RamachandranEnergy.cc

Go to the documentation of this file.

// -*- 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/RamachandranEnergy.cc
/// @brief  Ramachandran energy method class implementation
/// @author Phil Bradley
/// @author Andrew Leaver-Fay (aleaverfay@gmail.com)

// Unit Headers
#include <core/scoring/methods/RamachandranEnergy.hh>
#include <core/scoring/methods/RamachandranEnergyCreator.hh>

// Package Headers
#include <core/scoring/Ramachandran.hh>
#include <core/scoring/ScoringManager.hh>
#include <core/scoring/EnergyMap.hh>
#include <core/chemical/VariantType.hh>

// Project headers
#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 scoring {
namespace methods {


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

ScoreTypes
RamachandranEnergyCreator::score_types_for_method() const {
  ScoreTypes sts;
  sts.push_back( rama );
  return sts;
}


/// ctor
RamachandranEnergy::RamachandranEnergy() :
  parent( new RamachandranEnergyCreator ),
  potential_( ScoringManager::get_instance()->get_Ramachandran() )
{}

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

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

///
void
RamachandranEnergy::residue_energy(
  conformation::Residue const & rsd,
  pose::Pose const &,
  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;
  }

  if ( rsd.is_protein() && rsd.aa() <= chemical::num_canonical_aas ) {
    Real rama_score, drama_dphi, drama_dpsi;
    potential_.eval_rama_score_residue( rsd, rama_score, drama_dphi, drama_dpsi );
    emap[ rama ] += rama_score;
    }
}

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

Real
RamachandranEnergy::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,
  ScoreFunction const &, // sfxn,
  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);
  if ( tor_id.valid() && tor_id.type() == id::BB ) {
    //conformation::Residue const & rsd( pose.residue( tor_id.rsd() ) );
    if ( rsd.is_protein() && rsd.aa() != core::chemical::aa_unk && tor_id.torsion() <= 2 ) {
      Real rama_score, drama_dphi, drama_dpsi;
      potential_.eval_rama_score_residue( rsd, rama_score,
        drama_dphi, drama_dpsi );
      deriv = ( tor_id.torsion() == 1 ? drama_dphi : drama_dpsi );
    }
  }
  // note that the atomtree PHI dofs are in radians
  // use degrees since dE/dangle has angle in denominator
  return numeric::conversions::degrees( weights[ rama ] * deriv );

}



Real
RamachandranEnergy::eval_dof_derivative(
  id::DOF_ID const &,// dof_id,
  id::TorsionID const & tor_id,
  pose::Pose const & pose,
  ScoreFunction const &,// sfxn,
  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;
  }

  Real deriv(0.0);
  if ( tor_id.valid() && tor_id.type() == id::BB ) {
    conformation::Residue const & rsd( pose.residue( tor_id.rsd() ) );
    if ( rsd.is_protein() &&
         tor_id.torsion() <= 2 ) {
      Real rama_score, drama_dphi, drama_dpsi;
      potential_.eval_rama_score_residue( rsd, rama_score,
        drama_dphi, drama_dpsi );
      deriv = ( tor_id.torsion() == 1 ? drama_dphi : drama_dpsi );
    }
  }
  // note that the atomtree PHI dofs are in radians
  // use degrees since dE/dangle has angle in denominator
  return numeric::conversions::degrees( weights[ rama ] * deriv );
}

/// @brief Ramachandran Energy is context independent and thus indicates that no context graphs need to
/// be maintained by class Energies
void
RamachandranEnergy::indicate_required_context_graphs(
  utility::vector1< bool > & /*context_graphs_required*/
)
const
{}
core::Size
RamachandranEnergy::version() const
{
  return 1; // Initial versioning
}


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