CentroidDisulfideEnergy.cc

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/// @file   core/scoring/disulfides/CentroidDisulfideEnergy.cc
/// @brief  Centroid Disulfide Energy class implementation
/// @author Spencer Bliven <blivens@u.washington.edu>
/// @date   2/4/09


// Unit headers
#include <core/scoring/disulfides/CentroidDisulfideEnergy.hh>
#include <core/scoring/disulfides/CentroidDisulfideEnergyCreator.hh>

// Package headers
#include <core/scoring/disulfides/CentroidDisulfidePotential.hh>
#include <core/scoring/disulfides/CentroidDisulfideEnergyContainer.hh>

// Project headers
#include <core/chemical/VariantType.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/conformation/Residue.hh>
#include <core/pose/Pose.hh>
#include <core/scoring/EnergyMap.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/ScoringManager.hh>
#include <core/scoring/methods/Methods.hh>
#include <basic/Tracer.hh>

#include <core/chemical/ChemicalManager.fwd.hh>
#include <utility/vector1.hh>


namespace core {
namespace scoring {
namespace disulfides {


/// @details This must return a fresh instance of the CentroidDisulfideEnergy class,
/// never an instance already in use
methods::EnergyMethodOP
CentroidDisulfideEnergyCreator::create_energy_method(
  methods::EnergyMethodOptions const &
) const {
  return new CentroidDisulfideEnergy( ScoringManager::get_instance()->get_CentroidDisulfidePotential() );
}

ScoreTypes
CentroidDisulfideEnergyCreator::score_types_for_method() const {
  ScoreTypes sts;
  sts.push_back( dslfc_cen_dst );
  sts.push_back( dslfc_cb_dst );
  sts.push_back( dslfc_ang );
  sts.push_back( dslfc_cb_dih );
  sts.push_back( dslfc_bb_dih );
  return sts;
}


static basic::Tracer TR("core.scoring.disulfides.CentroidDisulfideEnergy");

CentroidDisulfideEnergy::CentroidDisulfideEnergy(
  CentroidDisulfidePotential const & potential
) :
  parent( new CentroidDisulfideEnergyCreator ),
  potential_( potential )
{}

CentroidDisulfideEnergy::~CentroidDisulfideEnergy() {}

// EnergyMethod Methods:

methods::EnergyMethodOP CentroidDisulfideEnergy::clone() const
{
  return new CentroidDisulfideEnergy( potential_ );
}


void CentroidDisulfideEnergy::setup_for_scoring(
    pose::Pose & pose,
    ScoreFunction const & ) const
{
  using namespace methods;

  if ( pose.energies().long_range_container( centroid_disulfide_energy ) == 0 ) {
    CentroidDisulfideEnergyContainerOP dec = new CentroidDisulfideEnergyContainer( pose );
    pose.energies().set_long_range_container( centroid_disulfide_energy, dec );
  } else {
    CentroidDisulfideEnergyContainerOP dec = CentroidDisulfideEnergyContainerOP (
        static_cast< CentroidDisulfideEnergyContainer * > (
          pose.energies().nonconst_long_range_container( centroid_disulfide_energy ).get() ));
    dec->update( pose );
  }
}

void CentroidDisulfideEnergy::indicate_required_context_graphs(
    utility::vector1< bool > & ) const
{}


// TwoBodyEnergy Methods:

void CentroidDisulfideEnergy::residue_pair_energy(
    conformation::Residue const & rsd1,
    conformation::Residue const & rsd2,
    pose::Pose const & pose,
    ScoreFunction const &,
    EnergyMap & emap
    ) const
{
  // ignore scoring residues which have been marked as "REPLONLY" residues (only the repulsive energy will be calculated)
  if ( rsd1.has_variant_type( core::chemical::REPLONLY ) || rsd2.has_variant_type( core::chemical::REPLONLY ) ){
    return;
  }


  Energy cbcb_distance_score;
  Energy centroid_distance_score;
  Energy cacbcb_angle_1_score;
  Energy cacbcb_angle_2_score;
  Energy cacbcbca_dihedral_score;
  Energy backbone_dihedral_score;

  //Require cysteines
  if ( rsd1.aa() != chemical::aa_cys || rsd2.aa() != chemical::aa_cys ) return;
  //Require Centroid
  if (rsd1.residue_type_set().name() != chemical::CENTROID ||
      rsd2.residue_type_set().name() != chemical::CENTROID )
    return;

  CentroidDisulfideEnergyContainerCOP dec = CentroidDisulfideEnergyContainerCOP (
      static_cast< CentroidDisulfideEnergyContainer const * > (
        pose.energies().long_range_container( methods::centroid_disulfide_energy ).get() ));
  //Require they're bonded
  if ( ! dec->residue_forms_disulfide( rsd1.seqpos() ) ||
      dec->other_neighbor_id( rsd1.seqpos() ) != (Size) rsd2.seqpos() ){
    return;
  }

  potential_.score_disulfide(
      rsd1, rsd2,
      cbcb_distance_score,
      centroid_distance_score,
      cacbcb_angle_1_score,
      cacbcb_angle_2_score,
      cacbcbca_dihedral_score,
      backbone_dihedral_score
      );

  emap[ dslfc_cen_dst ] += centroid_distance_score;
  emap[ dslfc_cb_dst ]  += cbcb_distance_score;
  emap[ dslfc_ang ]     += (cacbcb_angle_1_score + cacbcb_angle_2_score)*.5;
  emap[ dslfc_cb_dih ]  += cacbcbca_dihedral_score;
  emap[ dslfc_bb_dih ]  += backbone_dihedral_score;
}


bool CentroidDisulfideEnergy::defines_intrares_energy( EnergyMap const & ) const
{
  return false;
}


void CentroidDisulfideEnergy::eval_intrares_energy(
    conformation::Residue const &,
    pose::Pose const &,
    ScoreFunction const &,
    EnergyMap &
    ) const
{}

// LongRangeTwoBodyEnergy methods
methods::LongRangeEnergyType
CentroidDisulfideEnergy::long_range_type() const
{
  return methods::centroid_disulfide_energy;
}


bool CentroidDisulfideEnergy::defines_residue_pair_energy(
    pose::Pose const & pose,
    Size res1,
    Size res2
    ) const
{
  using namespace methods;
  if ( ! pose.energies().long_range_container( centroid_disulfide_energy )) return false;

  CentroidDisulfideEnergyContainerCOP dec = CentroidDisulfideEnergyContainerCOP (
      static_cast< CentroidDisulfideEnergyContainer const * > (
        pose.energies().long_range_container( centroid_disulfide_energy ).get() ));
  return dec->disulfide_bonded( res1, res2 );
}
core::Size
CentroidDisulfideEnergy::version() const
{
  return 1; // Initial versioning
}


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