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src/biu/OffLatticeProtein.hh

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#ifndef OFFLATTICEPROTEIN_H_
#define OFFLATTICEPROTEIN_H_


#include "LatticeProtein.hh"

namespace biu
{
    class OffLatticeProtein : public BackboneStructure3D
    {
    protected:

        DPointVec*  pData;          
        const Alphabet* alphabet;   
        Sequence*   sequence;       
    public:
        OffLatticeProtein(  const std::string& coordinatesFileName,
                            const Alphabet* const _alphabet);
                            
        OffLatticeProtein(  const DPointVec& data3D, 
                            const Alphabet* const _alphabet, 
                            const std::string& seqStr);
                   
        OffLatticeProtein(const OffLatticeProtein& offLatPro);
        virtual ~OffLatticeProtein();

        
        OffLatticeProtein& operator= (const OffLatticeProtein& offLatPro2);

        void writePDB(const std::string& pdbFileName);
        
        LatticeProtein* approximateToLattice( 
                            const LatticeModel* const lattice, 
                            const DistanceEnergyFunction* const energy) const;

    // abstract functions (BackboneStructure3D)
        
        virtual DPointVec get3Ddata() const;
        
        virtual double getDRMSD(const BackboneStructure3D& other) const;
    };

} // namespace biu

#endif /*OFFLATTICEPROTEIN_H_*/