Ramachandran.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:
//
// (c) Copyright Rosetta Commons Member Institutions.
// (c) This file is part of the Rosetta software suite and is made available under license.
// (c) The Rosetta software is developed by the contributing members of the Rosetta Commons.
// (c) For more information, see http://www.rosettacommons.org. Questions about this can be
// (c) addressed to University of Washington UW TechTransfer, email: license@u.washington.edu.

/// @file   core/scoring/Ramachandran.hh
/// @brief  Ramachandran potential class delcaration
/// @author Andrew Leaver-Fay (leaverfa@email.unc.edu)

#ifndef INCLUDED_core_scoring_Ramachandran_hh
#define INCLUDED_core_scoring_Ramachandran_hh

// Unit Headers
#include <core/scoring/Ramachandran.fwd.hh>
// AUTO-REMOVED #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>
#include <utility/vector1.hh>

// Numeric headers
#include <numeric/interpolation/spline/Bicubic_spline.hh>


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

#include <utility/vector1.hh>
#include <ObjexxFCL/FArray2D.fwd.hh>
#include <ObjexxFCL/FArray4D.fwd.hh>

// C++ Headers
#include <map>


namespace core {
namespace scoring {

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

public:
  Ramachandran();

  Ramachandran(
    std::string const & rama_map_filename,
    bool use_bicubic_interpolation
  );

  virtual ~Ramachandran() ; // auto-removing definition from header{}


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

  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
  eval_rama_score_residue(
    bool use_bicubic_interpolation,
    bool rama_not_squared,
    AA const res_aa,
    Real const phi,
    Real const psi,
    Real & rama,
    Real & drama_dphi,
    Real & drama_dpsi
  ) const;

  void
  random_phipsi_from_rama(
    AA const res_aa,
    Real & phi,
    Real & psi
  ) const;


  /// @brief functions for torsion-bin specific but otherwise random phi/psi angles
  /// @author Amelie Stein
  
  
  void
  random_phipsi_from_rama_by_torsion_bin(
                       AA const res_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( AA const res_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;

  //Real get_rama_score_residue_deriv( int res, Pose const & a_pose, ProteinTorsion torsion ) const;
  void eval_procheck_rama( Pose const & a_pose,
    Real & favorable, Real & allowed, Real & generous ) const;


private:

  void read_rama(
    std::string const & rama_map_filename,
    bool use_bicubic_interpolation);

  void init_rama_sampling_table( char const torsion_bin );
/*
  static
  void
  procheck_map_initializer( FArray1D_string & map );
*/
  static bool rama_initialized_;
  //static utility::vector1< utility::vector1 < FArray2D< Real > > > > ram_probabil_;
  static ObjexxFCL::FArray4D< Real > ram_probabil_;
  //static utility::vector1< utility::vector1 < FArray2D_int > > > ram_counts_;
  static ObjexxFCL::FArray4D_int ram_counts_;
  //static utility::vector1< utility::vector1 < FArray2D< Real > > > > ram_energ_;
  static ObjexxFCL::FArray4D< Real > ram_energ_;
  utility::vector1< numeric::interpolation::spline::BicubicSpline > rama_energy_splines_; // loops only

  static int const n_phi_ = 36;
  static int const n_psi_ = 36;
  static Real const binw_; // 360 / n_phi_ = 10;
  static Real const rama_sampling_thold_;
  static Real const rama_sampling_factor_;
  static int const n_aa_ = 20; // Ramachandran score defined for the cananical AAs only.
  static ObjexxFCL::FArray2D< Real > ram_entropy_;
  utility::vector1< utility::vector1< utility::vector1< Real > > > rama_sampling_table_; // vector of allowed phi/psi pairs for each residue
  utility::vector1 < utility::vector1< utility::vector1< utility::vector1< Real > > > > rama_sampling_table_by_torsion_bin_; // first entry will be a letter indicating the torsion bin, the rest is like in the regular rama_sampling_table_


/*
  static bool procheck_map_initialized_
  static FArray1D_string procheck_map_;
*/

};

}
}

#endif