DDPscore.cc

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// (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/Interface/DDPscore.cc
///@brief Implementation of distance dependent interface score
///@detailed The distance dependent score is a knowledge based potential specialized for
/// protein interfaces. This class loads and accesses the lookup tables.
///@author Hermann Zellner (hermann1.zellner@biologie.uni-regensburg.de)

#include <utility/vector1.hh>
#include <core/scoring/interface/DDPscore.hh>
#include <core/scoring/interface/DDPscoreCreator.hh>

// AUTO-REMOVED #include <basic/options/option.hh>
// AUTO-REMOVED #include <basic/options/keys/score.OptionKeys.gen.hh>
// AUTO-REMOVED #include <core/pose/Pose.hh>

// AUTO-REMOVED #include <basic/Tracer.hh>
#include <core/scoring/ScoringManager.hh>
// AUTO-REMOVED #include <core/scoring/ContextGraphTypes.hh>
// AUTO-REMOVED #include <numeric/constants.hh>

#include <core/conformation/Residue.hh>
// AUTO-REMOVED #include <core/chemical/AtomType.hh>
#include <core/scoring/EnergyMap.hh>


#include <core/kinematics/Jump.hh>

namespace core{
namespace scoring{
namespace interface{




methods::EnergyMethodOP
DDPscoreCreator::create_energy_method(
  methods::EnergyMethodOptions const &
) const {
  return new DDPscore;
}

ScoreTypes
DDPscoreCreator::score_types_for_method() const {
  ScoreTypes sts;
  sts.push_back( interface_dd_pair );
  return sts;
}


DDPscore::DDPscore() :
    parent( new DDPscoreCreator ),
    lookup_table_( core::scoring::ScoringManager::get_instance()->get_DDPLookupTable() )
{ }

methods::EnergyMethodOP DDPscore::clone() const
{
  return new DDPscore(*this);
}

void DDPscore::setup_for_scoring(pose::Pose&, const ScoreFunction& ) const
{
  //pose.update_residue_neighbors();
}

void DDPscore::setup_for_packing(
  pose::Pose&,
  utility::vector1< bool > const &,
  utility::vector1< bool > const & ) const
{
  //pose.update_residue_neighbors();
}

void DDPscore::setup_for_derivatives(pose::Pose&, const ScoreFunction& ) const
{
  //pose.update_residue_neighbors();
}

bool DDPscore::defines_intrares_energy(core::scoring::EnergyMap const &) const
{
        return false;
}

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


void DDPscore::residue_pair_energy(
  core::conformation::Residue const & rsd2,
  core::conformation::Residue const & rsd1,
  const core::pose::Pose &,
  const core::scoring::ScoreFunction &,
  core::scoring::EnergyMap & emap
) const
{
  assert (rsd1.seqpos() != rsd2.seqpos()); //only call for distinct residues

  if (rsd1.chain() != rsd2.chain()) // Only score contacts across the interface
  {
    core::Real distance = 1e3;
    for ( core::conformation::Atoms::const_iterator atom_it_1 = rsd1.atom_begin();
        atom_it_1 != rsd1.heavyAtoms_end(); atom_it_1++)
    {
      for ( core::conformation::Atoms::const_iterator atom_it_2 = rsd2.atom_begin();
          atom_it_2 != rsd2.heavyAtoms_end(); atom_it_2++)
      {
        if ( atom_it_1->xyz().distance(atom_it_2->xyz()) < distance )
        {
          distance = atom_it_1->xyz().distance(atom_it_2->xyz());
        }
      }
    }

    if (
        distance >= 10. ||
        distance < 1.5 ||
        lookup_table_.get_potentials( rsd1.aa(), rsd2.aa(), distance ) > 0. )
    {
      emap[ interface_dd_pair ] += 0.; // noop
    }
    else
    {
      emap[ interface_dd_pair ] += lookup_table_.get_potentials( rsd1.aa(), rsd2.aa(), distance );
    }
  }
  else
  {
    emap[ interface_dd_pair ] += 0.; // noop
  }

}



void DDPscore::indicate_required_context_graphs(utility::vector1< bool > & /*context_graphs_required*/ ) const
{

}

core::Distance DDPscore::atomic_interaction_cutoff() const{
        return 8.0;
}
core::Size
DDPscore::version() const
{
  return 1; // Initial versioning
}


} // InterfacePotentials
} // scoring
} // core