SLIKMC.h

/*
 * SLIKMC.h
 *
 *  Created on: Jun 10, 2012
 *      Author: Yajia
 */

#ifndef SLIKMC_H_
#define SLIKMC_H_

#include "PProtein.h"
#include <vector.h>
#include "RamachandranPlot.h"
#include "BFactor.h"
#include "SideChainRotater.h"
#include "Prior.h"

class SLIKMCSampler {
public:
    SLIKMCSampler( PProtein* chain);
    virtual ~SLIKMCSampler();

    void sample( const double time, const int s, const int e);

    void enableBfactors( PProtein* chain = NULL);

    void disableBfactors();

    void enableSidechain();

    void disableSidechain();

    void enableFreeEnd();

    void disableFreeEnd();

    void enableLog(const int skip = 0);

    void disableLog();

    void enableCollisionChecking();

    void disableCollisionChecking();

    void enableRamachandran();

    void disableRamachandran();

    void dispSettings();

    void enableCustomPriors();

    void disableCustomPriors();

    void addCustomPrior( Prior& prior);

private:
    bool MHStep( double P, double Q, double P_proposal, double Q_proposal);

    double getP_log( PProtein* chain);

    double getQ_log( PProtein* chain, const int num_solutions, int& status);

    double getMetricTensor_log(PProtein* protein, int& status);

    PProtein* protein;

    vector<PProtein*> subchains;

    static const int MAX_IK_SAMPLE = 100;

    static const int MAX_METROPOLIS_REJECT = 1;

    static const int MAX_COLLISION_DETECT = 1;

    BFactor* bfactor;
    RamachandranPlot* rplot;

    SidechainRotater* scRotater;

    bool use_BFactor;
    bool use_Rotamer;
    bool freeEnd;
    bool use_colChecking;
    bool use_RPlot;
    bool use_customPrior;

    bool init_Rotamer;
    bool logFile;
    int skipLength;

    vector<Prior*> priors;
};

const double EPSILON = 0.0000001;
#endif /* SLIKMC_H_ */