Ramachandran2B.hh

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// -*- mode:c++;tab-width:2;indent-tabs-mode:t;show-trailing-whitespace:t;rm-trailing-spaces:t -*-
// vi: set ts=2 noet:
//
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/// @file   core/scoring/Ramachandran.hh
/// @brief  Ramachandran potential class delcaration
/// @author Guoli Wang

#ifndef INCLUDED_core_scoring_Ramachandran2B_hh
#define INCLUDED_core_scoring_Ramachandran2B_hh

// Unit Headers
#include <core/scoring/Ramachandran2B.fwd.hh>
//#include <core/scoring/ProteinTorsion.hh>

// Project Headers
#include <core/types.hh>
#include <core/chemical/AA.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/conformation/Residue.fwd.hh>
#include <core/scoring/ScoreFunction.fwd.hh>

// Utility Headers
#include <utility/pointer/ReferenceCount.hh>

// ObjexxFCL Headers
#include <ObjexxFCL/FArray1D.hh>
#include <ObjexxFCL/FArray2D.hh>
// AUTO-REMOVED #include <ObjexxFCL/FArray2A.hh>
#include <ObjexxFCL/FArray3D.hh>
#include <ObjexxFCL/FArray4D.hh>

#include <utility/vector1.hh>

// C++ Headers
#include <map>


namespace core {
namespace scoring {


class Ramachandran2B : public utility::pointer::ReferenceCount
{
public:
  typedef pose::Pose Pose;
  typedef chemical::AA AA;

public:
  Ramachandran2B();
  virtual ~Ramachandran2B() ; // auto-removing definition from header{}

  Real
  eval_rama_score_residue(
    AA const res_aa,
    Real const phi,
    Real const psi
  ) const;

  // Guoli Wang
  void
  eval_rama_score_residue(
    conformation::Residue const & res,
    chemical::AA const left_aa,
    chemical::AA const right_aa,
    Real & rama,
    Real & drama_dphi,
    Real & drama_dpsi
  ) const;

  Real
  RamaE_Lower(
    conformation::Residue const &rsd,
    chemical::AA const &neighbor,
    Real &drama_dphi,
    Real &drama_dpsi
  ) const;

  Real
  RamaE_Lower(
    conformation::Residue const &rsd,
    chemical::AA const &neighbor
  ) const;

  Real
  RamaE_Upper(
    conformation::Residue const & rsd,
    chemical::AA const &neighbor,
    Real &drama_dphi,
    Real &drama_dpsi
  ) const;

  Real
  RamaE_Upper(
    conformation::Residue const & rsd,
    chemical::AA const &neighbor
  ) const;

  Real
  RamaE(
    conformation::Residue const & rsd,
    Real &drama_dphi,
    Real &drama_dpsi
  ) const;

  Real
  RamaE(
    conformation::Residue const & rsd
  ) const;
  // finished

  void
  eval_rama_score_residue(
    conformation::Residue const & res,
    Real & rama,
    Real & drama_dphi,
    Real & drama_dpsi
  ) const;

  void
  eval_rama_score_residue(
    AA const res_aa,
    Real const phi,
    Real const psi,
    Real & rama,
    Real & drama_dphi,
    Real & drama_dpsi
  ) const;

  void
  IdealizeRamaEnergy(
    Real const phi,
    Real const psi,
    Real & rama,
    Real & drama_dphi,
    Real & drama_dpsi,
    Real const entropy,
    ObjexxFCL::
    FArray2A< Real > const & rama_for_res
  ) const;

  // AS: for neighbor-dependent rama sampling
    void
  random_phipsi_from_rama_left(
                                 AA const left_aa,
                                 AA const pos_aa,
                                 Real & phi,
                                 Real & psi
                                 ) const;
  
    void
  random_phipsi_from_rama_right(
                  AA const pos_aa,
                  AA const right_aa,
                  Real & phi,
                  Real & psi
                  ) const;
  
  /// @brief function for torsion-bin specific but otherwise random phi/psi angles
  /// @author Amelie Stein
    
  void
  random_phipsi_from_rama_by_torsion_bin_left(
                        AA const left_aa,
                        AA const pos_aa,
                        Real & phi,
                        Real & psi,
                        char const torsion_bin
                        ) const;
  
  void
  random_phipsi_from_rama_by_torsion_bin_right(
                         AA const pos_aa,
                         AA const right_aa,
                         Real & phi,
                         Real & psi,
                         char const torsion_bin
                         ) const;
  
  
  core::Size get_torsion_bin_index(char torsion_bin) const;
  
  void
  init_rama_sampling_tables_by_torsion_bin(); 
  
  void
  get_entries_per_torsion_bin_left( 
                   AA const left_aa,
                   AA const pos_aa,
                   std::map< char, core::Size > & tb_frequencies ) const;
    
  void
  get_entries_per_torsion_bin_right( 
                    AA const pos_aa,
                    AA const right_aa,
                    std::map< char, core::Size > & tb_frequencies ) const;
    
  

  
  ///////////////////////////////
  // unused??
  void
  eval_rama_score_all(
    Pose & pose,
    ScoreFunction const & scorefxn
  ) const;

  void
  write_rama_score_all(
    Pose const & pose
  ) const;


private:

  void read_rama();
    void init_rama_sampling_table_left( const char torsion_bin ); // AS: for neighbor-dependent rama sampling in KIC/NGK
    void init_rama_sampling_table_right( const char torsion_bin ); 

  //static bool rama_initialized_;
  ObjexxFCL::FArray3D< Real > ram_energ_;
  ObjexxFCL::FArray1D< Real > ram_entropy_;
  ObjexxFCL::FArray4D< Real > ram_energ_left_;
  ObjexxFCL::FArray2D< Real > ram_entropy_left_;
  ObjexxFCL::FArray4D< Real > ram_energ_right_;
  ObjexxFCL::FArray2D< Real > ram_entropy_right_;

  static int const n_phi_ = 36;
  static int const n_psi_ = 36;
  static Real const binw_; // 360 / n_phi_ = 10;
  static int const n_aa_ = 20; // Ramachandran score defined for the cananical AAs only.
  static int const nullaa = 21; // Guoli Wang

  Real const rama_score_limit_;

    static ObjexxFCL::FArray4D< Real > left_ram_probabil_; // AS: probability of each phi/psi combination given the left & actual  AA 
    utility::vector1< utility::vector1< utility::vector1< utility::vector1< Real > > > > left_rama_sampling_table_; // vector of allowed phi/psi pairs for each residue triplet
    utility::vector1< utility::vector1< utility::vector1< utility::vector1< utility::vector1< Real > > > > > left_rama_sampling_table_by_torsion_bin_; 
  
    static ObjexxFCL::FArray4D< Real > right_ram_probabil_; // AS: probability of each phi/psi combination given the actual & right  AA 
    utility::vector1< utility::vector1< utility::vector1< utility::vector1< Real > > > > right_rama_sampling_table_; // vector of allowed phi/psi pairs for each residue triplet
    utility::vector1< utility::vector1< utility::vector1< utility::vector1< utility::vector1< Real > > > > > right_rama_sampling_table_by_torsion_bin_; 
  
  static Real const rama_sampling_thold_;
  static Real const rama_sampling_factor_;
  

};

}
}

#endif