DunbrackEnergy.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/pack/dunbrack/DunbrackEnergy.cc
/// @brief  Dunbrack energy method implementation
/// @author Andrew Leaver-Fay (aleaverfay@gmail.com)

// Unit headers
#include <core/pack/dunbrack/DunbrackEnergy.hh>
#include <core/pack/dunbrack/DunbrackEnergyCreator.hh>

// Package Headers
#include <core/scoring/EnergyMap.hh>
#include <core/pack/dunbrack/RotamerLibrary.hh>
#include <core/pack/dunbrack/RotamerLibraryScratchSpace.hh>

#include <core/scoring/ScoreType.hh>

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

#include <core/id/TorsionID.hh>

// Utility headers
#include <numeric/conversions.hh>

#include <utility/vector1.hh>



namespace core {
namespace pack {
namespace dunbrack {

using namespace scoring;
using namespace scoring::methods;

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

scoring::ScoreTypes
DunbrackEnergyCreator::score_types_for_method() const {
  ScoreTypes sts;
  sts.push_back( fa_dun );
  sts.push_back( fa_dun_dev );
  sts.push_back( fa_dun_rot );
  sts.push_back( fa_dun_semi );
  return sts;
}



/// ctor
DunbrackEnergy::DunbrackEnergy() :
  parent( new DunbrackEnergyCreator )
{}

DunbrackEnergy::~DunbrackEnergy() {}

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

/////////////////////////////////////////////////////////////////////////////
// methods for ContextIndependentOneBodyEnergies
/////////////////////////////////////////////////////////////////////////////

/// @details Allocate the scratch space object on the stack to
/// alieviate thread-safety concerns.  Scratch does not use new.
void
DunbrackEnergy::residue_energy(
  conformation::Residue const & rsd,
  pose::Pose const &,
  scoring::EnergyMap & emap
) const
{
  // ignore scoring residues which have been marked as "REPLONLY" residues (only the repulsive energy will be calculated)
  if ( rsd.has_variant_type( core::chemical::REPLONLY )){
      return;
  }

  //
  //static boost::detail::atomic_count count_present( 0 );
  //++count_present;
  //std::cout << "D" << count_present << std::flush;

  if ( rsd.is_virtual_residue() ) return;

  /* old    emap[ fa_dun ] = rot_lib_.rotamer_energy( rsd ); */
  pack::dunbrack::SingleResidueRotamerLibraryCAP rotlib = RotamerLibrary::get_instance().get_rsd_library( rsd.type() ) ;
  if ( rotlib ) {
    dunbrack::RotamerLibraryScratchSpace scratch;
    emap[ fa_dun ] += rotlib->rotamer_energy( rsd, scratch );
    emap[ fa_dun_rot ] += scratch.fa_dun_rot();
    emap[ fa_dun_semi ] += scratch.fa_dun_semi();
    emap[ fa_dun_dev  ] += scratch.fa_dun_dev();
  }
  //--count_present;
  //std::cout << "D" << count_present << std::flush;

}

bool DunbrackEnergy::defines_dof_derivatives( pose::Pose const & ) const { return true; }

Real
DunbrackEnergy::eval_residue_dof_derivative(
  conformation::Residue const & rsd,
  ResSingleMinimizationData const & ,//min_data,
  id::DOF_ID const & ,// dof_id,
  id::TorsionID const & tor_id,
  pose::Pose const & ,//pose,
  scoring::ScoreFunction const & ,//sfxn,
  scoring::EnergyMap const & weights
) const
{
  // ignore scoring residues which have been marked as "REPLONLY" residues (only the repulsive energy will be calculated)
  if ( rsd.has_variant_type( core::chemical::REPLONLY )){
      return 0.0;
  }

  Real deriv(0.0);
  Real deriv_dev(0.0);
  Real deriv_rot(0.0);
  Real deriv_semi(0.0);
  if ( tor_id.valid() ) {
    assert( rsd.seqpos() == tor_id.rsd() );
    //utility::vector1< Real > dE_dbb, dE_dchi;
    //    std::cerr << __FILE__<< ' ' << __LINE__ << ' ' << tor_id.rsd() << std::endl;
    pack::dunbrack::SingleResidueRotamerLibraryCAP rotlib =
      RotamerLibrary::get_instance().get_rsd_library( rsd.type() );
    if ( rsd.is_protein() && rotlib ) {
      dunbrack::RotamerLibraryScratchSpace scratch;
      rotlib->rotamer_energy_deriv( rsd, scratch );
      if ( tor_id.type() == id::BB  && tor_id.torsion() <= dunbrack::DUNBRACK_MAX_BBTOR ) {
        deriv = scratch.dE_dbb()[ tor_id.torsion() ];
        deriv_dev = scratch.dE_dbb_dev()[ tor_id.torsion() ];
        deriv_rot = scratch.dE_dbb_rot()[ tor_id.torsion() ];
        deriv_semi = scratch.dE_dbb_semi()[ tor_id.torsion() ];
      } else if ( tor_id.type() == id::CHI && tor_id.torsion() <= dunbrack::DUNBRACK_MAX_SCTOR ) {
        deriv = scratch.dE_dchi()[ tor_id.torsion() ];
        deriv_dev = scratch.dE_dchi_dev()[ tor_id.torsion() ];
        deriv_semi = scratch.dE_dchi_semi()[ tor_id.torsion() ];
      }
    }
  }
  return numeric::conversions::degrees( weights[ fa_dun ] * deriv + weights[ fa_dun_dev ] * deriv_dev + weights[ fa_dun_rot ] * deriv_rot + weights[ fa_dun_semi ] * deriv_semi);
}


///
Real
DunbrackEnergy::eval_dof_derivative(
  id::DOF_ID const &,// dof_id,
  id::TorsionID const & tor_id,
  pose::Pose const & pose,
  scoring::ScoreFunction const &,
  scoring::EnergyMap const & weights
) const
{
  // ignore scoring residues which have been marked as "REPLONLY" residues (only the repulsive energy will be calculated)
  if ( pose.residue( tor_id.rsd() ).has_variant_type( core::chemical::REPLONLY )){
      return 0.0;
  }

  //
  //static boost::detail::atomic_count count_present( 0 );
  //++count_present;
  //std::cout << "dD" << count_present << std::flush;

  Real deriv(0.0);
  Real deriv_dev(0.0);
  Real deriv_rot(0.0);
  Real deriv_semi(0.0);
  if ( tor_id.valid() ) {
    //utility::vector1< Real > dE_dbb, dE_dchi;
    //    std::cerr << __FILE__<< ' ' << __LINE__ << ' ' << tor_id.rsd() << std::endl;
    pack::dunbrack::SingleResidueRotamerLibraryCAP rotlib =
      RotamerLibrary::get_instance().get_rsd_library( pose.residue( tor_id.rsd() ).type() );

    if ( pose.residue( tor_id.rsd() ).is_virtual_residue() ) return 0.0;

    if ( rotlib ) {
      dunbrack::RotamerLibraryScratchSpace scratch;
      rotlib->rotamer_energy_deriv
        ( pose.residue( tor_id.rsd() ), scratch );

      /// ASSUMPTION: Derivatives for amino acids only!
      if ( pose.residue_type( tor_id.rsd() ).is_protein() ) {
        if ( tor_id.type() == id::BB  && tor_id.torsion() <= dunbrack::DUNBRACK_MAX_BBTOR ) {
          deriv = scratch.dE_dbb()[ tor_id.torsion() ];
          deriv_dev = scratch.dE_dbb_dev()[ tor_id.torsion() ];
          deriv_rot = scratch.dE_dbb_rot()[ tor_id.torsion() ];
          deriv_semi = scratch.dE_dbb_semi()[ tor_id.torsion() ];
        } else if ( tor_id.type() == id::CHI && tor_id.torsion() <= dunbrack::DUNBRACK_MAX_SCTOR ) {
          deriv = scratch.dE_dchi()[ tor_id.torsion() ];
          deriv_dev = scratch.dE_dchi_dev()[ tor_id.torsion() ];
          deriv_semi = scratch.dE_dchi_semi()[ tor_id.torsion() ];
        }
      }
    }
  }
  //--count_present;
  //std::cout << "dD" << count_present << std::flush;
  return numeric::conversions::degrees( weights[ fa_dun ] * deriv + weights[ fa_dun_dev ] * deriv_dev + weights[ fa_dun_rot ] * deriv_rot + weights[ fa_dun_semi ] * deriv_semi );
}

/// @brief DunbrackEnergy is context independent; indicates that no context graphs are required
void
DunbrackEnergy::indicate_required_context_graphs(
  utility::vector1< bool > & /*context_graphs_required*/
) const
{}
core::Size
DunbrackEnergy::version() const
{
  return 1; // Initial versioning
}



} // dunbrack
} // pack
} // core