CentroidDisulfidePotential.hh

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// vi: set ts=2 sw=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/disulfides/CentroidDisulfidePotential.hh
/// @brief  Centroid Disulfide Energy Potentials
/// @author Spencer Bliven <blivens@u.washington.edu>
/// @date   12/17/08

#ifndef INCLUDED_core_scoring_disulfides_CentroidDisulfidePotential_hh
#define INCLUDED_core_scoring_disulfides_CentroidDisulfidePotential_hh

//Unit headers
#include <core/scoring/disulfides/CentroidDisulfidePotential.fwd.hh>
#include <utility/pointer/ReferenceCount.hh>

//Project headers
#include <core/types.hh>
// AUTO-REMOVED #include <core/pose/Pose.fwd.hh>
#include <core/conformation/Residue.fwd.hh>
#include <core/scoring/constraints/Func.hh>

//Utility Headers
// AUTO-REMOVED #include <numeric/interpolation/Histogram.hh>
// AUTO-REMOVED #include <utility/vector1.hh>

#include <numeric/interpolation/Histogram.fwd.hh>


namespace core {
namespace scoring {
namespace disulfides {

/**
 * @details This class scores centroid disulfide bonds
 * It is intended to be a singleton with a single instance held by ScoringManager.
 *
 * The energy functions are derived from those present in Rosetta++
 */
class CentroidDisulfidePotential : public utility::pointer::ReferenceCount {
public:
  CentroidDisulfidePotential();
  virtual ~CentroidDisulfidePotential();

  /**
   * @brief Calculates scoring terms for the disulfide bond specified
   */
  void
  score_disulfide(core::conformation::Residue const & res1,
      core::conformation::Residue const & res2,
      core::Energy & cbcb_distance_score,
      core::Energy & centroid_distance_score,
      core::Energy & cacbcb_angle_1_score,
      core::Energy & cacbcb_angle_2_score,
      core::Energy & cacbcbca_dihedral_score,
      core::Energy & backbone_dihedral_score
      ) const;

  /**
   * @brief Calculates scoring terms and geometry
   */
  void score_disulfide(
      core::conformation::Residue const & res1,
      core::conformation::Residue const & res2,
      core::Real & cbcb_distance_sq,
      core::Real & centroid_distance_sq,
      core::Real & cacbcb_angle_1,
      core::Real & cacbcb_angle_2,
      core::Real & cacbcbca_dihedral,
      core::Real & backbone_dihedral,
      core::Energy & cbcb_distance_score,
      core::Energy & centroid_distance_score,
      core::Energy & cacbcb_angle_1_score,
      core::Energy & cacbcb_angle_2_score,
      core::Energy & cacbcbca_dihedral_score,
      core::Energy & backbone_dihedral_score,
      core::Real & cb_score_factor
      ) const;

  /**
   * @brief Decide whether there is a disulfide bond between two residues.
   *
   * Does not require that the residues be cysteines, so if this is important
   * you should check for CYS first. (The relaxed requirements are useful for
   * design.)
   */
  bool is_disulfide(core::conformation::Residue const & res1,
      core::conformation::Residue const & res2) const;


private:

  /**
   * @brief calculates some degrees of freedom between two centroid cys residues
   *
   * @param cbcb_distance_sq      The distance between Cbetas squared
   * @param centroid_distance_sq  The distance between centroids squared
   * @param cacbcb_angle_1        The Ca1-Cb1-Cb2 planar angle, in degrees
   * @param cacbcb_angle_2        The Ca2-Cb2-Cb1 planar angle, in degrees
   * @param cacbcbca_dihedral     The Ca1-Cb1-Cb2-Ca2 dihedral angle
   * @param backbone_dihedral     The N-Ca1-Ca2-C2 dihedral angle
   */
  static
  void
  disulfide_params(
      core::conformation::Residue const& res1,
      core::conformation::Residue const& res2,
      core::Real & cbcb_distance_sq,
      core::Real & centroid_distance_sq,
      core::Real & cacbcb_angle_1,
      core::Real & cacbcb_angle_2,
      core::Real & cacbcbca_dihedral,
      core::Real & backbone_dihedral);

private: //Scoring functions
  static Cb_Distance_FuncCOP cb_distance_func_;
  static Cen_Distance_FuncCOP cen_distance_func_;
  static CaCbCb_Angle_FuncCOP cacbcb_angle_func_;
  static NCaCaC_Dihedral_FuncCOP ncacac_dihedral_func_;
  static CaCbCbCa_Dihedral_FuncCOP cacbcbca_dihedral_func_;

  ///@brief the Cysteines with cb dist scores less than this threshold are
  /// very likely (99%) to be disulfide bonded.
  static const core::Real disulfide_cb_dist_cutoff;

}; // CentroidDisulfidePotential


/**
 * @brief Score based on the distance between Cb
 *
 * Based on the rosetta++ scores by Bill Schief in 2002.
 *
 * Uses a sum of three gaussians.
 */
class Cb_Distance_Func : public constraints::Func
{
public:
  Cb_Distance_Func();
  virtual ~Cb_Distance_Func();
  constraints::FuncOP clone() const { return new Cb_Distance_Func( *this ); }
  virtual core::Real func( core::Real const ) const;
  virtual core::Real dfunc( core::Real const ) const;
private:
  //Parameters for the 3 gaussians
  static const Real means_[3];
  static const Real sds_[3];
  //Weighting between the 3 gaussians
  static const Real weights_[3];
  //Score at infinity; The gaussians are subtracted from this base.
  static const Real base_score_;

};

/**
 * Score based on the distance between the two residues' centroids
 */
class Cen_Distance_Func : public constraints::Func
{
public:
  Cen_Distance_Func();
  virtual ~Cen_Distance_Func();
  constraints::FuncOP clone() const { return new Cen_Distance_Func( *this ); }
  virtual core::Real func( core::Real const ) const;
  virtual core::Real dfunc( core::Real const ) const;
private:
  static numeric::interpolation::HistogramCOP<core::Real,core::Real>::Type centroid_dist_scores_;
};

/**
 * Score based on the angle Ca Cb Cb
 */
class CaCbCb_Angle_Func : public constraints::Func
{
public:
  CaCbCb_Angle_Func();
  virtual ~CaCbCb_Angle_Func();
  constraints::FuncOP clone() const { return new CaCbCb_Angle_Func( *this ); }
  virtual core::Real func( core::Real const ) const;
  virtual core::Real dfunc( core::Real const ) const;
private:
  static numeric::interpolation::HistogramCOP<core::Real,core::Real>::Type CaCbCb_angle_scores_;
};

/**
 * Score based on the dihedral formed by the two Ca and Cb
 */
class NCaCaC_Dihedral_Func : public constraints::Func
{
public:
  NCaCaC_Dihedral_Func();
  virtual ~NCaCaC_Dihedral_Func();
  constraints::FuncOP clone() const { return new NCaCaC_Dihedral_Func( *this ); }
  virtual core::Real func( core::Real const ) const;
  virtual core::Real dfunc( core::Real const ) const;
private:
  static numeric::interpolation::HistogramCOP<core::Real,core::Real>::Type backbone_dihedral_scores_;
};

/**
 * Score based on the dihedral formed by N Ca Ca C
 */
class CaCbCbCa_Dihedral_Func : public constraints::Func
{
public:
  CaCbCbCa_Dihedral_Func();
  virtual ~CaCbCbCa_Dihedral_Func();
  constraints::FuncOP clone() const { return new CaCbCbCa_Dihedral_Func( *this ); }
  virtual core::Real func( core::Real const ) const;
  virtual core::Real dfunc( core::Real const ) const;
private:
  static numeric::interpolation::HistogramCOP<core::Real,core::Real>::Type CaCbCbCa_dihedral_scores_;
};

} // disulfides
} // scoring
} // core

#endif