#include <SmoothEnvPairPotential.hh>

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

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

References aa1, aa2, core::scoring::SmoothScoreTermCoeffs::add_gaussian(), core::scoring::SmoothScoreTermCoeffs::add_sigmoid(), cbeta12_, cbeta6_, cen_dist_cutoff_12_pad, cenpack_, env_, getline(), l, basic::database::open(), pair_, core::scoring::SmoothScoreTermCoeffs::shift(), SIGMOID_SLOPE, tag, and utility_exit_with_message.

Member Function Documentation

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

Referenced by evaluate_env_and_cbeta_deriv(), and evaluate_env_and_cbeta_scores().

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

References core::scoring::SigmoidWeightedCenList< T >::calculated(), cen_dist_cutoff_12_pad, core::graph::Node::const_upper_edge_list_end(), core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), fill_smooth_cenlist(), core::graph::Edge::get_node(), core::graph::Edge::get_second_node_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::SmoothEnvEnergy::setup_for_derivatives(), core::scoring::methods::SmoothEnvEnergy::setup_for_scoring(), and core::scoring::methods::SmoothCenPairEnergy::setup_for_scoring().

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

References core::scoring::SigmoidWeightedCenList< T >::calculated(), cen_dist_cutoff_12_pad, core::graph::Node::const_upper_edge_list_end(), core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), fill_smooth_dcenlist(), core::graph::Edge::get_node(), core::graph::Edge::get_second_node_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::SmoothEnvEnergy::setup_for_derivatives().

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

Referenced by 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::graph::Node::const_edge_list_end(), 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::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::SmoothEnvEnergy::eval_residue_derivatives().

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(), 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(), and core::conformation::Residue::seqpos().

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

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(), aa1, aa2, 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(), core::scoring::pair, pair_, core::conformation::Residue::polymeric_sequence_distance(), and SIGMOID_SLOPE.

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

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(), aa1, aa2, 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(), pair_, core::conformation::Residue::polymeric_sequence_distance(), and SIGMOID_SLOPE.

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

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().

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

Referenced by compute_dcentroid_environment().

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::scoring::methods::SmoothCenPairEnergy::finalize_total_energy(), and core::scoring::methods::SmoothEnvEnergy::finalize_total_energy().

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(), 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::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(), 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().