VGPFunction.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 __VGPFunction_H__
#define __VGPFunction_H__

#include <GapFunction.h>
#include <PdbLoader.h>
#include <SolvExpos.h>
#include <Spacer.h>
#include <vector3.h>
#include <math.h>

namespace Victor { namespace Align2{

    class VGPFunction : public GapFunction {
    public:

        // CONSTRUCTORS:

        VGPFunction(string pdbFileName, string chainID);

        VGPFunction(string pdbFileName, string chainID, double o, double e, unsigned int extType,
                double wH, double wS, double wB, double wC, double wD);

        VGPFunction(const VGPFunction &orig);

        virtual ~VGPFunction();


        // OPERATORS:

        VGPFunction& operator =(const VGPFunction &orig);


        // PREDICATES:

        virtual double getOpenPenalty(int p);

        virtual double getExtensionPenalty(int p);


        // MODIFIERS:

        virtual void copy(const VGPFunction &orig);

        virtual VGPFunction* newCopy();

        virtual void setOpenPenalty(double pen);

        virtual void setExtensionPenalty(double pen);


        // HELPERS:

        void pExtractPdbInfo(string pdbFileName, string chainID);


    protected:


    private:

        // ATTRIBUTES:

        double o; 
        double e; 
        unsigned int extType; 
        unsigned int extCounter; 
        vector<double> hContent; 
        vector<double> sContent; 
        vector<double> solvAccess; 
        vector<double> bbStraight; 
        vector<double> spaceProx; 
        double wH; 
        double wS; 
        double wB; 
        double wC; 
        double wD; 

    };

    // -----------------------------------------------------------------------------
    //                                 VGPFunction
    // -----------------------------------------------------------------------------

    // MODIFIERS:

    inline void
    VGPFunction::setOpenPenalty(double pen) {
        o = pen;
    }

    inline void
    VGPFunction::setExtensionPenalty(double pen) {
        e = pen;
    }

}} // namespace

#endif