core::scoring::sc::ElectrostaticSimilarityCalculator Class Reference

#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

core::scoring::sc::ElectrostaticSimilarityCalculator::ElectrostaticSimilarityCalculator

(

)

References Reset().

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

default

Member Function Documentation

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().

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().

References core::scoring::sc::MolecularSurfaceCalculator::AddResidue(), core::scoring::sc::ShapeSimilarityCalculator::Calc(), core::conformation::Residue::chain(), core::sequence::end, core::scoring::sc::ElectrostaticSimilarityResults::es_0_p, core::scoring::sc::ElectrostaticSimilarityResults::es_0_s, core::scoring::sc::ElectrostaticSimilarityResults::es_1_p, core::scoring::sc::ElectrostaticSimilarityResults::es_1_s, get_present_atoms(), core::scoring::sc::MolecularSurfaceCalculator::GetDots(), core::pose::initialize_atomid_map(), core::conformation::Residue::is_virtual(), molecule_atoms_, core::conformation::Residue::natoms(), core::scoring::sc::ElectrostaticSimilarityResults::polarity_avg0, core::scoring::sc::ElectrostaticSimilarityResults::polarity_avg1, core::scoring::sc::ElectrostaticSimilarityResults::polarity_mag_avg0, core::scoring::sc::ElectrostaticSimilarityResults::polarity_mag_avg1, prepare_correlation_lists(), protocols::hybridization::r1, protocols::hybridization::r2, reference_pose_, core::pose::Pose::residue(), results_, selector1_, selector2_, core::pose::Pose::size(), core::scoring::PoissonBoltzmannPotential::solve_pb(), core::pose::Pose::split_by_chain(), and core::scoring::TR().

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

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().

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

inline

References results_.

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

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().

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().

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

private

Prepare lists containing the point clouds for correlation analysis.

References core::scoring::PoissonBoltzmannPotential::get_potential().

Referenced by Calc().

void core::scoring::sc::ElectrostaticSimilarityCalculator::reference_pose ( core::pose::PoseCOP  reference_pose )

inline

References reference_pose(), and reference_pose_.

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

void core::scoring::sc::ElectrostaticSimilarityCalculator::Reset

(

)

References core::scoring::sc::ElectrostaticSimilarityResults::es_0_p, core::scoring::sc::ElectrostaticSimilarityResults::es_0_s, core::scoring::sc::ElectrostaticSimilarityResults::es_1_p, core::scoring::sc::ElectrostaticSimilarityResults::es_1_s, molecule_atoms_, core::scoring::sc::ElectrostaticSimilarityResults::polarity_avg0, core::scoring::sc::ElectrostaticSimilarityResults::polarity_avg1, core::scoring::sc::ElectrostaticSimilarityResults::polarity_mag_avg0, core::scoring::sc::ElectrostaticSimilarityResults::polarity_mag_avg1, core::scoring::sc::MolecularSurfaceCalculator::Reset(), results_, and sc_calc_.

Referenced by ElectrostaticSimilarityCalculator().

void core::scoring::sc::ElectrostaticSimilarityCalculator::selector1 ( select::residue_selector::ResidueSelectorCOP  selector1 )

inline

References selector1(), and selector1_.

Referenced by core::simple_metrics::composite_metrics::ElectrostaticSimilarityMetric::calculate(), and selector1().

void core::scoring::sc::ElectrostaticSimilarityCalculator::selector2 ( select::residue_selector::ResidueSelectorCOP  selector2 )

inline

References selector2(), and selector2_.

Referenced by core::simple_metrics::composite_metrics::ElectrostaticSimilarityMetric::calculate(), and selector2().

Member Data Documentation

utility::vector0< id::AtomID_Map<bool> > core::scoring::sc::ElectrostaticSimilarityCalculator::molecule_atoms_

private

Referenced by AddResidue(), Calc(), and Reset().

bool core::scoring::sc::ElectrostaticSimilarityCalculator::partially_solvated_

private

Referenced by get_present_atoms(), Init(), and partially_solvated().

core::pose::PoseCOP core::scoring::sc::ElectrostaticSimilarityCalculator::reference_pose_

private

Referenced by Calc(), Init(), and reference_pose().

ElectrostaticSimilarityResults core::scoring::sc::ElectrostaticSimilarityCalculator::results_

private

Referenced by Calc(), GetResults(), and Reset().

ShapeSimilarityCalculator core::scoring::sc::ElectrostaticSimilarityCalculator::sc_calc_

private

Referenced by AddResidue(), Init(), and Reset().

select::residue_selector::ResidueSelectorCOP core::scoring::sc::ElectrostaticSimilarityCalculator::selector1_

private

Referenced by Calc(), Init(), and selector1().

select::residue_selector::ResidueSelectorCOP core::scoring::sc::ElectrostaticSimilarityCalculator::selector2_

private

Referenced by Calc(), Init(), and selector2().

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

• src/core/scoring/sc/ElectrostaticSimilarityCalculator.hh
• src/core/scoring/sc/ElectrostaticSimilarityCalculator.cc