#include <ElectrostaticSimilarityCalculator.hh>

Public Member Functions
	ElectrostaticSimilarityCalculator ()

	~ElectrostaticSimilarityCalculator ()

int	Init ()

void	Reset ()

int	Calc (core::pose::Pose const &pose)
	Run the ES calculation for previously defined molecules (via AddResidue) More...

core::Size	AddResidue (core::pose::Pose const &pose, int molecule, Size seqpos)
	Add a residue to the molecular surface that is being evaluated. More...

ElectrostaticSimilarityResults const &	GetResults ()

void	partially_solvated (bool partially_solvated)

void	reference_pose (core::pose::PoseCOP reference_pose)

void	selector1 (select::residue_selector::ResidueSelectorCOP selector1)

void	selector2 (select::residue_selector::ResidueSelectorCOP selector2)

Private Member Functions
id::AtomID_Map< bool >	get_present_atoms (core::pose::Pose const &pose, id::AtomID_Map< bool > const &charged_side, id::AtomID_Map< bool > const &uncharged_side, id::AtomID_Map< bool > const &atoms_within_radius) const
	Get atoms of the selected surface patch. More...

void	prepare_correlation_lists (std::vector< const DOT * > const &dots, PoissonBoltzmannPotential const &pb_a, PoissonBoltzmannPotential const &pb_b, utility::vector1< Real > &charges_from_a, utility::vector1< Real > &charges_from_b) const
	Prepare lists containing the point clouds for correlation analysis. More...

Private Attributes
bool	partially_solvated_

utility::vector0< id::AtomID_Map< bool > >	molecule_atoms_

core::pose::PoseCOP	reference_pose_

select::residue_selector::ResidueSelectorCOP	selector1_

select::residue_selector::ResidueSelectorCOP	selector2_

ShapeSimilarityCalculator	sc_calc_

ElectrostaticSimilarityResults	results_

Constructor & Destructor Documentation

◆ ElectrostaticSimilarityCalculator()

core::scoring::sc::ElectrostaticSimilarityCalculator::ElectrostaticSimilarityCalculator ( )

References Reset().

◆ ~ElectrostaticSimilarityCalculator()

core::scoring::sc::ElectrostaticSimilarityCalculator::~ElectrostaticSimilarityCalculator ( )

default

Member Function Documentation

◆ AddResidue()

core::Size core::scoring::sc::ElectrostaticSimilarityCalculator::AddResidue	(	core::pose::Pose const &	pose,
		int	molecule,
		Size	seqpos
	)

Add a residue to the molecular surface that is being evaluated.

References core::scoring::sc::MolecularSurfaceCalculator::AddResidue(), core::conformation::Residue::is_virtual(), molecule_atoms_, core::conformation::Residue::natoms(), core::pose::Pose::residue(), and sc_calc_.

Referenced by core::simple_metrics::composite_metrics::ElectrostaticSimilarityMetric::setup_from_selectors().

◆ Calc()

int core::scoring::sc::ElectrostaticSimilarityCalculator::Calc ( core::pose::Pose const & pose )

Run the ES calculation for previously defined molecules (via AddResidue)

This is a function calcualtes the electrostatic similarity for the given pose in respect to a provided reference pose. Residue selectors for the pose and reference pose are used to specify the evaluated surface. The residues are added with AddResdiue().

Referenced by core::simple_metrics::composite_metrics::ElectrostaticSimilarityMetric::calculate().

◆ get_present_atoms()

id::AtomID_Map< bool > core::scoring::sc::ElectrostaticSimilarityCalculator::get_present_atoms	(	core::pose::Pose const &	pose,
		id::AtomID_Map< bool > const &	charged_side,
		id::AtomID_Map< bool > const &	uncharged_side,
		id::AtomID_Map< bool > const &	atoms_within_radius
	)		const

private

Get atoms of the selected surface patch.

References core::pose::initialize_atomid_map(), core::id::AtomID_Map< T >::n_atom(), core::id::AtomID_Map< T >::n_residue(), and partially_solvated_.

Referenced by Calc().

◆ GetResults()

ElectrostaticSimilarityResults const& core::scoring::sc::ElectrostaticSimilarityCalculator::GetResults ( )

inline

References results_.

Referenced by core::simple_metrics::composite_metrics::ElectrostaticSimilarityMetric::calculate().

◆ Init()

int core::scoring::sc::ElectrostaticSimilarityCalculator::Init ( )

References core::scoring::sc::MolecularSurfaceCalculator::Init(), core::scoring::sc::ElectrostaticSimilarityDefaults::PARTIALLY_SOLVATED, partially_solvated_, reference_pose_, sc_calc_, selector1_, and selector2_.

Referenced by core::simple_metrics::composite_metrics::ElectrostaticSimilarityMetric::calculate().

◆ partially_solvated()

void core::scoring::sc::ElectrostaticSimilarityCalculator::partially_solvated ( bool partially_solvated )

inline

References partially_solvated(), and partially_solvated_.

Referenced by core::simple_metrics::composite_metrics::ElectrostaticSimilarityMetric::calculate(), and partially_solvated().

◆ prepare_correlation_lists()

void core::scoring::sc::ElectrostaticSimilarityCalculator::prepare_correlation_lists	(	std::vector< const DOT * > const &	dots,
		PoissonBoltzmannPotential const &	pb_a,
		PoissonBoltzmannPotential const &	pb_b,
		utility::vector1< Real > &	charges_from_a,
		utility::vector1< Real > &	charges_from_b
	)		const