/*
 * File:   ring.h
 * Author: flong
 *
 * Created on February 3, 2012, 10:26 AM
 */

#ifndef RING_H
#define	RING_H

#ifndef KERNEL_H
#include "kernel.h"
#endif

#ifndef ATOM_H
#include "atom.h"
#endif

#ifndef LIB_ATOMASSEMBLY_H
#include "atomAssembly.h"
#endif

#ifndef BOND_H
#include "bond.h"
#endif

#ifndef ANGLE_H
#include "angle.h"
#endif

#ifndef ANGLE_H
#include "angle.h"
#endif

#ifndef PLANE_H
#include "plane.h"
#endif

//#ifndef CHEMPROPSET_H
//#include "chemPropSet.h"
//#endif

namespace LIBMOL
{
    class Atom;
    class AtomDict;

    class Bond;
    class BondDict;

    class Angle;
    class AngleDict;

    class Torsion;
    class TorsionDict;

    class PlaneDict;


    class Ring
    {
    public:

        // Default constructor
        Ring();

        // Copy constructor
        Ring(const Ring & tRing);

        // Destructor
        ~Ring();


        std::list<AtomDict>    atoms;
        std::list<BondDict>    bonds;
        std::vector<Angle>     angles;

        std::vector<Torsion> torsions;

        // some properties a ring has

    };

    class RingDict
    {
    public:
        // Default constructor
        RingDict();

        // Copy constructor
        RingDict(const RingDict & tR);

        // Constructor using a set of atoms
        RingDict(const std::vector<AtomDict> tAtoms);

        // Destructor
        ~RingDict();

        void setAtmsLink(std::vector<AtomDict> tAllAtoms);
        void setRingAtmsLinks();
        void setPlaneProp();
        void setBondIdxs(std::vector<BondDict> & tBonds, int & tStartIdx);

        bool                                     isPlanar;
        bool                                     isAromatic;
        bool                                     isAromaticP;
        bool                                     isAntiAroma;
        bool                                     isSugar;
        std::string                              sugarType;
        std::string                              rep;
        std::string                              sRep;
        std::string                              extId;

        std::vector<AtomDict>                    atoms;
        std::map<int, std::map<ID, int> >        atomsLink;
        std::map<int, std::vector<int> >         ringAtomLink;
        std::map<ID, REAL>                       sugarTors;
        std::vector<int>                         bondIdxs;

        std::vector<AtomDict>                    seqedAtoms;

    };

    class sugarRing: public RingDict
    {
    public :

        sugarRing();



        std::map<std::string, std::vector<AtomDict> >                cAtoms;


    };

    // about the internal structure of a ring
    extern bool AtomsInSameRing(AtomDict & tAt1, AtomDict tAt2,
                std::vector<RingDict> & tRings);

    extern int  checkIfAngleInSameRing(std::vector<AtomDict> & tAtoms,
                                       std::vector<RingDict> & tRings,
                                       int tIdxCen, int tIdx1, int tIdx2);

    extern void buildOneRing(std::vector<AtomDict> & tAtoms,
                             std::vector<AtomDict>   sSet,
                             std::vector<AtomDict> & doneSet);

    extern void ringAtmsLink(RingDict & tRing,
                             int        tIdx,
                             std::vector<int> & tAtmsLink);

    // Aromatic rings and Planes
    extern void mergePlaneRings(std::vector<RingDict>          & tAllRings,
                                std::vector<std::vector<int> > & tRingAtms);

    extern void mergePlaneRings(std::vector<RingDict>          & tAllRings,
                                std::vector<std::vector<int> > & tRingAtoms,
                                std::vector<AtomDict>          & tAtoms);

    // a copy mergePlaneRings used to kekulization so that its changes would not
    // affect other sections in libmol
    extern void mergePlaneRings2(std::vector<RingDict>          & tAllRings,
                                std::vector<std::vector<int> > & tRingAtoms,
                                std::vector<AtomDict>          & tAtoms);

    extern void findAllRingsConnectedOneRing(int tCurIdx, std::vector<RingDict> & tRings,
                                             std::vector<int>                   & DoneList,
                                             std::vector<int>                   & curLinkedRing);

    extern REAL setPiForOneAtom(int tIdx, std::vector<AtomDict> & tAtoms);
    extern REAL setPiForOneAtom(int tIdx, std::vector<AtomDict> & tAtoms,
                                std::vector<BondDict>  & tBonds);

    extern REAL setPiForOne_S_Sp3_Atom(int tIdx, std::vector<int>  & tAtmIdx,
                                      std::vector<AtomDict> & tAtoms);

    extern bool checkAromaSys(std::vector<int>      & tSubAtoms,
                              std::vector<AtomDict> & tAtoms);
    //extern REAL getTotalPiElec(std::vector<int>      & tSubAtoms,
    //                          std::vector<AtomDict> & tAtoms);
    extern bool checkAromaSys(std::vector<int>      & tSubAtoms,
                              std::vector<AtomDict> & tAtoms,
                              std::vector<BondDict> & tBonds);
    // modified to split isAromatic and isAromaticP
    extern REAL setPiForOneAtom(int tIdx, std::vector<AtomDict> & tAtoms,
                                int                   tMode);
    extern REAL setPiForOneAtomNoMetal(int tIdx, std::vector<AtomDict> & tAtoms,
                                        int                   tMode);
    extern REAL setPiForOneAtomAll(int tIdx, std::vector<AtomDict> & tAtoms,
                                        int                   tMode);

    extern bool checkAromaSys(std::vector<int>      & tSubAtoms,
                              std::vector<AtomDict> & tAtoms,
                              int                     tMode);

    extern REAL getTotalPiElec(std::vector<int>      & tSubAtoms,
                               std::vector<AtomDict> & tAtoms,
                               int                     tMode);

    extern bool isPyroleRing(RingDict & tRing);

    extern void setPyroleRings(std::vector<RingDict>  & tAllRings);

    extern void checkAndSetupPlanes(std::vector<RingDict>  & tAllRings,
                                    std::vector<PlaneDict> & tPlanes,
                                    std::vector<AtomDict>  & tAtoms);

    extern void checkAndSetupPlanes(std::vector<RingDict>  & tAllRings,
                                    std::vector<PlaneDict> & tPlanes,
                                    std::vector<AtomDict>  & tAtoms,
                                    bool                     tMdPls);

    extern void checkAndSetupPlanes2(std::vector<RingDict>  & tAllRings,
                                    std::vector<PlaneDict> & tPlanes,
                                    std::vector<AtomDict>  & tAtoms,
                                    std::vector<BondDict> & tBonds);

    extern bool checkUndRing(std::vector<int>   &    tAtmIdxs,
                            std::vector<AtomDict> & tAtoms);

    extern void TestAromaticity(std::vector<RingDict>  & tAllRings,
                                std::vector<AtomDict>  & tAtoms);

    extern bool checkAllARBondsInOneRing( std::vector<BondDict> & tBonds,
                                          RingDict               & tRing);

    extern void setAromaticBonds(std::vector<RingDict>  & tRings,
                                 std::vector<BondDict>  & tBonds);

    extern void detectRingsInAtoms(std::vector<AtomDict> & tAtoms);

    extern bool detectAllSp2AtomRing(RingDict               & tRing);

    // Sugar rings

    extern void setSugarRingInitComf(std::vector<AtomDict> & tAtoms,
                                     std::vector<TorsionDict>  & tTors,
                                     std::vector<RingDict>::iterator tRing);

    // 1. six-member rings

    extern void checkOneSugarRing(std::vector<AtomDict> & tAtoms,
                                  std::vector<RingDict>::iterator tRing);
    extern void setPyranoseChairComf(std::vector<AtomDict> & tAtoms,
                                      std::vector<RingDict>::iterator tRing);
    extern void setPyranoseChairComf(std::vector<AtomDict> & tAtoms,
                                     std::vector<RingDict>::iterator tRing,
                                     std::vector<TorsionDict> & tTors);



    extern void setTorsionAroundOneBondInRing(std::vector<TorsionDict> & tTors,
                                              std::vector<AtomDict> & tAtoms,
                                              int rAt1, int rAt2, int rAt3,
                                              int rAt4, REAL vInit);

    class ringTools
    {
    public :
        // Tool box. nothing to initiate. Default constructor
        ringTools();

        // Destructor
        ~ringTools();

        void detectRingFromAtoms(std::vector<AtomDict>                & tAtoms,
                                 std::map<ID, std::vector<RingDict> > & tRings,
                                 int                                    tDepth,
                                 int                                    tMaxRing);

        void checkOnePathSec(AtomDict                          & curAto,
                             int                                 tMaxRing,
                             std::vector<AtomDict>::iterator     iOriAto,
                             int                                 SeriNumPreAto,
                             int                                 curLev,
                             std::map<int, ID>                 & seenAtomIDs,
                             std::map<int, ID>                 & atomIDsInPath,
                             std::vector<AtomDict>             &     tAtoms,
                             std::map<ID, std::vector<RingDict> > &  tRings);

        void setAtomsRingRepreS(std::vector<AtomDict>                & tAtoms,
                                std::vector<RingDict>                & tRings);


        void outRingSec(AtomDict & tAtom);
        std::string outRingSecStr(AtomDict &tAtom);


    };

    class SugarDict {
    public :

        //Default
    };

}     // end of namespace LIBMOL

#endif	/* RING_H */