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src/biu/OffLatticeProtein.cc

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#include <biu/OffLatticeProtein.hh>
#include <fstream>

namespace biu
{
    OffLatticeProtein::OffLatticeProtein(const std::string& coordinatesFileName,
                        const Alphabet* const _alphabet)
        :   pData(new DPointVec()), 
            alphabet(_alphabet), 
            sequence(NULL) 
     {
        std::ifstream ifs;
        ifs.open(coordinatesFileName.c_str());
        if (!ifs) {
            std::cerr<< "ERROR OffLatticeProtein::OffLatticeProtein : "+
             coordinatesFileName+" kann nicht geöffnet werden.";
            delete pData;
            exit(-1);
        }

        double x, y, z;
        char aa;
        std::string remark, seqStr = "";
        
        // ignore remarks (#...)
        while(ifs.peek() == '#') {
            getline(ifs, remark);
        }
        while(ifs >> aa >> x >> y >> z) {
            pData->push_back(DblPoint(x, y, z));
            seqStr += aa;
        }
        ifs.close();

        assertbiu(alphabet->isAlphabetString(seqStr),
         "AA sequence contains characters which are not in the alphabet.");
        sequence = new Sequence(alphabet->getSequence(seqStr));
    }

    OffLatticeProtein::OffLatticeProtein(   const DPointVec& data3D, 
                                            const Alphabet* const _alphabet, 
                                            const std::string& seqStr) 
     : pData(new DPointVec(data3D)), alphabet(_alphabet), sequence(NULL) 
    {
        assertbiu(alphabet != NULL,  "alphabet is not allowed to be NULL.");
        sequence = new Sequence(alphabet->getSequence(seqStr));
        assertbiu(pData->size() == sequence->size(),
            "Structure and sequence have to have the same length.");
    }

    OffLatticeProtein::OffLatticeProtein( const OffLatticeProtein& offLatPro)
     :  pData(new DPointVec(*(offLatPro.pData))), 
        alphabet(offLatPro.alphabet),
        sequence(new Sequence(*(offLatPro.sequence))) 
    {
        assertbiu(alphabet != NULL,  "alphabet is not allowed to be NULL.");
        assertbiu(pData->size() == sequence->size(),
         "Structure and sequence have to have the same length.");
    }
    
    OffLatticeProtein::~OffLatticeProtein() {
        delete pData; pData = NULL;
        delete sequence; sequence = NULL;
    }

    
    OffLatticeProtein& 
    OffLatticeProtein::operator= ( const OffLatticeProtein& offLatPro2) 
    {
        if (this != &offLatPro2) {
            delete pData;
            pData = new DPointVec(*(offLatPro2.pData));
            delete sequence;
            sequence = new Alphabet::Sequence(*(offLatPro2.sequence));
            alphabet = offLatPro2.alphabet;
        }
        return *this;
    }

    void        
    OffLatticeProtein::writePDB(const std::string& pdbFileName) {
    //TODO
    }
    
    LatticeProtein* 
    OffLatticeProtein::approximateToLattice(const LatticeModel* const lattice,  
                const ContactEnergyFunction* const energy) const 
    {
    //TODO
        return NULL;
    }

    DPointVec   
    OffLatticeProtein::get3Ddata() const{
        return *pData;  
    }
    
    double      
    OffLatticeProtein::getDRMSD(const BackboneStructure3D& other) const{
// TODO implementieren
    /*  DPointVec other3Ddata = other.get3Ddata();
        assertbiu(pData->size() == other3Ddata->size(),
         "Structure and sequence have to have the same length.");
        double rmsd = 0;
        for(int k=0; k<i; k++)
                for(int l=k+1; l<=i; l++)
                        rmsd += pow( pos[k].dist(pos[l]) - (scaling * conformation[k].dist(conformation[l])), 2);
        rmsd /= ((i+1)*i /2);   // Index i => Kettenlaenge i+1
        return sqrt(rmsd);*/
        return 0.0;

    }




}