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Public Member Functions | Protected Member Functions | Protected Attributes | Private Member Functions | Private Attributes | List of all members
core::scoring::SmoothEnvPairPotential Class Reference

#include <SmoothEnvPairPotential.hh>

Inheritance diagram for core::scoring::SmoothEnvPairPotential:
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Public Member Functions

 SmoothEnvPairPotential ()
 
void compute_centroid_environment (pose::Pose &pose) const
 
void compute_dcentroid_environment (pose::Pose &pose) const
 
void finalize (pose::Pose &pose) const
 
void evaluate_env_and_cbeta_scores (pose::Pose const &pose, conformation::Residue const &rsd, Real &env_score, Real &cb_score6, Real &cb_score12) const
 
void evaluate_pair_and_cenpack_score (conformation::Residue const &rsd1, conformation::Residue const &rsd2, Real const cendist, Real &pair_contribution, Real &cenpack_contribution) const
 
void evaluate_env_and_cbeta_deriv (pose::Pose const &pose, conformation::Residue const &rsd, numeric::xyzVector< Real > &d_env_score, numeric::xyzVector< Real > &d_cb_score6, numeric::xyzVector< Real > &d_cb_score12) const
 
void evaluate_pair_and_cenpack_deriv (conformation::Residue const &rsd1, conformation::Residue const &rsd2, Real const cendist, Real &d_pair, Real &d_cenpack) const
 

Protected Member Functions

SigmoidWeightedCenList< Real > const & cenlist_from_pose (pose::Pose const &) const
 
SigmoidWeightedCenList< Real > & nonconst_cenlist_from_pose (pose::Pose &) const
 
SigmoidWeightedCenList< numeric::xyzVector< Real > > const & dcenlist_from_pose (pose::Pose const &) const
 
SigmoidWeightedCenList< numeric::xyzVector< Real > > & nonconst_dcenlist_from_pose (pose::Pose &) const
 

Protected Attributes

Real cen_dist_cutoff_12_pad
 

Private Member Functions

void fill_smooth_cenlist (SigmoidWeightedCenList< Real > &cenlist, Size const res1, Size const res2, Real const cendist) const
 
void fill_smooth_dcenlist (SigmoidWeightedCenList< numeric::xyzVector< Real > > &dcenlist, Size const res1, Size const res2, numeric::xyzVector< Real > const &cendist) const
 

Private Attributes

Real SIGMOID_SLOPE
 
SmoothScoreTermCoeffs cbeta6_
 
SmoothScoreTermCoeffs cbeta12_
 
SmoothScoreTermCoeffs cenpack_
 
utility::vector1< SmoothScoreTermCoeffs > env_
 
utility::vector1< utility::vector1< SmoothScoreTermCoeffs > > pair_
 

Constructor & Destructor Documentation

◆ SmoothEnvPairPotential()

core::scoring::SmoothEnvPairPotential::SmoothEnvPairPotential ( )

References core::scoring::SmoothScoreTermCoeffs::add_gaussian(), core::scoring::SmoothScoreTermCoeffs::add_sigmoid(), cbeta12_, cbeta6_, cen_dist_cutoff_12_pad, cenpack_, env_, protocols::mean_field::max(), protocols::mean_field::min(), pair_, core::scoring::SmoothScoreTermCoeffs::shift(), and SIGMOID_SLOPE.

Member Function Documentation

◆ cenlist_from_pose()

SigmoidWeightedCenList< Real > const & core::scoring::SmoothEnvPairPotential::cenlist_from_pose ( pose::Pose const &  pose) const
protected

Pose must already contain a cenlist object or this method will fail.

References core::pose::Pose::data().

Referenced by evaluate_env_and_cbeta_deriv(), and evaluate_env_and_cbeta_scores().

◆ compute_centroid_environment()

void core::scoring::SmoothEnvPairPotential::compute_centroid_environment ( pose::Pose &  pose) const

References core::conformation::Residue::atom(), core::scoring::SigmoidWeightedCenList< T >::calculated(), cen_dist_cutoff_12_pad, core::pose::Pose::conformation(), core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), core::scoring::SigmoidWeightedCenList< T >::fcen10(), core::scoring::SigmoidWeightedCenList< T >::fcen12(), core::scoring::SigmoidWeightedCenList< T >::fcen6(), fill_smooth_cenlist(), core::scoring::SigmoidWeightedCenList< T >::initialize(), core::conformation::Residue::is_protein(), core::pose::symmetry::is_symmetric(), core::conformation::Residue::nbr_atom(), nonconst_cenlist_from_pose(), core::pose::Pose::residue(), core::pose::Pose::size(), and core::conformation::Atom::xyz().

Referenced by core::energy_methods::SmoothEnvEnergy::setup_for_derivatives(), core::energy_methods::SmoothCenPairEnergy::setup_for_scoring(), and core::energy_methods::SmoothEnvEnergy::setup_for_scoring().

◆ compute_dcentroid_environment()

void core::scoring::SmoothEnvPairPotential::compute_dcentroid_environment ( pose::Pose &  pose) const

References core::conformation::Residue::atom(), core::scoring::SigmoidWeightedCenList< T >::calculated(), cen_dist_cutoff_12_pad, core::pose::Pose::conformation(), core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), core::scoring::SigmoidWeightedCenList< T >::fcen10(), core::scoring::SigmoidWeightedCenList< T >::fcen12(), core::scoring::SigmoidWeightedCenList< T >::fcen6(), fill_smooth_dcenlist(), core::scoring::SigmoidWeightedCenList< T >::initialize(), core::conformation::Residue::is_protein(), core::pose::symmetry::is_symmetric(), core::conformation::Residue::nbr_atom(), nonconst_cenlist_from_pose(), nonconst_dcenlist_from_pose(), core::pose::Pose::residue(), core::pose::Pose::size(), and core::conformation::Atom::xyz().

Referenced by core::energy_methods::SmoothEnvEnergy::setup_for_derivatives().

◆ dcenlist_from_pose()

SigmoidWeightedCenList< numeric::xyzVector< Real > > const & core::scoring::SmoothEnvPairPotential::dcenlist_from_pose ( pose::Pose const &  pose) const
protected

Pose must already contain a cenlist object or this method will fail.

References core::pose::Pose::data().

Referenced by evaluate_env_and_cbeta_deriv().

◆ evaluate_env_and_cbeta_deriv()

void core::scoring::SmoothEnvPairPotential::evaluate_env_and_cbeta_deriv ( pose::Pose const &  pose,
conformation::Residue const &  rsd,
numeric::xyzVector< Real > &  d_env_score,
numeric::xyzVector< Real > &  d_cb_score6,
numeric::xyzVector< Real > &  d_cb_score12 
) const

References core::conformation::Residue::aa(), core::conformation::Residue::atom(), cbeta12_, cbeta6_, cen_dist_cutoff_12_pad, cenlist_from_pose(), core::pose::Pose::conformation(), dcenlist_from_pose(), core::scoring::SmoothScoreTermCoeffs::dfunc(), core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), env_, core::scoring::SigmoidWeightedCenList< T >::fcen10(), core::scoring::SigmoidWeightedCenList< T >::fcen12(), core::scoring::SigmoidWeightedCenList< T >::fcen6(), core::conformation::Residue::is_protein(), core::pose::symmetry::is_symmetric(), core::conformation::Residue::nbr_atom(), core::pose::Pose::residue(), core::conformation::Residue::seqpos(), SIGMOID_SLOPE, and core::conformation::Atom::xyz().

Referenced by core::energy_methods::SmoothEnvEnergy::eval_residue_derivatives().

◆ evaluate_env_and_cbeta_scores()

void core::scoring::SmoothEnvPairPotential::evaluate_env_and_cbeta_scores ( pose::Pose const &  pose,
conformation::Residue const &  rsd,
Real &  env_score,
Real &  cb_score6,
Real &  cb_score12 
) const

References core::conformation::Residue::aa(), cbeta12_, cbeta6_, cenlist_from_pose(), core::pose::Pose::conformation(), env_, core::scoring::SigmoidWeightedCenList< T >::fcen10(), core::scoring::SigmoidWeightedCenList< T >::fcen12(), core::scoring::SigmoidWeightedCenList< T >::fcen6(), core::scoring::SmoothScoreTermCoeffs::func(), core::conformation::Residue::is_protein(), core::pose::symmetry::is_symmetric(), and core::conformation::Residue::seqpos().

Referenced by core::energy_methods::SmoothEnvEnergy::residue_energy().

◆ evaluate_pair_and_cenpack_deriv()

void core::scoring::SmoothEnvPairPotential::evaluate_pair_and_cenpack_deriv ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
Real const  cendist,
Real &  d_pair,
Real &  d_cenpack 
) const

References core::conformation::Residue::aa(), core::chemical::aa_cys, cenpack_, core::scoring::SmoothScoreTermCoeffs::dfunc(), core::chemical::DISULFIDE, core::scoring::SmoothScoreTermCoeffs::func(), core::conformation::Residue::has_variant_type(), core::conformation::Residue::is_bonded(), core::conformation::Residue::is_protein(), protocols::mean_field::max(), protocols::mean_field::min(), core::scoring::pair, pair_, core::conformation::Residue::polymeric_sequence_distance(), core::scoring::epr_deer::sigmoid(), and SIGMOID_SLOPE.

Referenced by core::energy_methods::SmoothCenPairEnergy::eval_residue_pair_derivatives().

◆ evaluate_pair_and_cenpack_score()

void core::scoring::SmoothEnvPairPotential::evaluate_pair_and_cenpack_score ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
Real const  cendist,
Real &  pair_contribution,
Real &  cenpack_contribution 
) const

References core::conformation::Residue::aa(), core::chemical::aa_cys, cenpack_, core::chemical::DISULFIDE, core::scoring::SmoothScoreTermCoeffs::func(), core::conformation::Residue::has_variant_type(), core::conformation::Residue::is_bonded(), core::conformation::Residue::is_protein(), protocols::mean_field::max(), protocols::mean_field::min(), pair_, core::conformation::Residue::polymeric_sequence_distance(), and SIGMOID_SLOPE.

Referenced by core::energy_methods::SmoothCenPairEnergy::residue_pair_energy().

◆ fill_smooth_cenlist()

void core::scoring::SmoothEnvPairPotential::fill_smooth_cenlist ( SigmoidWeightedCenList< Real > &  cenlist,
Size const  res1,
Size const  res2,
Real const  cendist 
) const
private

References core::scoring::SigmoidWeightedCenList< T >::fcen10(), core::scoring::SigmoidWeightedCenList< T >::fcen12(), core::scoring::SigmoidWeightedCenList< T >::fcen6(), and SIGMOID_SLOPE.

Referenced by compute_centroid_environment().

◆ fill_smooth_dcenlist()

void core::scoring::SmoothEnvPairPotential::fill_smooth_dcenlist ( SigmoidWeightedCenList< numeric::xyzVector< Real > > &  dcenlist,
Size const  res1,
Size const  res2,
numeric::xyzVector< Real > const &  cendist 
) const
private

References SIGMOID_SLOPE.

Referenced by compute_dcentroid_environment().

◆ finalize()

void core::scoring::SmoothEnvPairPotential::finalize ( pose::Pose &  pose) const

References core::scoring::SigmoidWeightedCenList< T >::calculated(), nonconst_cenlist_from_pose(), and nonconst_dcenlist_from_pose().

Referenced by core::energy_methods::SmoothCenPairEnergy::finalize_total_energy(), and core::energy_methods::SmoothEnvEnergy::finalize_total_energy().

◆ nonconst_cenlist_from_pose()

SigmoidWeightedCenList< Real > & core::scoring::SmoothEnvPairPotential::nonconst_cenlist_from_pose ( pose::Pose &  pose) const
protected

Either returns a non-const reference to the cenlist object already stored in the pose, or creates a new cenist object, places it in the pose, and returns a non-const reference to it.

References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::SIGMOID_WEIGHTED_CEN_LIST.

Referenced by compute_centroid_environment(), compute_dcentroid_environment(), and finalize().

◆ nonconst_dcenlist_from_pose()

SigmoidWeightedCenList< numeric::xyzVector< Real > > & core::scoring::SmoothEnvPairPotential::nonconst_dcenlist_from_pose ( pose::Pose &  pose) const
protected

Either returns a non-const reference to the cenlist object already stored in the pose, or creates a new cenist object, places it in the pose, and returns a non-const reference to it.

References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::SIGMOID_WEIGHTED_D_CEN_LIST.

Referenced by compute_dcentroid_environment(), and finalize().

Member Data Documentation

◆ cbeta12_

SmoothScoreTermCoeffs core::scoring::SmoothEnvPairPotential::cbeta12_
private

Referenced by evaluate_env_and_cbeta_deriv(), evaluate_env_and_cbeta_scores(), and SmoothEnvPairPotential().

◆ cbeta6_

SmoothScoreTermCoeffs core::scoring::SmoothEnvPairPotential::cbeta6_
private

Referenced by evaluate_env_and_cbeta_deriv(), evaluate_env_and_cbeta_scores(), and SmoothEnvPairPotential().

◆ cen_dist_cutoff_12_pad

Real core::scoring::SmoothEnvPairPotential::cen_dist_cutoff_12_pad
protected

Referenced by compute_centroid_environment(), compute_dcentroid_environment(), evaluate_env_and_cbeta_deriv(), and SmoothEnvPairPotential().

◆ cenpack_

SmoothScoreTermCoeffs core::scoring::SmoothEnvPairPotential::cenpack_
private

Referenced by evaluate_pair_and_cenpack_deriv(), evaluate_pair_and_cenpack_score(), and SmoothEnvPairPotential().

◆ env_

utility::vector1< SmoothScoreTermCoeffs > core::scoring::SmoothEnvPairPotential::env_
private

Referenced by evaluate_env_and_cbeta_deriv(), evaluate_env_and_cbeta_scores(), and SmoothEnvPairPotential().

◆ pair_

utility::vector1< utility::vector1< SmoothScoreTermCoeffs > > core::scoring::SmoothEnvPairPotential::pair_
private

Referenced by evaluate_pair_and_cenpack_deriv(), evaluate_pair_and_cenpack_score(), and SmoothEnvPairPotential().

◆ SIGMOID_SLOPE

Real core::scoring::SmoothEnvPairPotential::SIGMOID_SLOPE
private

Referenced by evaluate_env_and_cbeta_deriv(), evaluate_pair_and_cenpack_deriv(), evaluate_pair_and_cenpack_score(), fill_smooth_cenlist(), fill_smooth_dcenlist(), and SmoothEnvPairPotential().

The documentation for this class was generated from the following files:
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