RMS_Energy.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/methods/RMS_Energy.cc
/// @brief  RMS Energy function. Used to optimize the RMSD between two structures.
/// @author James Thompson


// Unit headers
#include <core/scoring/methods/RMS_Energy.hh>
#include <core/scoring/methods/RMS_EnergyCreator.hh>

// Package headers
// AUTO-REMOVED #include <core/conformation/Residue.hh>
// AUTO-REMOVED #include <core/conformation/Atom.hh>

// AUTO-REMOVED #include <core/scoring/EnvPairPotential.hh>
//#include <core/scoring/ScoringManager.hh>
// AUTO-REMOVED #include <core/scoring/EnergyGraph.hh>
#include <core/scoring/rms_util.hh>

// AUTO-REMOVED #include <core/io/pdb/pose_io.hh>

#include <basic/options/option.hh>

#include <core/pose/Pose.hh>

// AUTO-REMOVED #include <basic/prof.hh>
#include <utility/exit.hh>


// option key includes

#include <basic/options/keys/score.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>

#include <core/io/pdb/file_data.hh>
#include <core/scoring/EnergyMap.hh>
#include <utility/vector1.hh>



namespace core {
namespace scoring {
namespace methods {


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

ScoreTypes
RMS_EnergyCreator::score_types_for_method() const {
  ScoreTypes sts;
  sts.push_back( rms );
  return sts;
}


/// c-tor
RMS_Energy::RMS_Energy() :
  parent( new RMS_EnergyCreator )
{
  // configure native pose. Not perfect, ideally we should have some way of
  // guaranteeing that the native pose and pose provided for scoring have
  // the same ResidueTypeSet.
  if ( basic::options::option[ basic::options::OptionKeys::in::file::native ].user() ) {
    //core::import_pose::pose_from_pdb( native_pose_, basic::options::option[ basic::options::OptionKeys::in::file::native ]() );
     core::io::pdb::build_pose_from_pdb_as_is(native_pose_, basic::options::option[ basic::options::OptionKeys::in::file::native ]() );
  } else {
    utility_exit_with_message( "Error: must provide native pose when scoring with RMS_Energy!\n" );
  }

  // configure target RMSD.
  rms_target_ = basic::options::option[ basic::options::OptionKeys::score::rms_target ]();
}


/// clone
EnergyMethodOP
RMS_Energy::clone() const
{
  return new RMS_Energy();
}


/////////////////////////////////////////////////////////////////////////////
// scoring
/////////////////////////////////////////////////////////////////////////////

/// @brief Calculate the RMS difference between native_pose_ (provided by
/// the option -in::file::native and the given Pose. The actual energy calculation
/// is the difference between the RMSD and the target RMSD. Target RMSD is specified
/// the option -score::rms_target.

void
RMS_Energy::finalize_total_energy(
  pose::Pose & pose,
  ScoreFunction const &,
  EnergyMap & totals
) const {

  // PROF_START( basic::RMS );

  ///////////////////////////////////////
  //
  // RMS SCORE
  core::Real rmsd = core::scoring::CA_rmsd( native_pose_, pose );
  totals[ rms ]  = std::abs( rms_target_ - rmsd );

  // PROF_STOP( basic::RMS );
}
core::Size
RMS_Energy::version() const
{
  return 1; // Initial versioning
}

} // namespace methods
} // namespace scoring
} // namespace core