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core::scoring::CenRotEnvPairPotential Class Reference

#include <CenRotEnvPairPotential.hh>

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

 CenRotEnvPairPotential ()
 
void evaluate_cen_rot_pair_score (conformation::Residue const &rsd1, conformation::Residue const &rsd2, Real const cendist, Real &pair_contribution) const
 pair More...
 
void evaluate_cen_rot_pair_deriv (conformation::Residue const &rsd1, conformation::Residue const &rsd2, Real const cendist, Real &d_pair) const
 
void evaluate_cen_rot_pair_orientation_score (conformation::Residue const &rsd1, conformation::Residue const &rsd2, Real const cendist, Real &ang1_contribution, Real &ang2_contribution, Real &dih_contribution) const
 
void evaluate_cen_rot_pair_orientation_deriv (conformation::Residue const &rsd1, conformation::Residue const &rsd2, Real const cendist, Real const ang, Real &dE_dr, Real &dE_d_ang, Real &dE_d_dih) const
 
void evaluate_cen_rot_env_and_cbeta_score (pose::Pose const &pose, conformation::Residue const &rsd, Real &env_contribution, Real &cbeta6_contribution, Real &cbeta12_contribution) const
 env More...
 
void evaluate_cen_rot_env_and_cbeta_deriv (pose::Pose const &pose, conformation::Residue const &rsd, numeric::xyzVector< Real > &f2_cen_env, numeric::xyzVector< Real > &f2_cen_cb6, numeric::xyzVector< Real > &f2_cen_cb12, numeric::xyzVector< Real > &f2_cb_env, numeric::xyzVector< Real > &f2_cb_cb6, numeric::xyzVector< Real > &f2_cb_cb12) const
 
void compute_centroid_environment (pose::Pose &pose) const
 
void compute_dcentroid_environment (pose::Pose &pose) const
 
void finalize (pose::Pose &pose) 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 &cenvec) const
 

Private Attributes

Real SIGMOID_SLOPE
 
utility::vector1
< utility::vector1
< numeric::interpolation::spline::CubicSpline > > 
pairsplines_
 
utility::vector1
< numeric::interpolation::spline::CubicSpline > 
envsplines_
 
SmoothScoreTermCoeffs cbeta6_
 
SmoothScoreTermCoeffs cbeta12_
 
SmoothScoreTermCoeffs cenpack_
 
utility::vector1
< utility::vector1
< numeric::interpolation::spline::BicubicSpline > > 
angsplines_
 

Constructor & Destructor Documentation

core::scoring::CenRotEnvPairPotential::CenRotEnvPairPotential ( )

Member Function Documentation

SigmoidWeightedCenList< Real > const & core::scoring::CenRotEnvPairPotential::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_cen_rot_env_and_cbeta_deriv(), and evaluate_cen_rot_env_and_cbeta_score().

void core::scoring::CenRotEnvPairPotential::compute_centroid_environment ( pose::Pose pose) const
void core::scoring::CenRotEnvPairPotential::compute_dcentroid_environment ( pose::Pose pose) const
SigmoidWeightedCenList< numeric::xyzVector< Real > > const & core::scoring::CenRotEnvPairPotential::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_cen_rot_env_and_cbeta_deriv().

void core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_env_and_cbeta_deriv ( pose::Pose const &  pose,
conformation::Residue const &  rsd,
numeric::xyzVector< Real > &  f2_cen_env,
numeric::xyzVector< Real > &  f2_cen_cb6,
numeric::xyzVector< Real > &  f2_cen_cb12,
numeric::xyzVector< Real > &  f2_cb_env,
numeric::xyzVector< Real > &  f2_cb_cb6,
numeric::xyzVector< Real > &  f2_cb_cb12 
) const
void core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_env_and_cbeta_score ( pose::Pose const &  pose,
conformation::Residue const &  rsd,
Real env_contribution,
Real cbeta6_contribution,
Real cbeta12_contribution 
) const
void core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_pair_deriv ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
Real const  cendist,
Real d_pair 
) const
void core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_pair_orientation_deriv ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
Real const  cendist,
Real const  ang,
Real dE_dr,
Real dE_d_ang,
Real dE_d_dih 
) const
void core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_pair_orientation_score ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
Real const  cendist,
Real ang1_contribution,
Real ang2_contribution,
Real dih_contribution 
) const
void core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_pair_score ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
Real const  cendist,
Real pair_contribution 
) const
void core::scoring::CenRotEnvPairPotential::fill_smooth_cenlist ( SigmoidWeightedCenList< Real > &  cenlist,
Size const  res1,
Size const  res2,
Real const  cendist 
) const
private
void core::scoring::CenRotEnvPairPotential::fill_smooth_dcenlist ( SigmoidWeightedCenList< numeric::xyzVector< Real > > &  dcenlist,
Size const  res1,
Size const  res2,
numeric::xyzVector< Real > const &  cenvec 
) const
private

References SIGMOID_SLOPE.

Referenced by compute_dcentroid_environment().

void core::scoring::CenRotEnvPairPotential::finalize ( pose::Pose pose) const
SigmoidWeightedCenList< Real > & core::scoring::CenRotEnvPairPotential::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 cenlist 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().

SigmoidWeightedCenList< numeric::xyzVector< Real > > & core::scoring::CenRotEnvPairPotential::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

utility::vector1< utility::vector1< numeric::interpolation::spline::BicubicSpline > > core::scoring::CenRotEnvPairPotential::angsplines_
private
SmoothScoreTermCoeffs core::scoring::CenRotEnvPairPotential::cbeta12_
private
SmoothScoreTermCoeffs core::scoring::CenRotEnvPairPotential::cbeta6_
private
Real core::scoring::CenRotEnvPairPotential::cen_dist_cutoff_12_pad
protected
SmoothScoreTermCoeffs core::scoring::CenRotEnvPairPotential::cenpack_
private

Referenced by CenRotEnvPairPotential().

utility::vector1<numeric::interpolation::spline::CubicSpline> core::scoring::CenRotEnvPairPotential::envsplines_
private
utility::vector1< utility::vector1< numeric::interpolation::spline::CubicSpline > > core::scoring::CenRotEnvPairPotential::pairsplines_
private
Real core::scoring::CenRotEnvPairPotential::SIGMOID_SLOPE
private

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