SolvationPotential.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 _SOLVATIONPOTENTIAL_H_
#define _SOLVATIONPOTENTIAL_H_

// Includes:
#include <vector>
#include <Spacer.h>
#include <Potential.h>

// Global constants, typedefs, etc. (to avoid):
const double SOLVATION_CUTOFF_DISTANCE = 10.0;

using namespace Victor;
namespace Victor { namespace Energy {

   
    class SolvationPotential : public Potential {
    public:

        // CONSTRUCTORS/DESTRUCTOR:
        SolvationPotential(unsigned int _resol = 1);

        virtual ~SolvationPotential() {
            PRINT_NAME;
        }

        // PREDICATES:

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

        virtual long double calculateEnergy(AminoAcid& aa, Spacer& sp) {
            return calculateSolvation(aa, sp);
        }

        virtual long double calculateEnergy(
                AminoAcid& resid, AminoAcidCode type, Spacer& sp) {
            return calculateSolvation(resid, type, sp);
        }
        long double calculateSolvation(Spacer& sp);
        long double calculateSolvation(AminoAcid& aa, Spacer& sp,
                unsigned int start = 0, unsigned int end = 9999);
        long double calculateSolvation(AminoAcid& resid, AminoAcidCode type,
                Spacer& sp);
        long double pReturnMaxPropensity(const AminoAcidCode type) const;
        long double pReturnMinPropensity(const AminoAcidCode type) const;

        // MODIFIERS:

        // OPERATORS:

        // HELPERS:

        static inline long double propCoeff() {
            return 0.582;
        }

    protected:

    private:

        // PREDICATES
        long double pGetPropensity(const AminoAcidCode type,
                unsigned int count) const;
        long double pGetMaxPropensity(const AminoAcidCode type) const;
        long double pGetMinPropensity(const AminoAcidCode type) const;

        // MODIFIERS
        void pConstructMaxPropensities();
        void pConstructMinPropensities();

        // ATTRIBUTES:
        vector<vector<int> > sum;

        unsigned int binResolution;

        /* maximum and minimum propensities extracted from the solvation database
           file. The i-th element of each vector refers to the i-th amino acid type
           declared in the AminoAcidCode enumeration (i=0,...,19). */
        //ALA=0,CYS,ASP,GLU,PHE,GLY,HIS,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR
        //    0,  1,  2,  3,  4,  5,  6,  7,  8,  9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19  
        vector<long double> amino_max_propensities;
        vector<long double> amino_min_propensities;
        static unsigned int MAX_BINS;
        static string SOLV_PARAM_FILE;


    };

    // ---------------------------------------------------------------------------
    //                            SolvationPotential
    // -----------------x-------------------x-------------------x-----------------

    inline long double SolvationPotential::pReturnMaxPropensity(const AminoAcidCode type) const {
        return amino_max_propensities[type];
    }

    inline long double SolvationPotential::pReturnMinPropensity(const AminoAcidCode type) const {
        return amino_min_propensities[type];
    }


}} // namespace
#endif //_SOLVATIONPOTENTIAL_H_