NatbiasSecondaryStructureEnergy.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 ./src/protocols/fldsgn/potentials/sspot/NatbiasSecondaryStructureEnergy.cc
/// @brief native biased centroid score for secondary structures
/// @author Nobuyasu Koga ( nobuyasu@uw.edu )

// Unit headers
#include <protocols/fldsgn/potentials/sspot/NatbiasSecondaryStructureEnergy.hh>
#include <protocols/fldsgn/potentials/sspot/NatbiasSecondaryStructureEnergyCreator.hh>

// Package headers
#include <protocols/fldsgn/topology/SS_Info2.hh>
#include <protocols/fldsgn/topology/StrandPairing.hh>
#include <protocols/fldsgn/topology/HelixPairing.hh>
#include <protocols/fldsgn/topology/HSSTriplet.hh>
#include <protocols/fldsgn/potentials/sspot/NatbiasHelicesSheetPotential.hh>
#include <protocols/fldsgn/potentials/sspot/NatbiasHelixPairPotential.hh>
#include <protocols/fldsgn/potentials/sspot/NatbiasStrandPairPotential.hh>

// Project headers
#include <core/pose/Pose.hh>
// AUTO-REMOVED #include <core/scoring/dssp/Dssp.hh>
#include <core/scoring/EnergyMap.hh>
// AUTO-REMOVED #include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreType.hh>
#include <core/scoring/methods/EnergyMethod.hh>
// AUTO-REMOVED #include <core/scoring/methods/EnergyMethodOptions.hh>
#include <basic/Tracer.hh>

#include <utility/vector1.hh>


static basic::Tracer TR("protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy", basic::t_info);

namespace protocols {
namespace fldsgn {
namespace potentials {
namespace sspot {

//////////////////////////////////////////////////////////////////////////////////////////////////////
/// SecodaryStructureEnergy2Creator
/// @details This must return a fresh instance of the SecondaryStructureEnergy class,
/// never an instance already in use
NatbiasSecondaryStructureEnergyCreator::EnergyMethodOP
NatbiasSecondaryStructureEnergyCreator::create_energy_method( EnergyMethodOptions const & ) const
{
  return new NatbiasSecondaryStructureEnergy;
}

NatbiasSecondaryStructureEnergyCreator::ScoreTypes
NatbiasSecondaryStructureEnergyCreator::score_types_for_method() const
{
  ScoreTypes sts;
  sts.push_back( core::scoring::natbias_hs );
  sts.push_back( core::scoring::natbias_ss );
  sts.push_back( core::scoring::natbias_hh );
  sts.push_back( core::scoring::natbias_stwist );
  return sts;
}


/// @brief default constructor
NatbiasSecondaryStructureEnergy::NatbiasSecondaryStructureEnergy() :
  parent( new NatbiasSecondaryStructureEnergyCreator ),
  native_secstruct_( "" ),
  use_sspot_( false ),
  use_hhpot_( false ),
  use_hspot_( false ),
  use_nobias_( false ),
  sspot_( NULL ),
  hhpot_( NULL ),
  hspot_( NULL )
{}


/// @brief copy constructor
NatbiasSecondaryStructureEnergy::NatbiasSecondaryStructureEnergy( NatbiasSecondaryStructureEnergy const & src ):
  parent( src ),
  native_secstruct_( src.native_secstruct_ ),
  use_sspot_( src.use_sspot_ ),
  use_hhpot_( src.use_hhpot_ ),
  use_hspot_( src.use_hspot_ ),
  use_nobias_( src.use_nobias_ ),
  sspot_( src.sspot_ ),
  hhpot_( src.hhpot_ ),
  hspot_( src.hspot_ )
{}


/// @brief clone
NatbiasSecondaryStructureEnergy::EnergyMethodOP
NatbiasSecondaryStructureEnergy::clone() const
{
  return new NatbiasSecondaryStructureEnergy( *this );
}

/// @brief set native secondary structure
void
NatbiasSecondaryStructureEnergy::native_secstruct( String const & secstruct )
{
  native_secstruct_ = secstruct;
}

/// @brief set native NatbiasStrandPairPotential
void
NatbiasSecondaryStructureEnergy::set_natbias_spairpot( StrandPairingSetOP const spairset )
{
  using protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential;
  use_sspot_ = true;
  sspot_ = new NatbiasStrandPairPotential( spairset );
}


/// @brief set NatbiasHelixPairPotential
void
NatbiasSecondaryStructureEnergy::set_natbias_hpairpot( HelixPairingSetOP const hpairset )
{
  using protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential;
  use_hhpot_ = true;
  hhpot_ = new NatbiasHelixPairPotential( hpairset );
}

/// @brief set HelicesSheetPotential
void
NatbiasSecondaryStructureEnergy::set_natbias_helices_sheet_pot( HSSTripletSetOP const hss3set )
{
  using protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential;
  use_hspot_ = true;
  hspot_ = new NatbiasHelicesSheetPotential( hss3set );
}


/// @brief set native NatbiasStrandPairPotential
void
NatbiasSecondaryStructureEnergy::set_natbias_spairpot( NatbiasStrandPairPotentialOP const sspot )
{
  use_sspot_ = true;
  sspot_ = sspot;
}

/// @brief set NatbiasHelixPairPotential
void
NatbiasSecondaryStructureEnergy::set_natbias_hpairpot( NatbiasHelixPairPotentialOP const hhpot )
{
  use_hhpot_ = true;
  hhpot_ = hhpot;
}

/// @brief set NatbiasHelicesSheetPotential
void
NatbiasSecondaryStructureEnergy::set_natbias_helices_sheet_pot( NatbiasHelicesSheetPotentialOP const hspot )
{
  use_hspot_ = true;
  hspot_ = hspot;
}

/// @brief set up for scoring
void
NatbiasSecondaryStructureEnergy::setup_for_scoring( Pose & pose, ScoreFunction const & ) const
{
  pose.update_residue_neighbors();
}

/// @brief all scoring happens here
void
NatbiasSecondaryStructureEnergy::finalize_total_energy(
  Pose & pose,
  ScoreFunction const &,
  EnergyMap & totals
) const
{
  using protocols::fldsgn::topology::SS_Info2;
  using protocols::fldsgn::topology::SS_Info2_OP;

  runtime_assert( pose.total_residue() == native_secstruct_.length() );

  Real ss_score( 0.0 ), hh_score( 0.0 ), hs_score( 0.0 );

  SS_Info2_OP ssinfo = new SS_Info2( pose, native_secstruct_ );

  if( use_sspot_ ) sspot_->score( pose, *ssinfo, ss_score );

  if( use_hhpot_ ) hhpot_->score( ssinfo, hh_score );

  if( use_hspot_ ) hspot_->score( ssinfo, hh_score, hs_score );

  // set calculated score
  totals[ core::scoring::natbias_hs ] = hs_score;
  totals[ core::scoring::natbias_ss ] = ss_score;
  totals[ core::scoring::natbias_hh ] = hh_score;

  // TR << "hs_score: " << hs_score << " hh_score: " << hh_score << " ss_score: " << ss_score << std::endl;

}


/// @brief SecondaryStructureEnergy distance cutoff
core::Distance
NatbiasSecondaryStructureEnergy::atomic_interaction_cutoff() const
{
  return 6.0; /// now subtracted off 6.0 from cutoffs in centroid params files
//  return 0.0; /// since all the cutoffs for centroid mode are rolled into the cendist check
}

/// @brief SecondaryStructureEnergy
void
NatbiasSecondaryStructureEnergy::indicate_required_context_graphs( utility::vector1< bool > & /*context_graphs_required*/ ) const
{}

core::Size
NatbiasSecondaryStructureEnergy::version() const
{
  return 1; 
}

} // sspot
} // potentials
} // fldsgn
} // protocols