: Add support for wild cards in CHARMM parameter file (used in param 19, not used in 22). Documentation at http://www.charmm.org/html/documentation/c32b2/miscom.html
• EnergySet: implement: 1) copy constructor; 2) void deleteInteractionsWithAtom(Atom & _a); 3) void deleteInteractionsWithAtoms(AtomPointerVector & _atomVec);
• CharmmSystemBuilder: implement removeIdentity and mutate functions
• Create PDBToplogy object for adding residues to positions
• System: copy bonds in copy costructor
• PDBWriter: proper support for MODELs and alt coordinates
• Position: add support for saveAltCoor to include the current identity/conformer