#include <EnvPairPotential.hh>

Inheritance diagram for core::scoring::EnvPairPotential:

Collaboration diagram for core::scoring::EnvPairPotential:

Public Member Functions
	EnvPairPotential ()

void	compute_centroid_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

Protected Member Functions
CenListInfo const &	cenlist_from_pose (pose::Pose const &) const

CenListInfo &	nonconst_cenlist_from_pose (pose::Pose &) const

Protected Attributes
Real const	cen_dist_cutoff2

Private Member Functions
void	fill_cenlist (CenListInfo &cenlist, Size const res1, Size const res2, Real const cendist) const
	fill the cenlist using interpolation More...

void	truncate_cenlist_values (CenListInfo &cenlist) const

Private Attributes
ObjexxFCL::FArray2D< Real >	env_log_

ObjexxFCL::FArray1D< Real >	cbeta_den6_

ObjexxFCL::FArray1D< Real >	cbeta_den12_

ObjexxFCL::FArray3D< Real >	pair_log_

ObjexxFCL::FArray1D< Real >	cenpack_log_

Real const	cen_dist6sqr_

Real const	cen_dist10sqr_

Real const	cen_dist12sqr_

Real const	cen_dist5_pad

Real const	cen_dist6_pad

Real const	cen_dist7_pad

Real const	cen_dist10_pad

Real const	cen_dist12_pad

Real const	cen_dist5_pad_plus

Real const	cen_dist6_pad_plus

Real const	cen_dist7_pad_plus

Real const	cen_dist10_pad_plus

Real const	cen_dist12_pad_plus

Real const	cen_dist5_pad_minus

Real const	cen_dist7_pad_minus

Real const	cen_dist10_pad_minus

Real const	cen_dist12_pad_minus

Real const	cen_dist5_pad_hinv

Real const	cen_dist6_pad_hinv

Real const	cen_dist7_pad_hinv

Real const	cen_dist10_pad_hinv

Real const	cen_dist12_pad_hinv

Real const	cen_dist_cutoff_12_pad

Detailed Description

Definition at line 147 of file EnvPairPotential.hh.

Constructor & Destructor Documentation

core::scoring::EnvPairPotential::EnvPairPotential ( )

Definition at line 73 of file EnvPairPotential.cc.

References cbeta_den12_, cbeta_den6_, cenpack_log_, env_log_, and pair_log_.

Member Function Documentation

CenListInfo const & core::scoring::EnvPairPotential::cenlist_from_pose ( pose::Pose const & pose) const

protected

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

Definition at line 505 of file EnvPairPotential.cc.

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

Referenced by core::scoring::MembranePotential::evaluate_cbeta(), core::scoring::MembranePotential::evaluate_env(), evaluate_env_and_cbeta_scores(), and protocols::scoring::InterchainPotential::evaluate_env_score().

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

Definition at line 301 of file EnvPairPotential.cc.

References core::scoring::CenListInfo::calculated(), cen_dist_cutoff_12_pad, core::graph::Node::const_upper_edge_list_end(), core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), fill_cenlist(), core::graph::Edge::get_node(), core::graph::Edge::get_second_node_ind(), core::scoring::CenListInfo::initialize(), nonconst_cenlist_from_pose(), core::pose::Pose::residue(), core::scoring::EnergyEdge::square_distance(), and truncate_cenlist_values().

Referenced by protocols::scoring::methods::InterchainPairEnergy::setup_for_scoring(), protocols::scoring::methods::InterchainEnvEnergy::setup_for_scoring(), core::scoring::methods::EnvEnergy::setup_for_scoring(), core::scoring::methods::MembraneCenPairEnergy::setup_for_scoring(), core::scoring::methods::CenPairEnergy::setup_for_scoring(), core::scoring::methods::MembraneCbetaEnergy::setup_for_scoring(), core::scoring::methods::MembraneLipo::setup_for_scoring(), and core::scoring::methods::MembraneEnvEnergy::setup_for_scoring().

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

Definition at line 358 of file EnvPairPotential.cc.

References core::conformation::Residue::aa(), cbeta_den12_, cbeta_den6_, cenlist_from_pose(), env_log_, core::scoring::CenListInfo::fcen10(), core::scoring::CenListInfo::fcen12(), core::scoring::CenListInfo::fcen6(), core::conformation::Residue::is_protein(), and core::conformation::Residue::seqpos().

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

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

void core::scoring::EnvPairPotential::fill_cenlist	(	CenListInfo &	cenlist,
		Size const	res1,
		Size const	res2,
		Real const	cendist
	)		const

private

fill the cenlist using interpolation

Detailed:: cems-----------------------------------------------------------------------— interpolation notes –Historically we have broken the centroid density statistics into three bins: i) pairs less than 6 angstroms ii) pairs less than 10 angstroms ems iii) and pairs between 6 and 12 angstroms the resulting abruptness in the scoring functions due to the arbitrary radius cutoffs has caused some problems during gradient minimization. therefore this was replaced with an interpolated binning schema as follows: When a pairwise distance lies within "+/- dr" of the bin boundary (6,10,12) then partial credit is given to the enclosing bins. So for example, if fgap=0.5 angstroms, and a pair radius were 6.4 angstroms, then a fractional count is given to BOTH the "less-than-6" bin AND to the "between-6-and-10" bin. The sum of these fractions always adds to one. So that we dont have to re-do the statistics we currently use we want to keep "fgap" small. ideally fgap should be large compared to the search algorithm step size, and larger than the expected roundoff error in any refold operation, and otherwise as small as possible. Also we want to cleverly choose the interpolation function so that the average number of counts getting into the bins is the same as under the old schema. As long as dr is small then we can use either r+/-fgap or alternatively r^2+/-fgap^2 and this will be approximately satsified. since the squared from is easier to work we will use this. in the code below the frag^2 term is called a _pad, and we allow for different pad_sizes on the three radii. cems-----------------------------------------------------------------------—

Definition at line 227 of file EnvPairPotential.cc.

References cen_dist10_pad_hinv, cen_dist10_pad_plus, cen_dist12_pad_hinv, cen_dist12_pad_plus, cen_dist6_pad_hinv, cen_dist6_pad_plus, core::scoring::CenListInfo::fcen10(), core::scoring::CenListInfo::fcen12(), and core::scoring::CenListInfo::fcen6().

Referenced by compute_centroid_environment().

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

Definition at line 350 of file EnvPairPotential.cc.

References core::scoring::CenListInfo::calculated(), and nonconst_cenlist_from_pose().

Referenced by core::scoring::methods::EnvEnergy::finalize_total_energy(), and core::scoring::methods::CenPairEnergy::finalize_total_energy().

CenListInfo & core::scoring::EnvPairPotential::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.

Definition at line 516 of file EnvPairPotential.cc.

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

Referenced by compute_centroid_environment(), core::scoring::MembranePotential::compute_membrane_embedding(), protocols::scoring::InterchainPotential::finalize(), finalize(), core::scoring::MembranePotential::finalize(), and core::scoring::Membrane_FAPotential::finalize().