P_AA.hh

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// vi: set ts=2 noet:
//
// (c) Copyright Rosetta Commons Member Institutions.
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// (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
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/// @file   core/scoring/P_AA.hh
/// @brief  Amino acid probability arrays and functions
/// @author Stuart G. Mentzer (Stuart_Mentzer@objexx.com)
/// @author Andrew Leaver-Fay -- porting Stuart's code

#ifndef INCLUDED_core_scoring_P_AA_hh
#define INCLUDED_core_scoring_P_AA_hh

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

// Package headers
#include <core/scoring/types.hh>

// Project headers
#include <core/types.hh>
#include <core/chemical/AA.hh>
#include <core/conformation/Residue.fwd.hh>
#include <core/id/TorsionID.fwd.hh>

// Utility headers
#include <utility/pointer/ReferenceCount.hh>
#include <utility/vector1.hh>

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

namespace core {
namespace scoring {

class P_AA : public utility::pointer::ReferenceCount
{

private:

  /// @brief Amino acid probability array: P(aa)
  //typedef  utility::keys::SmallKeyVector< conformation::amino::AminoAcidKey, Probability >  Probability_AA;
  //extern Probability_AA P_AA;
  typedef utility::vector1< Probability > Probability_AA;
  Probability_AA P_AA_;

  /// @brief Amino acid conditional probability wrt number of neighbors array: P(aa|neighbors)
  //typedef  utility::keys::SmallKeyVector< conformation::amino::AminoAcidKey, FArray1D_Probability >  Probability_AA_n;
  //extern Probability_AA_n P_AA_n;
  typedef utility::vector1< utility::vector1< Probability > > Probability_AA_n;
  Probability_AA_n P_AA_n_;

  /// @brief Amino acid conditional probability wrt (phi,psi) array: P(aa|phi,psi)
  //typedef  utility::keys::SmallKeyVector< conformation::amino::AminoAcidKey, FArray2D_Probability >  Probability_AA_pp;
  //extern Probability_AA_pp P_AA_pp;
  typedef utility::vector1< FArray2D_Probability > Probability_AA_pp;
  Probability_AA_pp P_AA_pp_;

  utility::vector1< numeric::interpolation::spline::BicubicSpline > P_AA_pp_energy_splines_;

public:
  P_AA();

  virtual ~P_AA();
private:


  /// @brief Initialize the amino acid probability data structures
  void
  P_AA_initialize();


  /// @brief Read the amino acid probability file into P_AA
  void
  read_P_AA();


  /// @brief Read the amino acid conditional probability wrt (neighbors) file into P_AA_n
  void
  read_P_AA_n();


  /// @brief Read the amino acid conditional probability wrt (phi,psi) file into P_AA_pp
  void
  read_P_AA_pp();

public:
  /// @brief Probability energies from P(aa|phi,psi)
  //Energy
  //P_AA_pp_energy( conformation::amino::AminoAcid const & aa );
  Energy
  P_AA_pp_energy( conformation::Residue const & ) const;

  /// @brief Low-level probability energies from P(aa|phi,psi)
  /// @brief Probability energies from P(aa|phi,psi): Low level calculation for non-terminus position
  //Energy
  //P_AA_pp_energy( conformation::amino::AminoAcidKey const & key, Angle const phi, Angle const psi );
  Energy
  P_AA_pp_energy( chemical::AA aa, Angle const phi, Angle const psi ) const;

  EnergyDerivative
  get_Paa_pp_deriv(
    conformation::Residue const & res,
    id::TorsionID const & tor_id
  ) const;

  /// @brief Probability energies for P(aa)
  Energy
  P_AA_energy( conformation::Residue const & ) const;


};

} // namespace scoring
} // namespace core


#endif // INCLUDED_core_scoring_P_AA_HH