core::scoring::CenRotEnvPairPotential Class Reference

#include <CenRotEnvPairPotential.hh>

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

(

)

References aa1, aa2, core::scoring::SmoothScoreTermCoeffs::add_gaussian(), core::scoring::SmoothScoreTermCoeffs::add_sigmoid(), angsplines_, cbeta12_, cbeta6_, cen_dist_cutoff_12_pad, cenpack_, e_Natural, envsplines_, l, basic::database::open(), pairsplines_, core::scoring::SmoothScoreTermCoeffs::shift(), SIGMOID_SLOPE, tag, numeric::interpolation::spline::BicubicSpline::train(), numeric::interpolation::spline::CubicSpline::train(), and utility_exit_with_message.

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(), and basic::datacache::BasicDataCache::get_const_ptr().

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

References core::scoring::SigmoidWeightedCenList< T >::calculated(), cen_dist_cutoff_12_pad, core::graph::Node::const_edge_list_end(), core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), fill_smooth_cenlist(), core::graph::Edge::get_node(), core::graph::Edge::get_other_ind(), core::scoring::SigmoidWeightedCenList< T >::initialize(), numeric::xyzVector< class >::length_squared(), nonconst_cenlist_from_pose(), nres, core::pose::Pose::residue(), core::pose::Pose::total_residue(), and xyz.

Referenced by core::scoring::methods::CenRotEnvEnergy::setup_for_derivatives(), and core::scoring::methods::CenRotEnvEnergy::setup_for_scoring().

void core::scoring::CenRotEnvPairPotential::compute_dcentroid_environment

(

pose::Pose &

pose

)

const

References core::scoring::SigmoidWeightedCenList< T >::calculated(), cen_dist_cutoff_12_pad, core::graph::Node::const_edge_list_end(), core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), fill_smooth_dcenlist(), core::graph::Edge::get_node(), core::graph::Edge::get_other_ind(), core::scoring::SigmoidWeightedCenList< T >::initialize(), numeric::xyzVector< class >::length_squared(), nonconst_cenlist_from_pose(), nonconst_dcenlist_from_pose(), nres, core::pose::Pose::residue(), core::pose::Pose::total_residue(), and xyz.

Referenced by core::scoring::methods::CenRotEnvEnergy::setup_for_derivatives(), and core::scoring::methods::CenRotEnvEnergy::setup_for_scoring().

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(), and basic::datacache::BasicDataCache::get_const_ptr().

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

References core::conformation::Residue::aa(), core::conformation::Residue::atom(), cbeta12_, cbeta6_, cen_dist_cutoff_12_pad, cenlist_from_pose(), core::graph::Node::const_edge_list_end(), dcenlist_from_pose(), core::scoring::SmoothScoreTermCoeffs::dfunc(), core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), envsplines_, core::scoring::SigmoidWeightedCenList< T >::fcen10(), core::scoring::SigmoidWeightedCenList< T >::fcen12(), core::scoring::SigmoidWeightedCenList< T >::fcen6(), core::graph::Edge::get_node(), core::graph::Edge::get_other_ind(), core::conformation::Residue::is_protein(), numeric::xyzVector< class >::length_squared(), core::conformation::Residue::nbr_atom(), core::pose::Pose::residue(), core::conformation::Residue::seqpos(), SIGMOID_SLOPE, and xyz.

Referenced by core::scoring::methods::CenRotEnvEnergy::eval_residue_derivatives().

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

env

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

Referenced by core::scoring::methods::CenRotEnvEnergy::residue_energy().

void core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_pair_deriv	(	conformation::Residue const &	rsd1,
		conformation::Residue const &	rsd2,
		Real const	cendist,
		Real &	d_pair
	)		const

References core::conformation::Residue::aa(), aa1, aa2, pairsplines_, and core::conformation::Residue::polymeric_sequence_distance().

Referenced by core::scoring::methods::CenRotPairEnergy::eval_residue_pair_derivatives().

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

References core::conformation::Residue::aa(), core::chemical::aa_ala, core::chemical::aa_gly, core::chemical::aa_pro, angsplines_, core::conformation::Residue::is_protein(), and core::conformation::Residue::polymeric_sequence_distance().

Referenced by core::scoring::methods::CenRotPairEnergy::eval_residue_pair_derivatives().

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

References core::conformation::Residue::aa(), aa1, aa2, core::chemical::aa_ala, core::chemical::aa_gly, core::chemical::aa_pro, numeric::angle_radians(), angsplines_, core::conformation::Residue::atom(), core::conformation::Residue::is_protein(), core::conformation::Residue::nbr_atom(), core::conformation::Residue::polymeric_sequence_distance(), xyz, and core::conformation::Atom::xyz().

Referenced by core::scoring::methods::CenRotPairEnergy::residue_pair_energy().

void core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_pair_score	(	conformation::Residue const &	rsd1,
		conformation::Residue const &	rsd2,
		Real const	cendist,
		Real &	pair_contribution
	)		const

pair

References core::conformation::Residue::aa(), aa1, aa2, core::conformation::Residue::is_protein(), pairsplines_, and core::conformation::Residue::polymeric_sequence_distance().

Referenced by core::scoring::methods::CenRotPairEnergy::residue_pair_energy().

void core::scoring::CenRotEnvPairPotential::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().

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 numeric::xyzVector< class >::length(), and SIGMOID_SLOPE.

Referenced by compute_dcentroid_environment().

void core::scoring::CenRotEnvPairPotential::finalize

(

pose::Pose &

pose

)

const

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

Referenced by core::scoring::methods::CenRotEnvEnergy::finalize_total_energy().

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(), basic::datacache::BasicDataCache::get_ptr(), basic::datacache::BasicDataCache::has(), basic::datacache::BasicDataCache::set(), 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(), basic::datacache::BasicDataCache::get_ptr(), basic::datacache::BasicDataCache::has(), basic::datacache::BasicDataCache::set(), 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

Referenced by CenRotEnvPairPotential(), evaluate_cen_rot_pair_orientation_deriv(), and evaluate_cen_rot_pair_orientation_score().

SmoothScoreTermCoeffs core::scoring::CenRotEnvPairPotential::cbeta12_

private

Referenced by CenRotEnvPairPotential(), evaluate_cen_rot_env_and_cbeta_deriv(), and evaluate_cen_rot_env_and_cbeta_score().

SmoothScoreTermCoeffs core::scoring::CenRotEnvPairPotential::cbeta6_

private

Referenced by CenRotEnvPairPotential(), evaluate_cen_rot_env_and_cbeta_deriv(), and evaluate_cen_rot_env_and_cbeta_score().

Real core::scoring::CenRotEnvPairPotential::cen_dist_cutoff_12_pad

protected

Referenced by CenRotEnvPairPotential(), compute_centroid_environment(), compute_dcentroid_environment(), and evaluate_cen_rot_env_and_cbeta_deriv().

SmoothScoreTermCoeffs core::scoring::CenRotEnvPairPotential::cenpack_

private

Referenced by CenRotEnvPairPotential().

utility::vector1<numeric::interpolation::spline::CubicSpline> core::scoring::CenRotEnvPairPotential::envsplines_

private

Referenced by CenRotEnvPairPotential(), evaluate_cen_rot_env_and_cbeta_deriv(), and evaluate_cen_rot_env_and_cbeta_score().

utility::vector1< utility::vector1< numeric::interpolation::spline::CubicSpline > > core::scoring::CenRotEnvPairPotential::pairsplines_

private

Referenced by CenRotEnvPairPotential(), evaluate_cen_rot_pair_deriv(), and evaluate_cen_rot_pair_score().

Real core::scoring::CenRotEnvPairPotential::SIGMOID_SLOPE

private

Referenced by CenRotEnvPairPotential(), evaluate_cen_rot_env_and_cbeta_deriv(), fill_smooth_cenlist(), and fill_smooth_dcenlist().

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

• src/core/scoring/CenRotEnvPairPotential.hh
• src/core/scoring/CenRotEnvPairPotential.cc