SmoothEnvEnergy.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
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/// @file   core/scoring/methods/SmoothEnvEnergy.cc
/// @brief  Smooth, differentiable, version of centroid env
/// @author Frank DiMaio


// Unit headers
// AUTO-REMOVED #include <core/scoring/methods/util.hh>
#include <core/scoring/methods/SmoothEnvEnergy.hh>
#include <core/scoring/methods/SmoothEnvEnergyCreator.hh>

// Package headers
#include <core/scoring/SmoothEnvPairPotential.hh>
#include <core/scoring/ScoringManager.hh>
#include <core/scoring/DerivVectorPair.hh>
#include <core/chemical/VariantType.hh>
// AUTO-REMOVED #include <core/scoring/EnergyGraph.hh>

// Project headers
#include <core/pose/Pose.hh>
// AUTO-REMOVED #include <core/conformation/Conformation.hh>
#include <core/conformation/Residue.hh>

#include <core/kinematics/Jump.hh>
#include <core/scoring/EnergyMap.hh>
#include <utility/vector1.hh>

// Utility headers

// C++

namespace core {
namespace scoring {
namespace methods {


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

ScoreTypes
SmoothEnvEnergyCreator::score_types_for_method() const {
  ScoreTypes sts;
  sts.push_back( cen_env_smooth );
  sts.push_back( cbeta_smooth );
  return sts;
}



/// c-tor
SmoothEnvEnergy::SmoothEnvEnergy() :
  parent( new SmoothEnvEnergyCreator ),
  potential_( ScoringManager::get_instance()->get_SmoothEnvPairPotential() )
{}


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


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


///
void
SmoothEnvEnergy::setup_for_scoring( pose::Pose & pose, ScoreFunction const & ) const {
  // compute interpolated number of neighbors at various distance cutoffs
  pose.update_residue_neighbors();
  potential_.compute_centroid_environment( pose );
}


///////////////////////////////////////
//
// ENV SCORE AND CBETA SCORE
void
SmoothEnvEnergy::residue_energy(
  conformation::Residue const & rsd,
  pose::Pose const & pose,
  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.aa() > core::chemical::num_canonical_aas ) return;

  Real env_score( 0.0 ), cb_score6( 0.0 ), cb_score12( 0.0 ), cb_score( 0.0 );

  potential_.evaluate_env_and_cbeta_scores( pose, rsd, env_score, cb_score6, cb_score12 );

  env_score *= 2.019;
  cb_score = 2.667 * ( cb_score6 + cb_score12 ) * 0.3;

  //fpd get rid of secstruct weighing
  //core::Real rsd_wt = get_residue_weight_by_ss( pose.conformation().secstruct( rsd.seqpos() ) );

  emap[ cen_env_smooth ] += env_score;
  emap[ cbeta_smooth ] += cb_score;
} // residue_energy


void
SmoothEnvEnergy::eval_residue_derivatives(
  conformation::Residue const & rsd,
  ResSingleMinimizationData const &,
  pose::Pose const & pose,
  EnergyMap const & weights,
  utility::vector1< DerivVectorPair > & atom_derivs
) const {
  if ( rsd.has_variant_type( core::chemical::REPLONLY ) ) return;
  if ( rsd.aa() > core::chemical::num_canonical_aas ) return;
  

  Real weight_env = weights[ cen_pair_smooth ];
  Real weight_cbeta = weights[ cenpack_smooth ];

  numeric::xyzVector<Real> d_env_score, d_cb_score6, d_cb_score12, d_cb_score;
  potential_.evaluate_env_and_cbeta_deriv( pose, rsd, d_env_score, d_cb_score6, d_cb_score12);

  // again, multiply by magic constants
  d_env_score *= weight_env * 2.019;
  d_cb_score = weight_cbeta * 2.667 * ( d_cb_score6 + d_cb_score12 ) * 0.3;

  numeric::xyzVector<core::Real> atom_x = rsd.atom( rsd.nbr_atom() ).xyz();

  numeric::xyzVector<core::Real> const f2_env( d_env_score );
  numeric::xyzVector<core::Real> atom_y = -f2_env + atom_x;
  Vector const f1_env( atom_x.cross( atom_y ) );

  numeric::xyzVector<core::Real> const f2_cbeta( d_cb_score );
  atom_y = -f2_cbeta + atom_x;
  Vector const f1_cbeta( atom_x.cross( atom_y ) );

  atom_derivs[ rsd.nbr_atom() ].f1() += f1_env + f1_cbeta;
  atom_derivs[ rsd.nbr_atom() ].f2() += f2_env + f2_cbeta;
}


void
SmoothEnvEnergy::finalize_total_energy(
  pose::Pose & pose,
  ScoreFunction const &,
  EnergyMap &
) const {
  potential_.finalize( pose );
}

core::Size
SmoothEnvEnergy::version() const {
  return 1; // Initial versioning
}

}
}
}