IntLoader.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 _INT_LOADER_H_
#define _INT_LOADER_H_

// Includes:
#include <Spacer.h>
#include <LigandSet.h>
#include <Loader.h>
#include <Debug.h>
#include <string>
#include <iostream>

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

namespace Victor { namespace Biopool { 

    class IntLoader : public Loader {
    public:

        // CONSTRUCTORS/DESTRUCTOR:

        IntLoader(istream& _input = cin) : input(_input), atomIndex() {
        }
        // this class uses the implicit copy operator.

        virtual ~IntLoader() {
            PRINT_NAME;
        }

        // MODIFIERS:
        virtual void loadGroup(Group& group);
        virtual void loadSideChain(SideChain& sc, AminoAcid* aaRef);
        virtual void loadAminoAcid(AminoAcid& aa);
        virtual void loadSpacer(Spacer& sp);
        virtual void loadLigand(Ligand& l);

    protected:
        void setBonds(Spacer& sp);

    private:
        void zAtomToCartesian(Atom& atbLP, double bondLength, Atom& atbAP,
                double bondAngle, Atom& attAP, double torsionAngle,
                int chiral, Atom& at);
        bool inSideChain(const AminoAcid& aa, const Atom& at);
        Atom& addToAminoAcid(AminoAcid* aa, Atom* at);
        void keepPlacingAlongZAxis(int bLP, double bondLength, int bAP,
                double bondAngle, Atom* at);
        istream& input; // input stream
        vector<Atom> atomIndex;
        bool connect; // are segments to be connected to each other?
    };

}} //namespace
#endif //_INT_LOADER_H_