geometricFit.h

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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//

#ifndef BALL_STRUCTURE_DOCKING_GEOMETRICFIT_H
#define BALL_STRUCTURE_DOCKING_GEOMETRICFIT_H

#ifndef BALL_DATATYPE_REGULARDATA3D_H
#include <BALL/DATATYPE/regularData3D.h>
#endif

#ifndef BALL_KERNEL_SYSTEM_H
#include <BALL/KERNEL/system.h>
#endif

#ifndef BALL_MATHS_COMPLEX_H
#include <BALL/MATHS/complex.h>
#endif

#ifndef BALL_MATHS_FFT3D_H
#include <BALL/MATHS/FFT3D.h>
#endif

#ifndef BALL_STRUCTURE_DOCKING_DOCKINGALGORITHM_H
#include <BALL/STRUCTURE/DOCKING/dockingAlgorithm.h>
#endif

namespace BALL
{
  class BALL_EXPORT GeometricFit 
    : public DockingAlgorithm
  {
    public:
      BALL_CREATE(GeometricFit)
      
      
      struct BALL_EXPORT Option 
      {
        // the parameter r,
        // "Any grid point is considered inside the molecule if there is at 
        // least one atom nucleus within a distance r from it." 
        // Default value is 1.8 Angstrom
        static const String NEAR_RADIUS;

        // Default grid spacing. 
        // Default value is 1.0 Angstrom
        static const String GRID_SPACING;
  
        // grid size = (ceil)(molecule size / grid spacing);
        static const String GRID_SIZE;  

        // The thickness of the surface of the protein
        // Default value is 1.0 Angstrom
        static const String SURFACE_THICKNESS;

        // Degree interval is the delta parameter, 
        // which is the degrees that protein B rotates every time
        // Default value is 20 degrees
        static const String DEGREE_INTERVAL;

        // How many peaks should the program keep for each rotation
        static const String TOP_N;

        static const String SURFACE_TYPE; 

        // How many results should be kept in total (also in DockingAlgorithms)
        static const String BEST_NUM;

        // Verbosity of the Algorithm (also in DockingAlgorithm)
        static const String VERBOSITY;
        
        // Euler angels for redocking
        static const String PHI_MIN;
        static const String PHI_MAX;
        static const String DEG_PHI;
        
        static const String THETA_MIN;
        static const String THETA_MAX;
        static const String DEG_THETA;
        
        static const String PSI_MIN;
        static const String PSI_MAX;
        static const String DEG_PSI;
        
        // penalty value of the inside points
        // Default value for static protein is -15, for mobile protein 1
        static const String PENALTY_STATIC;
        static const String PENALTY_MOBILE;

        // Number of processes in total for a parallel run
        static const String NUMBER_OF_PROCESSES;
        
        // Full path to the slave to spawn
        static const String SLAVE_PATH;
      };
    
      struct BALL_EXPORT Default
      {
        // Default parameter r,
        // Default value is 1.8 Angstrom
        static const float NEAR_RADIUS;

        // Default grid spacing. 
        // Default value is 1.0 Angstrom
        static const float GRID_SPACING;

        // grid size = (ceil)(molecule size / grid spacing);
        static const int GRID_SIZE; 

        // Default thickness of the surface of the protein
        // Default value is 1.0 Angstrom
        static const float SURFACE_THICKNESS;

        // Degree interval is the delta parameter, 
        // which is the degrees that protein B rotates every time
        // Default value is 20 degrees
        static const double DEGREE_INTERVAL;

        static const int SURFACE_TYPE;

        // How many peaks should the program keep for each rotation
        static const int TOP_N;

        // How many overall top best peaks should the program keep 
        // after doing all rotations.
        static const int BEST_NUM;

        // Verbosity of the algorithm
        // Default value is 0
        // For values > 1, some information is printed on Log
        // For values > 5, timing information is included
        static const int VERBOSITY;
        
        // Euler angels for redocking
        static const float PHI_MIN;
        static const float PHI_MAX;
        static const float DEG_PHI;
        
        static const float THETA_MIN;
        static const float THETA_MAX;
        static const float DEG_THETA;
        
        static const float PSI_MIN;
        static const float PSI_MAX;
        static const float DEG_PSI;
        
        // penalty value of the inside points
        // Default value for static protein is -15, for mobile protein 1
        static const int PENALTY_STATIC;
        static const int PENALTY_MOBILE;

        // number of processes for a parallel run
        static const int NUMBER_OF_PROCESSES;

        // Full path to the slave to spawn
        static const String SLAVE_PATH;
      };

      class BALL_EXPORT Peak_
      {
        public:

          // constructor
          Peak_();

          // destructor
          ~Peak_();

          // Operator <
          bool operator < (const Peak_& p) const;

          double  value;
          Vector3 orientation;
          Vector3 translation;
      };

      class BALL_EXPORT RotationAngles_
      {
        public: 

          // constructor
          RotationAngles_();
          
          // constructor
          RotationAngles_( int step );

          // destructor
          ~RotationAngles_()  {};

          // generate all non-degenerate rotation angles.
          // This algorithm is based on ???
          bool generateSomeAngles( const float deg_phi,   const float deg_psi, const float deg_theta,
                                   const float phi_min,   const float phi_max,
                                   const float psi_min,   const float psi_max,
                                   const float theta_min, const float theta_max );

          // generate all non-degenerate rotation angles.
          // This algorithm is based on ???
          bool generateAllAngles( const int deg );

          int getRotationNum()
          {
            return ang_num_;
          }

          int getXAng( int n ) // get the euler angle rotate around x axis
          {
            return phi_[n];
          }

          int getYAng( int n ) // get the euler angle rotate around y axis
          {
            return theta_[n];
          }

          int getZAng( int n ) // get the euler angle rotate around z axis
          {
            return psi_[n];
          }

          // TODO: This class is a bit strange...
          vector<int> phi_;
          vector<int> theta_;
          vector<int> psi_;

        private:
          int ang_num_;
          int max_rotation_;
      };

      // PROTEIN_A is the static protein, i.e., the bigger one;
      // PROTEIN_B is the mobile protein, i.e., the smaller one.
      enum ProteinIndex{  PROTEIN_A = 1, PROTEIN_B    = 2 };

      // The surface type to use for construction of the grids.
      enum SurfaceType {  CONNOLLY  = 1, VAN_DER_WAALS = 2, FTDOCK = 3 };

      // Default constructor
      // Creates an empty GeometricFit object
      GeometricFit();

      GeometricFit(System &system1, System &system2);

      GeometricFit(Options& new_options);
      
      GeometricFit(System &system1,System &system2 ,Options& new_options);
        
        
/*       // Copy constructor */
/*       // Copies an existing GeometricFit object */
/*       GeometricFit( const GeometricFit& geo_fit ); */

      // Destructor
      ~GeometricFit();

      virtual void setup(System& system1, System& system2, Options& new_options);
      
      virtual void setup(System& system1, System& system2);   
  
      void start();

#ifdef BALL_HAS_MPI

      void MPI_Slave_start(int argc, char**argv);
#endif

      // return the overall docking progress as a percentage
      float getProgress() const;
      
      // 
      bool hasFinished() const;

      Vector3 getTranslation(Index con_num) const;

      Vector3 getOrientation(Index con_num) const;

      ConformationSet getConformationSet(Index total_number = 0);
      
      // the member variables

      Options options;
      
    protected:

      // Free all allocated memory and destroys the options and results
      void destroy_();

      // find the inside points
      void findInsidePoints_( System& system, ProteinIndex pro_idx );

      // find out the surface points according to the Connolly's surface definition.
      void findConnollySurfacePoints_( System& system, ProteinIndex pro_idx );

      // find out the surface points according to the van der Waal's surface definition.
      void findVanDerWaalsSurfacePoints_( System& system, ProteinIndex pro_idx );

      // find the inside points using the same algorithm as FTDock
      void findFTDockInsidePoints_( System& system, ProteinIndex pro_idx );

      // find out the surface points according to the FTDock surface definition.
      void findFTDockSurfacePoints_( System& system, ProteinIndex pro_idx );

      Vector3 getMassCenter_( System& system );

      float getRadius_( System& system );

      void doPreTranslation_( ProteinIndex pro_idx );

      void initGridSizes_();

      int optimizeGridSize_( int raw_size );

      void initFFTGrid_( ProteinIndex pro_idx );

      // make grid from System
      void makeFFTGrid_( ProteinIndex pro_idx );

      // get the global peaks and put them into a list
      void getGlobalPeak_(Peak_* peak_list);

      // change the orientation of protein around its center according to euler_ang
      void changeProteinOrientation_( System& system, Vector3 euler_ang );

      // calculate the conjugate of each point in FFT grid
      void calcConjugate_( ProteinIndex pro_idx );

      // calculate the product of the two FFT grids
      void FFTGridMulti_();

      // get the transformation of the peak value according to its position in matrix
      Vector3 getTranslation_( const Vector3& mat_pos );

      Vector3 getSeparation_( const Vector3& mat_pos );


      // here we have two units for the size
      // index : in the unit of grid points
      // coord : in the unit of Angstrom

      // the FFT grid for protein A
      FFT3D*  FFT_grid_a_;
      
      // the FFT grid for protein B
      FFT3D*  FFT_grid_b_;

      float radius_a_;
      float radius_b_;

      Vector3 FFT_grid_lower_index_;
      Vector3 FFT_grid_upper_index_;
      Vector3 FFT_grid_lower_coord_;
      Vector3 FFT_grid_upper_coord_;     
      
      Vector3 FFT_grid_size_index_;

      // the translation we do to the system b before FFT
      // it is to reduse the size of the FFT_grid
      Vector3 pre_translation_a_;
      Vector3 pre_translation_b_;

      Vector3 FFT_grid_origin_;

      // current execution progress
      int current_round_;

      // execution round of whole work
      int total_round_;

      // ordered set of the top_n peaks
      std::multiset<Peak_> peak_set_;

      // Needed to produce the correct results in getRankedConformations
      System system_backup_a_;
      System system_backup_b_;

      // Vectors to store orientation and translation of the results in the ranked conformations
      vector<Vector3> translations_;
      vector<Vector3> orientations_;

    }; // class GeometricFit

} // namespace BALL

#endif