SmoothCenPairEnergy.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/methods/SmoothCenPairEnergy.cc
/// @brief  Smooth, differentiable, version of cenpair
/// @author Frank DiMaio


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

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

#include <numeric/xyzVector.hh>
// AUTO-REMOVED #include <numeric/xyz.functions.hh>

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

namespace core {
namespace scoring {
namespace methods {

methods::EnergyMethodOP
SmoothCenPairEnergyCreator::create_energy_method(
  methods::EnergyMethodOptions const &
) const {
  return new methods::SmoothCenPairEnergy;
}

/// @brief Return the set of score types claimed by the EnergyMethod
/// this EnergyMethodCreator creates in its create_energy_method() function
ScoreTypes
SmoothCenPairEnergyCreator::score_types_for_method() const {
  ScoreTypes sts;
  sts.push_back( cen_pair_smooth );
  sts.push_back( cenpack_smooth );
  return sts;
}


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


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


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


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


//////////////////////////////////////////////////////////////
//
//     CENTROID PAIR SCORE
//      and
//     "CENTROID PACK" SCORE (helps reproduce pairwise correlations
//                            between centroids, observed in PDB)
//
void
SmoothCenPairEnergy::residue_pair_energy(
  conformation::Residue const & rsd1,
  conformation::Residue const & rsd2,
  pose::Pose const &,
  ScoreFunction const &,
  EnergyMap & emap
) const {
  // ignore scoring residues which have been marked as "REPLONLY" residues (only the repulsive energy will be calculated)
  if ( rsd1.has_variant_type( core::chemical::REPLONLY ) || rsd2.has_variant_type( core::chemical::REPLONLY ) ) return;
  if ( rsd1.aa() > core::chemical::num_canonical_aas || rsd2.aa() > core::chemical::num_canonical_aas ) return;

  /// assumes centroids are being used
  conformation::Atom const & cen1 ( rsd1.atom( rsd1.nbr_atom() ) ), cen2 (rsd2.atom( rsd2.nbr_atom() ) );
  Real const cendist = cen1.xyz().distance_squared( cen2.xyz() );

  /// accumulate total energies
  Real pair_score( 0.0 ), cenpack_score( 0.0 );
  potential_.evaluate_pair_and_cenpack_score( rsd1, rsd2, cendist, pair_score, cenpack_score );

  //fpd I'll just keep these magic constants here
  pair_score *= 2.019f;
  cenpack_score *= 2.0f;

  //fpd Get rid of secstruct weighing
  emap[ cen_pair_smooth ] += pair_score;
  emap[ cenpack_smooth ]  += cenpack_score;
}

void
SmoothCenPairEnergy::eval_residue_pair_derivatives(
    conformation::Residue const & rsd1,
    conformation::Residue const & rsd2,
    ResSingleMinimizationData const &,
    ResSingleMinimizationData const &,
    ResPairMinimizationData const &,
    pose::Pose const &,
    EnergyMap const & weights,
    utility::vector1< DerivVectorPair > & r1_atom_derivs,
    utility::vector1< DerivVectorPair > & r2_atom_derivs
  ) const {
  if ( rsd1.has_variant_type( core::chemical::REPLONLY ) || rsd2.has_variant_type( core::chemical::REPLONLY ) ) return;
  if ( rsd1.aa() > core::chemical::num_canonical_aas || rsd2.aa() > core::chemical::num_canonical_aas ) return;

  Real weight1 = weights[ cen_pair_smooth ];
  Real weight2 = weights[ cenpack_smooth ];

  /// assumes centroids are being used
  conformation::Atom const & cen1 ( rsd1.atom( rsd1.nbr_atom() ) ), cen2 (rsd2.atom( rsd2.nbr_atom() ) );
  Real const cendist = cen1.xyz().distance_squared( cen2.xyz() );
  Real dpair_dr, dcenpack_dr;
  potential_.evaluate_pair_and_cenpack_deriv( rsd1, rsd2, cendist, dpair_dr, dcenpack_dr );

  // again, multiply by magic constants
  dpair_dr *= 2.019f;
  dcenpack_dr *= 2.0f;

  Vector atom_x = rsd1.atom(rsd1.nbr_atom()).xyz();
  Vector atom_y = rsd2.atom(rsd2.nbr_atom()).xyz();

  Vector f1( atom_x.cross( atom_y ) );
  Vector f2( atom_x - atom_y );
  Real const dis( f2.length() );
  dpair_dr /= dis;
  dcenpack_dr /= dis;

  f1 *= (weight1 * dpair_dr + weight2 * dcenpack_dr);
  f2 *= (weight1 * dpair_dr + weight2 * dcenpack_dr);

  r1_atom_derivs[ rsd1.nbr_atom() ].f1() += f1;
  r1_atom_derivs[ rsd1.nbr_atom() ].f2() += f2;
  r2_atom_derivs[ rsd2.nbr_atom() ].f1() -= f1;
  r2_atom_derivs[ rsd2.nbr_atom() ].f2() -= f2;
}


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

/// @brief SmoothCenPairEnergy distance cutoff
Distance
SmoothCenPairEnergy::atomic_interaction_cutoff() const {
  //return 6.0;
  return 7.5;
}

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

}
}
}