EnvPairPotential.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/methods/EnvPairPotential.hh
/// @brief  Statistically derived rotamer pair potential class implementation
/// @author Phil Bradley
/// @author Andrew Leaver-Fay

#ifndef INCLUDED_core_scoring_EnvPairPotential_hh
#define INCLUDED_core_scoring_EnvPairPotential_hh

#include <core/types.hh>

// Unit headers
#include <core/scoring/EnvPairPotential.fwd.hh>

// Package headers
// AUTO-REMOVED #include <core/scoring/EnergyGraph.fwd.hh>
#include <core/conformation/Residue.fwd.hh>

// Project headers
#include <core/pose/Pose.fwd.hh>

#include <basic/datacache/CacheableData.hh>

// Utility headers
// AUTO-REMOVED #include <utility/vector1.hh>

#include <ObjexxFCL/FArray1D.hh>
#include <ObjexxFCL/FArray2D.hh>
#include <ObjexxFCL/FArray3D.hh>

#include <utility/vector1.hh>


// C++


namespace core {
namespace scoring {

////////////////////////////////////////////////////////////////////////////////////////////////////
/// @brief Keep track of the cenlist information

class CenListInfo : public basic::datacache::CacheableData {

public:

  CenListInfo(): calculated_(false) {};

  CenListInfo( CenListInfo const & src );

  basic::datacache::CacheableDataOP
  clone() const
  {
    return new CenListInfo( *this );
  }

  Size
  size() const {
    return fcen6_.size();
  }

  Real
  fcen6( Size const seqpos ) const
  {
    return fcen6_[ seqpos ];
  }

  Real &
  fcen6( Size const seqpos )
  {
    return fcen6_[ seqpos ];
  }

  Real
  fcen10( Size const seqpos ) const
  {
    return fcen10_[ seqpos ];
  }

  Real &
  fcen10( Size const seqpos )
  {
    return fcen10_[ seqpos ];
  }

  Real
  fcen12( Size const seqpos ) const
  {
    return fcen12_[ seqpos ];
  }

  Real &
  fcen12( Size const seqpos )
  {
    return fcen12_[ seqpos ];
  }

  bool
  calculated() const
  {
    return calculated_;
  }

  bool &
  calculated()
  {
    return calculated_;
  }

  void
  initialize( pose::Pose const & pose );

  // Setter functions
  void
  set_fcen6( Size const seqpos, Real value )
  {
    fcen6_[ seqpos ] = value;
  }

  void
  set_fcen10( Size const seqpos, Real value )
  {
    fcen10_[ seqpos ] = value;
  }

  void
  set_fcen12( Size const seqpos, Real value )
  {
    fcen12_[ seqpos ] = value;
  }

private:
  utility::vector1< Real > fcen6_;
  utility::vector1< Real > fcen10_;
  utility::vector1< Real > fcen12_;
  bool calculated_;
};

class EnvPairPotential : public utility::pointer::ReferenceCount {

public:
  EnvPairPotential();

  ///
  void
  compute_centroid_environment(
    pose::Pose & pose
  ) const;

  void
  finalize( pose::Pose & pose ) const;

  ///
  void
  evaluate_env_and_cbeta_scores(
    pose::Pose const & pose,
    conformation::Residue const & rsd,
    Real & env_score,
    Real & cb_score6,
    Real & cb_score12
  ) const;

  ///
  void
  evaluate_pair_and_cenpack_score(
    conformation::Residue const & rsd1,
    conformation::Residue const & rsd2,
    Real const cendist,
    Real & pair_contribution,
    Real & cenpack_contribution
  ) const;

protected:
  Real const cen_dist_cutoff2;


  CenListInfo const & cenlist_from_pose( pose::Pose const & ) const;
  CenListInfo & nonconst_cenlist_from_pose( pose::Pose & ) const;

private:

  void
  fill_cenlist(
    CenListInfo & cenlist,
    Size const res1,
    Size const res2,
    Real const cendist
  ) const;

  void
  truncate_cenlist_values( CenListInfo & cenlist ) const;

private: // data

  ObjexxFCL::FArray2D< Real > env_log_;
  ObjexxFCL::FArray1D< Real > cbeta_den6_;
  ObjexxFCL::FArray1D< Real > cbeta_den12_;
  ObjexxFCL::FArray3D< Real > pair_log_;
  ObjexxFCL::FArray1D< Real > cenpack_log_;

  Real const cen_dist6sqr_;
  Real const cen_dist10sqr_;
  Real const cen_dist12sqr_;

  //cems transition regions between environment bins
  //cems transition is from +/- sqrt(36+pad6) +/- sqrt(100+pad10) etc
  Real const cen_dist5_pad;
  Real const cen_dist6_pad;
  Real const cen_dist7_pad;
  Real const cen_dist10_pad;
  Real const cen_dist12_pad;

  Real const cen_dist5_pad_plus ;
  Real const cen_dist6_pad_plus ;
  Real const cen_dist7_pad_plus ;
  Real const cen_dist10_pad_plus;
  Real const cen_dist12_pad_plus;

  Real const cen_dist5_pad_minus ;
  Real const cen_dist7_pad_minus ;
  Real const cen_dist10_pad_minus;
  Real const cen_dist12_pad_minus;

  Real const cen_dist5_pad_hinv ;
  Real const cen_dist6_pad_hinv ;
  Real const cen_dist7_pad_hinv ;
  Real const cen_dist10_pad_hinv;
  Real const cen_dist12_pad_hinv;

  Real const cen_dist_cutoff_12_pad;

};
} // ns scoring
} // ns core

#endif