RNA_BaseBaseEnergy.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/rna/RNA_BaseBaseEnergy.cc
/// @brief  Statistically derived rotamer pair potential class implementation
/// @author Phil Bradley
/// @author Andrew Leaver-Fay
/// @author Rhiju Das


// Unit headers
#include <core/scoring/rna/RNA_BaseBaseEnergy.hh>

// Package headers
#include <core/scoring/rna/RNA_LowResolutionPotential.hh>
#include <core/scoring/rna/RNA_FilteredBaseBaseInfo.hh>
#include <core/scoring/rna/RNA_RawBaseBaseInfo.hh>
#include <core/scoring/rna/RNA_ScoringInfo.hh>
#include <core/scoring/ScoringManager.hh>
#include <core/scoring/EnergyGraph.hh>

// Project headers
#include <core/pose/Pose.hh>
#include <core/conformation/Residue.hh>


// Utility headers

#include <ObjexxFCL/format.hh>


// C++


namespace core {
namespace scoring {
namespace rna {

/// c-tor THIS CLASS REQUIRES AN EnergyMethodCreator TO WORK PROPERLY
RNA_BaseBaseEnergy::RNA_BaseBaseEnergy():
  rna_low_resolution_potential_( ScoringManager::get_instance()->get_RNA_LowResolutionPotential() )
{
  /*add_score_type( rna_base_pair );
  add_score_type( rna_base_axis );
  add_score_type( rna_base_stagger );
  add_score_type( rna_base_stack );
  add_score_type( rna_base_stack_axis );*/
}


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


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

  // Following will not repeat any work if any pairwise terms (e.g., base-backbone) have
  // already been calculated... would be better to
  // wrap it inside residue_pair_energy (so it could be used by the packer!).
  // Also maybe this should be unified with RNA_PairwiseLowResolutionEnergy...
  //rna_low_resolution_potential_.update_rna_base_base_interactions( pose );

}


/////////////////////////////////////////////////////////////////////////////
void
RNA_BaseBaseEnergy::setup_for_derivatives( pose::Pose & pose, ScoreFunction const & ) const
{
  pose.update_residue_neighbors();
  rna_low_resolution_potential_.update_rna_base_base_interactions( pose );

  rna::RNA_ScoringInfo & rna_scoring_info( rna::nonconst_rna_scoring_info_from_pose( pose ) );
  rna::RNA_RawBaseBaseInfo const & raw_base_base_info( rna_scoring_info.rna_raw_base_base_info() );
  rna::RNA_FilteredBaseBaseInfo & rna_filtered_base_base_info( rna_scoring_info.rna_filtered_base_base_info() );

  rna_filtered_base_base_info.carry_out_filtering( raw_base_base_info );
}


/////////////////////////////////////////////////////////////////////////////
// This all needs to eventually be refactored for the packer.
void
RNA_BaseBaseEnergy::finalize_total_energy(
  pose::Pose & pose,
  ScoreFunction const &,
  EnergyMap & totals
) const
{

  //This needs to take care of a bunch of base pair book-keeping.
  // Get Pose cached pairwise "raw" base-base info. This was
  // updated above, in setup_for_scoring
  rna::RNA_ScoringInfo & rna_scoring_info( rna::nonconst_rna_scoring_info_from_pose( pose ) );
  rna::RNA_RawBaseBaseInfo const & raw_base_base_info( rna_scoring_info.rna_raw_base_base_info() );

  // Create Pose cached non-pairwise, "filtered" base-base info.
  // This forces each base edge to have only one pairing partner.
  rna::RNA_FilteredBaseBaseInfo & rna_filtered_base_base_info( rna_scoring_info.rna_filtered_base_base_info() );

  rna_filtered_base_base_info.carry_out_filtering( raw_base_base_info );

  // From filtered base-base info, pull out total scores.
  totals[ rna_base_pair ]        += rna_filtered_base_base_info.get_total_base_pair_score();
  totals[ rna_base_axis ]        += rna_filtered_base_base_info.get_total_base_axis_score();
  totals[ rna_base_stagger ]     += rna_filtered_base_base_info.get_total_base_stagger_score();
  totals[ rna_base_stack ]       += rna_filtered_base_base_info.get_total_base_stack_score();
  totals[ rna_base_stack_axis ]  += rna_filtered_base_base_info.get_total_base_stack_axis_score();



  rna_low_resolution_potential_.finalize( pose ); //Set calculated to false!

  rna_filtered_base_base_info.set_calculated( false );

}

/////////////////////////////////////////////////////////////////////////////
void
RNA_BaseBaseEnergy::eval_atom_derivative(
  id::AtomID const & atom_id,
  pose::Pose const & pose,
  kinematics::DomainMap const &,
  ScoreFunction const &,
  EnergyMap const & weights,
  Vector & F1,
  Vector & F2
  ) const
{

  // updated above, in setup_for_scoring
  rna_low_resolution_potential_.eval_atom_derivative_base_base( atom_id, pose, weights, F1, F2 );

  return;
}


/////////////////////////////////////////////////////////////////////////////////////


/// @brief RNA_BaseBaseEnergy distance cutoff
Distance
RNA_BaseBaseEnergy::atomic_interaction_cutoff() const
{
  return 0.0; /// Uh, I don't know.
}

}
}
}