symE.cc

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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/symE/symE.c
/// @brief   Implementation of symmetric design bonus class
/// @author Sam DeLuca (samuel.l.deluca@vanderbilt.edu)

// Unit headers
#include <core/scoring/sym_e/symE.hh>
#include <core/scoring/sym_e/symECreator.hh>

// Package headers
#include <core/scoring/Energies.hh>
// AUTO-REMOVED #include <core/scoring/ScoreFunction.hh>
//#include <core/scoring/ScoringManager.hh>
#include <core/scoring/LREnergyContainer.hh>
#include <core/scoring/DenseEnergyContainer.hh>

// Project headers
// AUTO-REMOVED #include <core/conformation/Conformation.hh>
// AUTO-REMOVED #include <core/io/pdb/pose_io.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/score.OptionKeys.gen.hh>
#include <core/pose/Pose.hh>
// AUTO-REMOVED #include <basic/database/open.hh>
#include <basic/Tracer.hh>

#include <core/chemical/AtomType.hh>
#include <core/conformation/Residue.hh>
#include <core/kinematics/Jump.hh>
#include <utility/vector1.hh>


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

namespace core {
namespace scoring {
namespace sym_e {


/// @details This must return a fresh instance of the symE class,
/// never an instance already in use
methods::EnergyMethodOP
symECreator::create_energy_method(
  methods::EnergyMethodOptions const &
) const {
  return new symEnergy;
}

ScoreTypes
symECreator::score_types_for_method() const {
  ScoreTypes sts;
  sts.push_back( symE_bonus );
  return sts;
}



symEnergy::symEnergy() :
  parent( new symECreator )
{}

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

void symEnergy::setup_for_scoring(pose::Pose &pose, const ScoreFunction &) const
{

  using namespace methods;
  if(pose.energies().long_range_container(sym_bonus_lr) == 0)
  {
    DenseEnergyContainerOP lr_container = new DenseEnergyContainer(pose.total_residue(), symE_bonus);
    //LREnergyContainerOP lr_container = new LREnergyContainer(pose);
    pose.energies().set_long_range_container(sym_bonus_lr, lr_container);
  } else {
    DenseEnergyContainerOP lr_container_copied = DenseEnergyContainerOP(static_cast<DenseEnergyContainer*>(pose.energies().nonconst_long_range_container(sym_bonus_lr).get() ));
    if(lr_container_copied->size() !=pose.total_residue() )
    {
      DenseEnergyContainerOP lr_container = new DenseEnergyContainer(pose.total_residue(), symE_bonus);
      //LREnergyContainerOP lr_container = new LREnergyContainer(pose);
      pose.energies().set_long_range_container(sym_bonus_lr, lr_container);
    }
    //lr_container_copied->update(pose);
  }

  pose.update_residue_neighbors();
}

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

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

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

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

bool symEnergy::defines_residue_pair_energy(const core::pose::Pose& , platform::Size , platform::Size ) const
{
  return true;
}


methods::LongRangeEnergyType symEnergy::long_range_type() const
{
  return methods::sym_bonus_lr;
}


void symEnergy::residue_pair_energy(conformation::Residue const &rsd1, conformation::Residue const &rsd2,  pose::Pose const &pose,  scoring::ScoreFunction const &, EnergyMap & emap) const
{
  Size rsd1Pos = rsd1.seqpos();
  Size rsd2Pos = rsd2.seqpos();
  Size totalLength = pose.total_residue();

  int symUnits = basic::options::option[ basic::options::OptionKeys::score::symE_units ]();
  core::Real symBonus = basic::options::option[ basic::options::OptionKeys::score::symE_bonus ]();

  if(symUnits >0)
  {

    if(rsd1Pos % (totalLength/symUnits) ==  rsd2Pos % (totalLength/symUnits) && rsd1Pos != rsd2Pos)
    {

      if (rsd1.name() == rsd2.name())
      {
        emap[ symE_bonus ] += symBonus;
      }
    }
  }

}
core::Size
symEnergy::version() const
{
  return 1; // Initial versioning
}
} //symE
} //scoring
} //core