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Public Member Functions | Private Member Functions | Private Attributes | List of all members
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< boolget_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 
)
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
ElectrostaticSimilarityResults const& core::scoring::sc::ElectrostaticSimilarityCalculator::GetResults ( )
inline
int core::scoring::sc::ElectrostaticSimilarityCalculator::Init ( )
void core::scoring::sc::ElectrostaticSimilarityCalculator::partially_solvated ( bool  partially_solvated)
inline
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
void core::scoring::sc::ElectrostaticSimilarityCalculator::Reset ( )
void core::scoring::sc::ElectrostaticSimilarityCalculator::selector1 ( select::residue_selector::ResidueSelectorCOP  selector1)
inline
void core::scoring::sc::ElectrostaticSimilarityCalculator::selector2 ( select::residue_selector::ResidueSelectorCOP  selector2)
inline

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
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().


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