BioProteinStructureAlignment.h

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#ifndef BIOPROTEINSTRUCTUREALIGNMENT_H
#define BIOPROTEINSTRUCTUREALIGNMENT_H

#include "BioProteinChain.h"
#include "BioOutputStream.h"
#include "BioProteinSequenceLocalAlignment.h"
#include "BioProteinSequenceGlobalAlignment.h"

class BioProteinStructureAlignment
{

float rmsd_;
//BioMatrix translation_,centroid_,rotation_;
string subMatrix_ ;

float localSeqIdentity_, globalSeqIdentity_;

BioProteinChain tempRefCoords;
BioProteinChain tempQueCoords;

float superimpose(float **coords1, float **coords2, int npoints);
void computeMainChainAlignment(BioProteinChain& tempRefCoords,  BioProteinChain& tempQueCoords);
void computeCAlphaAlignment(BioProteinChain& tempRefCoords,  BioProteinChain& tempQueCoords);



public:

BioProteinStructureAlignment(const string& f1, const string& f2, const string& = "BLOSUM62");
BioProteinStructureAlignment( BioProteinChain& tempRefCoords,  BioProteinChain& tempQueCoords);
float getMainChainRmsd();
float getCAlphaRmsd();
/*
BioMatrix getRotationMatrix();
BioMatrix getTranslationMatrix();
BioMatrix getCentroid();
*/
float getLocalSequenceIdentity();
float getGlobalSequenceIdentity();
//BioProteinChain getRotatedProteinChain();
//void showStructureAlignment();

~BioProteinStructureAlignment();
};

#endif