DisulfideMatchingEnergy.cc

Go to the documentation of this file.

// -*- mode:c++;tab-width:2;indent-tabs-mode:t;show-trailing-whitespace:t;rm-trailing-spaces:t -*-
// vi: set ts=2 sw=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/disulfides/DisulfideMatchingEnergy.cc
/// @brief  Centroid Disulfide Energy class implementation
/// @author rvernon@u.washington.edu
/// @date   02/09/10


// Unit headers
#include <core/scoring/disulfides/DisulfideMatchingEnergy.hh>
#include <core/scoring/disulfides/DisulfideMatchingEnergyCreator.hh>

// Package headers
#include <core/scoring/disulfides/DisulfideMatchingPotential.hh>
#include <core/scoring/disulfides/DisulfideMatchingEnergyContainer.hh>

// Project headers
#include <core/chemical/VariantType.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 <utility/vector1.hh>


namespace core {
namespace scoring {
namespace disulfides {


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

ScoreTypes
DisulfideMatchingEnergyCreator::score_types_for_method() const {
  ScoreTypes sts;
  sts.push_back( dslfc_rot );
  sts.push_back( dslfc_trans );
  sts.push_back( dslfc_RT );
  return sts;
}


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



DisulfideMatchingEnergy::DisulfideMatchingEnergy(
  DisulfideMatchingPotential const & potential
) :
  parent( new DisulfideMatchingEnergyCreator ),
  potential_( potential )
{}

DisulfideMatchingEnergy::~DisulfideMatchingEnergy() {}

// EnergyMethod Methods:

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


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

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

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


// TwoBodyEnergy Methods:

void DisulfideMatchingEnergy::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 match_rot;
  Energy match_trans;
  Energy match_RT;

  //Require cysteines
  if ( rsd1.aa() != chemical::aa_cys || rsd2.aa() != chemical::aa_cys ) return;
  //Require Centroid (NOT NO MORE!)
  //if (rsd1.residue_type_set().name() != chemical::CENTROID ||
  //    rsd2.residue_type_set().name() != chemical::CENTROID )
  //  return;

  DisulfideMatchingEnergyContainerCOP dec = DisulfideMatchingEnergyContainerCOP (
      static_cast< DisulfideMatchingEnergyContainer const * > (
        pose.energies().long_range_container( methods::disulfide_matching_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,
      match_rot,
      match_trans,
      match_RT
      );

  emap[ dslfc_rot ]   += match_rot;
  emap[ dslfc_trans ] += match_trans;
  emap[ dslfc_RT ]    += match_RT;
}



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


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

// LongRangeTwoBodyEnergy methods
methods::LongRangeEnergyType
DisulfideMatchingEnergy::long_range_type() const
{
  return methods::disulfide_matching_energy;
}


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

  DisulfideMatchingEnergyContainerCOP dec = DisulfideMatchingEnergyContainerCOP (
      static_cast< DisulfideMatchingEnergyContainer const * > (
        pose.energies().long_range_container( disulfide_matching_energy ).get() ));
  return dec->disulfide_bonded( res1, res2 );
}
core::Size
DisulfideMatchingEnergy::version() const
{
  return 1; // Initial versioning
}


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