#include <CenRotEnvPairPotential.hh>

Inheritance diagram for core::scoring::CenRotEnvPairPotential:

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 core::scoring::SmoothScoreTermCoeffs::add_gaussian(), core::scoring::SmoothScoreTermCoeffs::add_sigmoid(), angsplines_, cbeta12_, cbeta6_, cen_dist_cutoff_12_pad, cenpack_, envsplines_, pairsplines_, core::scoring::SmoothScoreTermCoeffs::shift(), and SIGMOID_SLOPE.

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

References core::conformation::Residue::atom(), core::scoring::SigmoidWeightedCenList< T >::calculated(), cen_dist_cutoff_12_pad, core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), fill_smooth_cenlist(), core::scoring::SigmoidWeightedCenList< T >::initialize(), nonconst_cenlist_from_pose(), core::pose::Pose::residue(), core::pose::Pose::size(), and protocols::kinmatch::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::conformation::Residue::atom(), core::scoring::SigmoidWeightedCenList< T >::calculated(), cen_dist_cutoff_12_pad, core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), fill_smooth_dcenlist(), core::scoring::SigmoidWeightedCenList< T >::initialize(), nonconst_cenlist_from_pose(), nonconst_dcenlist_from_pose(), core::pose::Pose::residue(), core::pose::Pose::size(), and protocols::kinmatch::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().

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

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(), 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(), core::chemical::aa_ala, core::chemical::aa_gly, core::chemical::aa_pro, angsplines_, core::conformation::Residue::atom(), core::conformation::Residue::is_protein(), core::conformation::Residue::nbr_atom(), core::conformation::Residue::polymeric_sequence_distance(), protocols::kinmatch::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(), 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 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(), 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().