RigidCLL.h

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#ifndef RigidCLLH
#define RigidCLLH

#include <vector>
#include <list>
#include <string>

using namespace std;

#ifndef RIGIDCLL_DEBUG
  #define RIGIDCLL_DEBUG 1
#endif

typedef double RigidTransform[4][4];
 
class AtomInfo {
 public:
  unsigned int id;      
  unsigned int rID;     
  double op[3];         
  double cp[3];         
  double r;             
  unsigned int c[3];    
  AtomInfo(unsigned int identifier,unsigned int rigid,double x,double y,double z,double radius);

  inline void move(RigidTransform t); 

  double distance(AtomInfo *a);
};

ostream& operator<<(ostream& os,const AtomInfo &a);

class AtomPair {
 public:
  unsigned int a1;    
  unsigned int r1;    
  unsigned int a2;    
  unsigned int r2;    
  double d2;          
  AtomPair(AtomInfo *atom1,AtomInfo *atom2,double dst2);

  bool operator<(const AtomPair a) const;
  
  bool operator==(AtomPair &a);
};

ostream& operator<<(ostream& os,const AtomPair &a);

typedef struct {
  unsigned int firstAtom; 
  unsigned int lastAtom;  
} RigidInfo;

class CellInfo {
 public:
  unsigned int mobileID;             
  unsigned int fixedID;              
  inline CellInfo();
  inline void Reset();

  void AddFixedAtom(unsigned int id,unsigned int *fixedLL);

  inline void AddMobileAtom(unsigned int id,unsigned int *mobileLL);

};

class RigidCLL {

 private:

  vector<AtomInfo> fixedAtoms;         
  vector<AtomInfo> mobileAtoms;        
  vector<RigidInfo> rigids;            
  unsigned int* fixedLL;               
  unsigned int* mobileLL;              
  CellInfo ***grid;                    
  double o[3];                         
  unsigned int s[3];                   
  double cutoff;                       
  double d;                            
  double d2;                           
  unsigned int rID;                    
  RigidInfo cr;                        
  unsigned int nFixed;                 
  unsigned int nMobile;                
  unsigned int lastInGrid;             
  bool **checkInteraction;             
  void InitRigidCLL();

  inline void UpdateCell(AtomInfo *a);

  void InsertFixedInGrid(unsigned int n);

  inline void InsertMobileInGrid(unsigned int n);
    

  void DeleteGrid();

  void DeleteInteractions();

  void InitInteractions();

  inline void ResetQuery();

  inline void Move(RigidTransform *t);

  inline bool Check27(AtomInfo *a1);

 public:

  RigidCLL();

  RigidCLL(char *name);
    
  ~RigidCLL();

  unsigned int GetNumRigids();


  void SetCutOff(double c);

  double GetCutOff();

  double GetBBSize(unsigned int axis);
    
  void AddFixedAtom(unsigned int id,double x,double y,double z,double r);

  void AddFixedAtom(unsigned int id,double *p,double r);

  unsigned int NewRigid();

  void AddAtom(unsigned int id,double x,double y,double z,double r);

  void AddAtom(unsigned int id,double *p,double r);

  void EndRigid();
  
  void ActivateInteraction(unsigned int r1,unsigned int r2);

  void DeactivateInteraction(unsigned int r1,unsigned int r2);

  void WarmUp(RigidTransform *t);

  void Reset();

  bool StericClash(RigidTransform *t);

  bool CLLStericClash(RigidTransform *t);

  bool BruteForceStericClash(RigidTransform *t);

    
  void Interactions(RigidTransform *t,list<AtomPair> *c);

  void CLLInteractions(RigidTransform *t,list<AtomPair> *c);

  void BruteForceInteractions(RigidTransform *t,list<AtomPair> *c);
};

#endif