core::scoring::sc::ElectrostaticComplementarityCalculator Class Reference

#include <ElectrostaticComplementarityCalculator.hh>

Public Member Functions
	ElectrostaticComplementarityCalculator ()
	~ElectrostaticComplementarityCalculator ()
int	Init (core::pose::Pose const &pose)
void	Reset ()
int	Calc (core::pose::Pose const &pose)
int	Calc (core::pose::Pose const &pose, core::Size jump_id)
core::Size	AddResidue (core::pose::Pose const &pose, int molecule, Size seqpos)
ElectrostaticComplementarityResults const &	GetResults ()
void	ignore_radius (Real ignore_radius)
void	interface_trim_radius (Real interface_trim_radius)
void	partially_solvated (bool partially_solvated)

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
bool	is_within_radius (numeric::xyzVector< Real > xyz, std::vector< const DOT * > const &dots) const
void	get_atoms_within_radius (core::pose::Pose const &pose, id::AtomID_Map< bool > &atoms_within_radius, std::vector< const DOT * > const &dots, id::AtomID_Map< bool > const &molecule1, id::AtomID_Map< bool > const &molecule2) const
	Figure out which atoms are within the radius and part of one of the molecules. More...
std::vector< const DOT * >	trim_dots_to_resl (std::vector< const DOT * > const &dots) const
	Do something similar to k-means to reduce the number of dots. 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

Private Attributes
Real	ignore_radius_
Real	ignore_radius_resolution_
Real	interface_trim_radius_
bool	partially_solvated_
utility::vector0< id::AtomID_Map< bool > >	molecule_atoms_
ShapeComplementarityCalculator	sc_calc_
ElectrostaticComplementarityResults	results_

Constructor & Destructor Documentation

ElectrostaticComplementarityCalculator()

core::scoring::sc::ElectrostaticComplementarityCalculator::ElectrostaticComplementarityCalculator

(

)

References Reset().

~ElectrostaticComplementarityCalculator()

core::scoring::sc::ElectrostaticComplementarityCalculator::~ElectrostaticComplementarityCalculator ( )

default

Member Function Documentation

AddResidue()

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

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 Calc(), and core::simple_metrics::composite_metrics::ElectrostaticComplementarityMetric::setup_from_selectors().

Calc() [1/2]

int core::scoring::sc::ElectrostaticComplementarityCalculator::Calc

(

core::pose::Pose const &

pose

)

References core::scoring::sc::MolecularSurfaceCalculator::band, core::scoring::sc::ShapeComplementarityCalculator::Calc(), core::scoring::sc::ElectrostaticComplementarityResults::ec_0_p, core::scoring::sc::ElectrostaticComplementarityResults::ec_0_s, core::scoring::sc::ElectrostaticComplementarityResults::ec_1_p, core::scoring::sc::ElectrostaticComplementarityResults::ec_1_s, get_atoms_within_radius(), get_present_atoms(), core::scoring::sc::MolecularSurfaceCalculator::GetTrimmedDots(), ignore_radius_, core::pose::initialize_atomid_map(), interface_trim_radius_, molecule_atoms_, core::scoring::sc::ElectrostaticComplementarityResults::polarity_avg0, core::scoring::sc::ElectrostaticComplementarityResults::polarity_avg1, core::scoring::sc::ElectrostaticComplementarityResults::polarity_mag_avg0, core::scoring::sc::ElectrostaticComplementarityResults::polarity_mag_avg1, prepare_correlation_lists(), results_, sc_calc_, core::scoring::sc::MolecularSurfaceCalculator::settings, core::scoring::PoissonBoltzmannPotential::solve_pb(), core::scoring::TR(), and trim_dots_to_resl().

Referenced by Calc(), and core::simple_metrics::composite_metrics::ElectrostaticComplementarityMetric::calculate().

Calc() [2/2]

int core::scoring::sc::ElectrostaticComplementarityCalculator::Calc	(	core::pose::Pose const &	pose,
		core::Size	jump_id
	)

References AddResidue(), Calc(), core::pose::Pose::fold_tree(), molecule_atoms_, core::chemical::ResidueTypeBase::name(), core::pose::Pose::num_jump(), core::kinematics::FoldTree::partition_by_jump(), core::pose::Pose::residue(), core::pose::Pose::size(), core::scoring::TR(), and core::conformation::Residue::type().

get_atoms_within_radius()

void core::scoring::sc::ElectrostaticComplementarityCalculator::get_atoms_within_radius ( core::pose::Pose const &  pose, id::AtomID_Map< bool > &  atoms_within_radius, std::vector< const DOT * > const &  dots, id::AtomID_Map< bool > const &  molecule1, id::AtomID_Map< bool > const &  molecule2  ) const

private

Figure out which atoms are within the radius and part of one of the molecules.

References core::pose::initialize_atomid_map(), is_within_radius(), core::id::AtomID_Map< T >::n_atom(), core::id::AtomID_Map< T >::n_residue(), core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by Calc().

get_present_atoms()

id::AtomID_Map< bool > core::scoring::sc::ElectrostaticComplementarityCalculator::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

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()

ElectrostaticComplementarityResults const& core::scoring::sc::ElectrostaticComplementarityCalculator::GetResults ( )

inline

References results_.

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

ignore_radius()

void core::scoring::sc::ElectrostaticComplementarityCalculator::ignore_radius ( Real  ignore_radius )

inline

References ignore_radius(), and ignore_radius_.

Referenced by core::simple_metrics::composite_metrics::ElectrostaticComplementarityMetric::calculate(), and ignore_radius().

Init()

int core::scoring::sc::ElectrostaticComplementarityCalculator::Init

(

core::pose::Pose const &

pose

)

References core::scoring::sc::ElectrostaticComplementarityDefaults::IGNORE_RADIUS, ignore_radius_, core::scoring::sc::ElectrostaticComplementarityDefaults::IGNORE_RADIUS_RESOLUTION, ignore_radius_resolution_, core::scoring::sc::MolecularSurfaceCalculator::Init(), core::pose::initialize_atomid_map(), core::scoring::sc::ElectrostaticComplementarityDefaults::INTERFACE_TRIM_RADIUS, interface_trim_radius_, molecule_atoms_, core::scoring::sc::ElectrostaticComplementarityDefaults::PARTIALLY_SOLVATED, partially_solvated_, and sc_calc_.

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

interface_trim_radius()

void core::scoring::sc::ElectrostaticComplementarityCalculator::interface_trim_radius ( Real  interface_trim_radius )

inline

References interface_trim_radius(), and interface_trim_radius_.

Referenced by core::simple_metrics::composite_metrics::ElectrostaticComplementarityMetric::calculate(), and interface_trim_radius().

is_within_radius()

bool core::scoring::sc::ElectrostaticComplementarityCalculator::is_within_radius ( numeric::xyzVector< Real >  xyz, std::vector< const DOT * > const &  dots  ) const

private

References ignore_radius_, ignore_radius_resolution_, and protocols::kinmatch::xyz().

Referenced by get_atoms_within_radius().

partially_solvated()

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

inline

References partially_solvated(), and partially_solvated_.

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

prepare_correlation_lists()

void core::scoring::sc::ElectrostaticComplementarityCalculator::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

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

Referenced by Calc().

Reset()

void core::scoring::sc::ElectrostaticComplementarityCalculator::Reset

(

)

References core::scoring::sc::ElectrostaticComplementarityResults::ec_0_p, core::scoring::sc::ElectrostaticComplementarityResults::ec_0_s, core::scoring::sc::ElectrostaticComplementarityResults::ec_1_p, core::scoring::sc::ElectrostaticComplementarityResults::ec_1_s, molecule_atoms_, core::scoring::sc::ElectrostaticComplementarityResults::polarity_avg0, core::scoring::sc::ElectrostaticComplementarityResults::polarity_avg1, core::scoring::sc::ElectrostaticComplementarityResults::polarity_mag_avg0, core::scoring::sc::ElectrostaticComplementarityResults::polarity_mag_avg1, core::scoring::sc::MolecularSurfaceCalculator::Reset(), results_, and sc_calc_.

Referenced by ElectrostaticComplementarityCalculator().

trim_dots_to_resl()

std::vector< const DOT * > core::scoring::sc::ElectrostaticComplementarityCalculator::trim_dots_to_resl ( std::vector< const DOT * > const &  dots ) const

private

Do something similar to k-means to reduce the number of dots.

References ignore_radius_resolution_.

Referenced by Calc().

Member Data Documentation

ignore_radius_

Real core::scoring::sc::ElectrostaticComplementarityCalculator::ignore_radius_

private

Referenced by Calc(), ignore_radius(), Init(), and is_within_radius().

ignore_radius_resolution_

Real core::scoring::sc::ElectrostaticComplementarityCalculator::ignore_radius_resolution_

private

Referenced by Init(), is_within_radius(), and trim_dots_to_resl().

interface_trim_radius_

Real core::scoring::sc::ElectrostaticComplementarityCalculator::interface_trim_radius_

private

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

molecule_atoms_

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

private

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

partially_solvated_

bool core::scoring::sc::ElectrostaticComplementarityCalculator::partially_solvated_

private

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

results_

ElectrostaticComplementarityResults core::scoring::sc::ElectrostaticComplementarityCalculator::results_

private

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

sc_calc_

ShapeComplementarityCalculator core::scoring::sc::ElectrostaticComplementarityCalculator::sc_calc_

private

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

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

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