protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator Class Reference

#include <BuriedUnsatisfiedPolarsCalculator.hh>

Inheritance diagram for protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator:

Collaboration diagram for protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator:

Public Member Functions
	BuriedUnsatisfiedPolarsCalculator (std::string sasa_calc, std::string hbond_calc, core::Real burial_cutoff=basic::options::option[basic::options::OptionKeys::pose_metrics::atomic_burial_cutoff])
	BuriedUnsatisfiedPolarsCalculator (std::string sasa_calc, std::string hbond_calc, std::set< core::Size > const &special_region, core::Real burial_cutoff=basic::options::option[basic::options::OptionKeys::pose_metrics::atomic_burial_cutoff])
core::pose::metrics::PoseMetricCalculatorOP	clone () const
std::string const &	name_of_hbond_calc () const
std::string const &	name_of_sasa_calc () const
Public Member Functions inherited from core::pose::metrics::EnergyDependentCalculator
	EnergyDependentCalculator ()
void	notify_energy_change ()
void	get (std::string const &key, basic::MetricValueBase &val, Pose const &this_pose)
std::string	get (std::string const &key, Pose const &this_pose)
Public Member Functions inherited from core::pose::metrics::PoseMetricCalculator
	PoseMetricCalculator ()
virtual void	notify_structure_change ()

Protected Member Functions
virtual void	lookup (std::string const &key, basic::MetricValueBase *valptr) const
virtual std::string	print (std::string const &key) const
virtual void	recompute (core::pose::Pose const &this_pose)
	this function doesn't actually recompute anything by itself, but calls the More...

Private Member Functions
void	assert_calculators ()

Static Private Member Functions
static core::Size	satisfaction_cutoff (std::string atom_type)

Private Attributes
core::Size	all_bur_unsat_polars_
core::Size	special_region_bur_unsat_polars_
core::id::AtomID_Map< bool >	atom_bur_unsat_
utility::vector1< core::Size >	residue_bur_unsat_polars_
std::string	name_of_hbond_calc_
std::string	name_of_sasa_calc_
core::Real	burial_sasa_cutoff_
std::set< core::Size >	special_region_

Detailed Description

Definition at line 37 of file BuriedUnsatisfiedPolarsCalculator.hh.

Constructor & Destructor Documentation

protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::BuriedUnsatisfiedPolarsCalculator	(	std::string	sasa_calc,
		std::string	hbond_calc,
		core::Real	burial_cutoff = basic::options::option[basic::options::OptionKeys::pose_metrics::atomic_burial_cutoff]
	)

Definition at line 80 of file BuriedUnsatisfiedPolarsCalculator.cc.

References assert_calculators(), atom_bur_unsat_, core::id::AtomID_Map< T >::clear(), residue_bur_unsat_polars_, and special_region_.

Referenced by clone().

protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::BuriedUnsatisfiedPolarsCalculator	(	std::string	sasa_calc,
		std::string	hbond_calc,
		std::set< core::Size > const &	special_region,
		core::Real	burial_cutoff = basic::options::option[basic::options::OptionKeys::pose_metrics::atomic_burial_cutoff]
	)

Definition at line 98 of file BuriedUnsatisfiedPolarsCalculator.cc.

References assert_calculators(), atom_bur_unsat_, core::id::AtomID_Map< T >::clear(), and residue_bur_unsat_polars_.

Member Function Documentation

void protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::assert_calculators ( )

private

Definition at line 117 of file BuriedUnsatisfiedPolarsCalculator.cc.

References name_of_hbond_calc_, name_of_sasa_calc_, and protocols::toolbox::pose_metric_calculators::TR().

Referenced by BuriedUnsatisfiedPolarsCalculator().

core::pose::metrics::PoseMetricCalculatorOP protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::clone ( ) const

inlinevirtual

Implements core::pose::metrics::PoseMetricCalculator.

Definition at line 56 of file BuriedUnsatisfiedPolarsCalculator.hh.

References burial_sasa_cutoff_, BuriedUnsatisfiedPolarsCalculator(), name_of_hbond_calc_, and name_of_sasa_calc_.

void protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::lookup ( std::string const &  key, basic::MetricValueBase *  valptr  ) const

protectedvirtual

Implements core::pose::metrics::EnergyDependentCalculator.

Definition at line 138 of file BuriedUnsatisfiedPolarsCalculator.cc.

References all_bur_unsat_polars_, atom_bur_unsat_, residue_bur_unsat_polars_, and special_region_bur_unsat_polars_.

std::string const& protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::name_of_hbond_calc ( ) const

inline

Definition at line 59 of file BuriedUnsatisfiedPolarsCalculator.hh.

References name_of_hbond_calc_.

Referenced by protocols::dna::PDBOutput::output_buried_unsatisfied_hbonds().

std::string const& protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::name_of_sasa_calc ( ) const

inline

Definition at line 60 of file BuriedUnsatisfiedPolarsCalculator.hh.

References name_of_sasa_calc_.

Referenced by protocols::dna::PDBOutput::output_buried_unsatisfied_hbonds().

std::string protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::print ( std::string const &  key) const

protectedvirtual

Implements core::pose::metrics::EnergyDependentCalculator.

Definition at line 170 of file BuriedUnsatisfiedPolarsCalculator.cc.

References all_bur_unsat_polars_, residue_bur_unsat_polars_, and special_region_bur_unsat_polars_.

void protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::recompute ( core::pose::Pose const &  this_pose)

protectedvirtual

this function doesn't actually recompute anything by itself, but calls the

two member calculators and then processes the information out of the two of them

Implements core::pose::metrics::EnergyDependentCalculator.

Definition at line 194 of file BuriedUnsatisfiedPolarsCalculator.cc.

References all_bur_unsat_polars_, core::io::serialization::at(), atom_bur_unsat_, core::conformation::Residue::atom_type(), core::chemical::ResidueType::atom_type(), core::chemical::ResidueType::attached_H_begin(), core::chemical::ResidueType::attached_H_end(), burial_sasa_cutoff_, core::chemical::AtomType::is_acceptor(), core::chemical::AtomType::is_donor(), core::pose::Pose::metric(), core::conformation::Residue::n_bonded_neighbor_all_res(), core::chemical::AtomType::name(), name_of_hbond_calc_, name_of_sasa_calc_, core::conformation::Residue::nheavyatoms(), core::chemical::ResidueType::number_bonded_hydrogens(), core::pose::Pose::residue(), residue_bur_unsat_polars_, core::id::AtomID_Map< T >::resize(), satisfaction_cutoff(), core::id::AtomID_Map< T >::set(), special_region_, special_region_bur_unsat_polars_, core::pose::Pose::total_residue(), and core::conformation::Residue::type().

core::Size protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::satisfaction_cutoff ( std::string  atom_type)

staticprivate

Definition at line 257 of file BuriedUnsatisfiedPolarsCalculator.cc.

Referenced by recompute().

Member Data Documentation

core::Size protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::all_bur_unsat_polars_

private

Definition at line 77 of file BuriedUnsatisfiedPolarsCalculator.hh.

Referenced by lookup(), print(), and recompute().

core::id::AtomID_Map< bool > protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::atom_bur_unsat_

private

Definition at line 79 of file BuriedUnsatisfiedPolarsCalculator.hh.

Referenced by BuriedUnsatisfiedPolarsCalculator(), lookup(), and recompute().

core::Real protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::burial_sasa_cutoff_

private

Definition at line 84 of file BuriedUnsatisfiedPolarsCalculator.hh.

Referenced by clone(), and recompute().

std::string protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::name_of_hbond_calc_

private

Definition at line 83 of file BuriedUnsatisfiedPolarsCalculator.hh.

Referenced by assert_calculators(), clone(), name_of_hbond_calc(), and recompute().

std::string protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::name_of_sasa_calc_

private

Definition at line 83 of file BuriedUnsatisfiedPolarsCalculator.hh.

Referenced by assert_calculators(), clone(), name_of_sasa_calc(), and recompute().

utility::vector1< core::Size > protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::residue_bur_unsat_polars_

private

Definition at line 80 of file BuriedUnsatisfiedPolarsCalculator.hh.

Referenced by BuriedUnsatisfiedPolarsCalculator(), lookup(), print(), and recompute().

std::set< core::Size > protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::special_region_

private

Definition at line 86 of file BuriedUnsatisfiedPolarsCalculator.hh.

Referenced by BuriedUnsatisfiedPolarsCalculator(), and recompute().

core::Size protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::special_region_bur_unsat_polars_

private

Definition at line 78 of file BuriedUnsatisfiedPolarsCalculator.hh.

Referenced by lookup(), print(), and recompute().

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

• src/protocols/toolbox/pose_metric_calculators/BuriedUnsatisfiedPolarsCalculator.hh
• src/protocols/toolbox/pose_metric_calculators/BuriedUnsatisfiedPolarsCalculator.cc