BFactor.h

/*
 * BFactor.h
 *
 *  Created on: Jun 13, 2012
 *      Author: Yajia
 */

#ifndef BFACTOR_H_
#define BFACTOR_H_
#include "PProtein.h"
#include <vector.h>
using namespace Math3D;
using namespace std;

class BFactor {
public:
    BFactor(PProtein* protein);

    double evalAtomPositions( PProtein* chain, const int s, const int e);

    void output( char* filename);
private:
    vector< string> residue_name;
    vector< vector<string> > atom_name;
    vector< vector<Vector3> > atom_pos;
    vector< vector<double> > atom_bfactors;
    vector< vector<double> > atom_variance;

    double getProbDensity_log( const Vector3& mean, const double variance, const Vector3& position) const;

    double getProbDensity_log( const double mean, const double variance, const double x);
};

#endif /* BFACTOR_H_ */