Rotamer.h

/*
 * Rotamer.h
 *
 *  Created on: Jan 24, 2013
 *      Author: Yajia
 */

#ifndef ROTAMER_H_
#define ROTAMER_H_
#include <vector>
#include <string.h>
#include <iostream>
#include <map>
#include <PProtein.h>
using namespace std;

class ChiDistribution;
class RotamerGrid;
class RotamerGridSpecial;
class RotamerGridKey;
class Rotamer;

struct RotamerGridKeyComparator {
     bool operator()(RotamerGridKey lhv, RotamerGridKey rhv) const;
};

typedef map<RotamerGridKey, RotamerGrid, RotamerGridKeyComparator> GridMap;
typedef map<RotamerGridKey, RotamerGridSpecial, RotamerGridKeyComparator> GridMapSpecial;
typedef map<RotamerGridKey, RotamerGrid, RotamerGridKeyComparator>::iterator GridMapIter;
typedef map<RotamerGridKey, RotamerGridSpecial, RotamerGridKeyComparator>::iterator GridMapIterSpecial;

class ChiDistribution {
public:
    double prob;
    vector< double> means;
    vector< double> stds;
};

class RotamerGrid{
    friend class Rotamer;
public:
    //number of effective chi angles
    int n_chi;
    vector<double> acc_rotamer;
    //accumulated distribution for each rotamer
    vector<ChiDistribution> dist_rotamer;
};

class RotamerGridSpecial: public RotamerGrid {
    friend class Rotamer;
public:
    int degree_begin;
    int degree_end;
    int stepLength;
    bool check() const;
    vector<double> dist_terminal;
    vector< vector<double> > acc_terminal;
    vector< vector<double> > chi_terminal;
};

class RotamerGridKey {
    friend class Rotamer;
    friend struct RotamerGridKeyComparator;
public:
    RotamerGridKey( const string& name, const int& phi, const int& psi);

    string toString() const;

    void print() const;

    bool operator==(const RotamerGridKey& key) const;
private:
    string name;
    int phi;
    int psi;
};

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

    void sample( const string& residue_name, const double& phi, const double& psi, int& rotamer_grid, vector<double>& dAngles);

    void sample_common( const string& residue_name, const int& phi, const int& psi, int& rotamer_grid, vector<double>& dAngles);

    void sample_Special( const string& residue_name, const int& phi, const int& psi, int& rotamer_grid, vector<double>& dAngles);

    void output( char* filename);

    //Evaluate the conformation of sidechain and return log(prob);
    double evalSidechain_log(PChain* chain, const int s, const int e);
//  double evalResidue(const string& residue_name, const double& phi, const double& psi, const int& rotamer_index, const vector<double>& angles);

    void initSidechainDatabase( PProtein* protein);
private:
    void init();
    void read( const string& res_name);

    void read_common( const string& res_name);

    void read_special( const string& res_name);

    GridMap gridMap;
    GridMapSpecial gridMapSpecial;

    //For special amino acids.
    vector<int> degree_start;
    vector<int> degree_end;
    vector<int> stepLength;

    static const int ASN = 0;
    static const int ASP = 1;
    static const int PHE = 2;
    static const int TRP = 3;
    static const int HIS = 4;
    static const int TYR = 5;
    static const int GLN = 6;
    static const int GLU = 7;

    int type( const string& res_name);

    bool isSpecial( const string& res_name);
    map<string, int> typeMap;
};

#endif /* ROTAMER_H_ */