Chi1Chi2.h

/*  This file is part of Victor.

    Victor is free software: you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation, either version 3 of the License, or
    (at your option) any later version.

    Victor is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    GNU General Public License for more details.

    You should have received a copy of the GNU General Public License
    along with Victor.  If not, see <http://www.gnu.org/licenses/>.
 */


#ifndef _CHI1CHI2_H_
#define _CHI1CHI2_H_


// Includes:
#include <TorsionPotential.h>
#include <vector>
#include <Spacer.h>
#include <AminoAcidCode.h>
#include <IoTools.h>

// Global constants, typedefs, etc. (to avoid):

using namespace Victor::Biopool;
using namespace Victor::Energy;
using namespace Victor;
namespace Victor { namespace Energy {

    class Chi1Chi2 : public TorsionPotential {
    public:

        // CONSTRUCTORS/DESTRUCTOR:
        Chi1Chi2(string knownledge = "data/tor.par"); // OTHER KNOWNLEDGE

        virtual ~Chi1Chi2() {
            pResetData();
        }

        // PREDICATES:
        virtual long double calculateEnergy(Spacer& sp);
        virtual long double calculateEnergy(AminoAcid& aa);

        virtual long double calculateEnergy(AminoAcid& aa, Spacer& sp) {
            return calculateEnergy(aa);
        }
        virtual long double calculateEnergy(Spacer& sp, unsigned int index1, unsigned int index2);

        virtual long double calculateEnergy(AminoAcid& diheds, AminoAcidCode code) {
            ERROR("ERROR. NOT IMPLEMENTED FOR THIS CLASS.", exception)
        }
        virtual double pReturnMaxPropensities(int amino);

        virtual double pReturnMaxPropensitiesPreAngle(int amino, int prephi, int prepsi) {
            ERROR("ERROR. NOT IMPLEMENTED FOR THIS CLASS.", exception)
        }

        virtual int sGetPropBin2(double p) {
            ERROR("ERROR. NOT IMPLEMENTED FOR THIS CLASS.", exception)
        }

        // MODIFIERS:

        // OPERATORS:

    protected:

        // HELPERS:
        virtual void pConstructData();
        virtual void pResetData();
        virtual double pGetMaxPropensities(int amino);
        //not implemented in this class. No pre-angle considered.

        virtual double pGetMaxPropensities(int amino, int prephi, int prepsi) {
            ERROR("ERROR. NOT IMPLEMENTED FOR THIS CLASS.", exception)
        }
        virtual void sAddProp(int code, int x, int y);
        virtual int sGetPropChiBin(double p);
        virtual void pConstructMaxPropensities();

    private:

        // ATTRIBUTES:
        string TOR_PARAM_FILE; // File with prop torsion angles
        int amino_count[AminoAcid_CODE_SIZE];
        // total number of entries for all amino acids
        vector<vector<vector<int>* >* > propensities; // the propensities table.
        vector<vector<int>* > all_propensities; // the sum of propropensities table.
        int CHI_RANGE;
        double total;
        vector<double> amino_max_propensities; //vector with max amino propensities
        // according to knowledge.

    };

    // ---------------------------------------------------------------------------
    //                            Chi1Chi2
    // -----------------x-------------------x-------------------x-----------------
}} // namespace
#endif //_CHI1CHI2_H_