ShortRangeTwoBodyEnergy.cc

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//
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/// @file   core/scoring/methods/ShortRangeTwoBodyEnergy.cc
/// @brief  Short-Range, Two-Body Energy Method base class implementation
/// @author Andrew Leaver-Fay

// Unit Headers
#include <core/scoring/methods/ShortRangeTwoBodyEnergy.hh>

// Package Headers
#include <core/scoring/EnergyMap.hh>
#include <core/scoring/methods/EnergyMethodCreator.hh>

// Project Headers
#include <core/conformation/Residue.hh>
#include <core/conformation/RotamerSetBase.hh>

// ObjexxFCL Headers
#include <ObjexxFCL/FArray2D.hh>

#include <utility/vector1.hh>



namespace core {
namespace scoring {
namespace methods {

ShortRangeTwoBodyEnergy::ShortRangeTwoBodyEnergy( EnergyMethodCreatorOP creator ) : parent( creator ) {}

ShortRangeTwoBodyEnergy::~ShortRangeTwoBodyEnergy() {}

bool
ShortRangeTwoBodyEnergy::divides_backbone_and_sidechain_energetics() const
{
  return false;
}

void
ShortRangeTwoBodyEnergy::evaluate_rotamer_pair_energies(
  conformation::RotamerSetBase const & set1,
  conformation::RotamerSetBase const & set2,
  pose::Pose const & pose,
  ScoreFunction const & sfxn,
  EnergyMap const & weights,
  ObjexxFCL::FArray2D< core::PackerEnergy > & energy_table
) const
{
  using namespace conformation;
  using namespace numeric;

  EnergyMap emap;

  for ( Size ii = 1; ii <= set1.get_n_residue_types(); ++ii ) {
    Size const ii_offset = set1.get_residue_type_begin( ii );
    Residue const & ii_example_rotamer( *set1.rotamer( ii_offset ));
    Vector const & ii_coord( ii_example_rotamer.atom( ii_example_rotamer.type().nbr_atom() ).xyz());
    Real const ii_radius( ii_example_rotamer.type().nbr_radius() );

    for ( Size jj = 1; jj <= set2.get_n_residue_types(); ++jj ) {
      Size const jj_offset = set2.get_residue_type_begin( jj );
      Residue const & jj_example_rotamer( *set2.rotamer( jj_offset ));
      Vector const & jj_coord( jj_example_rotamer.atom( jj_example_rotamer.type().nbr_atom() ).xyz());
      Real const jj_radius( jj_example_rotamer.type().nbr_radius() );

      if ( ii_coord.distance_squared( jj_coord ) < std::pow(ii_radius+jj_radius+atomic_interaction_cutoff(), 2 )) {
        for ( Size kk = 1, kke = set1.get_n_rotamers_for_residue_type( ii ); kk <= kke; ++kk ) {
          Size const kk_rot_id = ii_offset + kk - 1;
          for ( Size ll = 1, lle = set2.get_n_rotamers_for_residue_type( jj ); ll <= lle; ++ll ) {
            Size const ll_rot_id = jj_offset + ll - 1;

            emap.zero();
            residue_pair_energy( *set1.rotamer( kk_rot_id ), *set2.rotamer( ll_rot_id ), pose, sfxn, emap );
            energy_table( ll_rot_id, kk_rot_id ) += static_cast< core::PackerEnergy > (weights.dot( emap ));
          }
        }
      }
    }
  }

}

void
ShortRangeTwoBodyEnergy::evaluate_rotamer_background_energies(
  conformation::RotamerSetBase const & set,
  conformation::Residue const & residue,
  pose::Pose const & pose,
  ScoreFunction const & sfxn,
  EnergyMap const & weights,
  utility::vector1< core::PackerEnergy > & energy_vector
) const
{
  EnergyMap emap;
  for ( Size ii = 1, ii_end = set.num_rotamers(); ii <= ii_end; ++ii ) {
    emap.zero();
    residue_pair_energy( *set.rotamer( ii ), residue, pose, sfxn, emap );
    energy_vector[ ii ] += static_cast< core::PackerEnergy > (weights.dot( emap ));
  }
}

void
ShortRangeTwoBodyEnergy::evaluate_rotamer_background_energy_maps(
  conformation::RotamerSetBase const & set,
  conformation::Residue const & residue,
  pose::Pose const & pose,
  ScoreFunction const & sfxn,
  EnergyMap const & , // weights
  utility::vector1< EnergyMap > & emaps
) const
{
  EnergyMap emap;
  for ( Size ii = 1, ii_end = set.num_rotamers(); ii <= ii_end; ++ii ) {
    emap.zero();
    residue_pair_energy( *set.rotamer( ii ), residue, pose, sfxn, emap );
    emaps[ ii ] += emap;
  }
}

}
}
}