// name: AtomPositions.h
// author: J. Michael Word
// date written: 8/1/97
// purpose: Interface for AtomPositions

// **************************************************************
// NOTICE: This is free software and the source code is freely
// available. You are free to redistribute or modify under the
// conditions that (1) this notice is not removed or modified
// in any way and (2) any modified versions of the program are
// also available for free.
//               ** Absolutely no Warranty **
// Copyright (C) 1999 J. Michael Word
// **************************************************************

#ifndef ATOMPOSITIONS_H
#define ATOMPOSITIONS_H 1

#include "PDBrec.h"
#include "ResBlk.h"
#include "DotSph.h"
#include "BumperPoint.h"
#include "Mover.h"
#include "CliqueList.h"
#include "neighbors.h"
#include "utility.h"
#include "AtomDescr.h"
#include "GraphToHoldScores.h"

extern bool UseSEGIDasChain; //jjh 130503, defined in reduce.cpp

class AtomPositions {
public:
   AtomPositions(int nblocks, bool onlyA, bool xplor, bool old, bool bbmodel, int nbCutoff,
		  float minRegHBcut, float minChargedHBcut,
		  float badBumpGapCut,
		  DotSphManager& dotBucket, float probeRadius,
		  float pmag, float occCutoff,
		  bool verbose, bool showOrientScore,
		  bool cliqueTicks, std::ostream& os)
      : _onlyA(onlyA), _useXplorNames(xplor), _useOldNames(old), _bbModel(bbmodel),
	_nBondCutoff(nbCutoff),
	_min_regular_hb_cutoff(minRegHBcut),
	_min_charged_hb_cutoff(minChargedHBcut),
	_bad_bump_gap_cutoff(badBumpGapCut),
	_dotBucket(dotBucket),
	_probeRadius(probeRadius), _pmag(pmag),
	_occupancyCuttoff(occCutoff),
	_outputNotice(verbose),
	_showOrientScore(showOrientScore),
	_cliqueTicks(cliqueTicks), _os(os),
	scoreAtomsAndDotsInAtomsToScoreVector_( false ),
	scoreAtomsInAtomsInHighOrderOverlapList_( false ),
	atoms_to_score_ptr_(0), atoms_in_high_order_overlap_ptr_(0),
	_clqOfInt( false ) {}

  ~AtomPositions() {
	  for (std::map<std::string, Mover*>::const_iterator i = _motionDesc.begin(); i != _motionDesc.end(); ++i)
		   delete i->second;
	   std::for_each(_excludePoints.begin(), _excludePoints.end(), DeleteObject());
	  for (std::multimap<LocBlk, PDBrec*>::const_iterator it = _xyzBlocks.begin(); it != _xyzBlocks.end(); ++it)
		   delete it->second;
  }

  int forceOrientations(const std::string& ofilename, std::vector<std::string>& notes);

   void put(PDBrec* r) {
	   PDBrec* temp = new PDBrec(*r);
	   _xyzBlocks.insert(std::make_pair(LocBlk(r->loc()), temp));
   }

   // move atom to new xyz pos.
   void reposition(const Point3d& prev, const PDBrec& r);

   std::list<PDBrec*> neighbors(const Point3d& p,
                         Coord mindist, Coord maxdist) const {
      return ::neighbors(p, mindist, maxdist, _xyzBlocks);
   }

   void insertRot(const PDBrec& hr, const PDBrec& c1,
                  const PDBrec& c2, const PDBrec& c3,
		  bool doOHSH, bool doNH3, bool doMethyl);

   void insertRotAromMethyl(const PDBrec& hr, const PDBrec& c1,
                  const PDBrec& c2, const PDBrec& c3); // for Arom methyls - Aram 08/13/12
   std::list<char> insertFlip(const ResBlk& rblk);
   void      insertFlip(PDBrec* hr, std::list<char> alts_list);

   void doNotAdjust(const PDBrec& a);

   void finalizeMovers();

   CliqueList findCliques() const;

   int orientSingles(const std::list<MoverPtr>& singles);
   int orientClique(const std::list<MoverPtr>& clique, int limit); // returns -1 if abandoned
   int exhaustiveSearchOfClique(const std::list<MoverPtr>& clique);

   void describeChanges(std::list<PDBrec*>& records,
	   std::list<PDBrec*>::iterator& infoPtr, std::vector<std::string>& notes);

   int numChanges() const { return _motionDesc.size(); }

   void manageMetals(const ResBlk& rblk);

   void generateWaterPhantomHs(std::list<PDBrec*>& waters);

   double atomScore(const PDBrec& a, const Point3d& p,
		float nearbyRadius, const std::list<PDBrec*>& exclude,  // JSS: no need to copy
		const DotSph& dots, float prRadius, bool onlyBumps,
		float &bumpSubScore, float &hbSubScore, bool &hasBadBump);

	//double determineScoreForMoverIn3WayOverlap(
	//	std::list< AtomDescr > * atomsIn3WayOverlap,
	//	Mover* mover
	//);

	void CollectBumping(const AtomDescr& ad, std::list<PDBrec*>& bumping);
   float & getMaxFoundVDWRad() { return _maxVDWFound;}
   int getNBondCutoff() const {return _nBondCutoff;}

   float determineScoreForMover(
   	Mover* mover,
   	std::vector< std::pair< AtomDescr, DotsForAtom * > >  & atoms_to_score,
   	double & penalty
   );

   //float scoreMoverInHighOrderOverlap(
	//	std::list< AtomDescr > & atomsInHighOrderOverlap,
	//	Mover * mover );

	bool outputNotice() const {return _outputNotice;}

private:
   AtomPositions(const AtomPositions& a);            // can't copy
   AtomPositions& operator=(const AtomPositions& a); // can't assign

   std::multimap<LocBlk, PDBrec*> _xyzBlocks;
   std::map<std::string, Mover*>       _motionDesc;
   std::list<BumperPoint*>          _excludePoints;

   const bool                _onlyA;
   const bool                _useXplorNames;
   const bool                _useOldNames;
   const bool		     _bbModel;
   const int                 _nBondCutoff;
   const float               _min_regular_hb_cutoff;
   const float               _min_charged_hb_cutoff;
   const float               _bad_bump_gap_cutoff;
   DotSphManager&            _dotBucket;
   const float               _probeRadius;
   const float               _pmag;
   const float               _occupancyCuttoff;
   const bool                _outputNotice;
   const bool                _showOrientScore;
   const bool                _cliqueTicks;
   std::ostream&             _os;
	float	_maxVDWFound;

   bool
	initializeCliqueMovers(
		std::list< Mover* > const & clique,
		std::vector< Mover* > & item,
		int const numItems
	);

	void
	setNumStatesForNodes(
		std::vector< Mover* > & item,
		int const numItems,
		std::vector< int > & num_states,
		std::vector< std::vector< float > > & penalties
	);


private:

	bool scoreAtomsAndDotsInAtomsToScoreVector_;
	bool scoreAtomsInAtomsInHighOrderOverlapList_;
	std::vector< std::pair< AtomDescr, DotsForAtom * > > * atoms_to_score_ptr_;
	std::list< AtomDescr > * atoms_in_high_order_overlap_ptr_;

	int  _clqDots;				//ANDREW: for keeping track of how many dots go into the score for a network
	int  _bgDots;				//ANDREW: used only when the flag DEBUGDOTCOUNTS is set.
	bool _clqOfInt;			//ANDREW: this will let me detect once whether the clique I'm examining is the one I'm interested in
									//and keep that fact around when the scoring is being done.


public:
   int SearchClique(std::list<MoverPtr> clique, int time_limit);

};
#endif