Added the 'atoms' field to protein, ligand and surface
Encapsulated proteinHBondDonors and proteinHBondAcceptors into entities.protein
Encapsulated maxD into entities.protein
Revised createSurfaceRepresentation to accept entity instead of atoms as parameter
Encapsulated objects into entities
Encapsulated options into entities
Encapsulated refresh() into entities
Added refresh() to entities during initialization
Inlined parseBox, createBox, parseProtein and parseLigand