protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator Class Reference

#include <BuriedUnsatisfiedPolarsCalculator.hh>

Inheritance diagram for protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator:

Public Member Functions
	BuriedUnsatisfiedPolarsCalculator (std::string const &sasa_calc, std::string const &hbond_calc, core::Real const burial_cutoff=-1.0, bool const generous=true, bool const legacy=false, bool const vsasa=true)
	default constructor ( keeping this for historical reasons and compatibility with other code that calls this ) More...
	BuriedUnsatisfiedPolarsCalculator (std::string const &sasa_calc, std::string const &hbond_calc, std::set< core::Size > const &special_region, core::Real const burial_cutoff=-1.0, bool const generous=true, bool const legacy=false, bool const vsasa=true)
	default constructor with special_region ( keeping this for historical reasons and compatibility with other code that calls this ) More...
	BuriedUnsatisfiedPolarsCalculator (std::string const &sasa_calc, std::string const &hbond_calc, core::id::AtomID_Map< bool > const &special_region, core::Real const burial_cutoff, core::Real const probe_r, core::Real const residue_surface_cutoff, core::Real const max_hbond_energy, bool const generous, bool const legacy, bool const vsasa, bool const use_sc_neighbors, bool const skip_surface_res)
	constructor where all options must be defined, for calling from code More...
core::pose::metrics::PoseMetricCalculatorOP	clone () const override
	copy constructor implicit in clone call More...
std::string const &	name_of_hbond_calc () const
std::string const &	name_of_sasa_calc () const
void	set_special_region (std::set< core::Size > const &special_region)
void	set_special_region (core::id::AtomID_Map< bool > const &special_region)
Public Member Functions inherited from core::pose::metrics::EnergyDependentCalculator
	EnergyDependentCalculator ()
void	notify_energy_change () override
void	get (std::string const &key, basic::MetricValueBase &val, Pose const &this_pose) override
std::string	get (std::string const &key, Pose const &this_pose) override
Public Member Functions inherited from core::pose::metrics::PoseMetricCalculator
	PoseMetricCalculator ()
virtual void	notify_structure_change ()

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

Private Member Functions
void	calculate_sasa (core::pose::Pose const &pose, core::id::AtomID_Map< core::Real > &atom_sasa, utility::vector1< core::Real > &residue_sasa) const
void	assert_calculators ()

Static Private Member Functions
static core::Size	satisfaction_cutoff (std::string atom_type)
	ONLY USED FOR LEGACY BEHAVIOR (legacy=true), cutoff to determine if unsat. More...

Private Attributes
core::Size	all_bur_unsat_polars_
core::Size	bb_heavy_unsats_
core::Size	all_heavy_unsats_
core::Size	countable_nonheavy_unsats_
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::id::AtomID_Map< bool >	special_region_
bool	special_region_entire_residue_
core::Real	burial_cutoff_
core::Real	probe_radius_
core::Real	residue_surface_cutoff_
core::Real	max_hbond_energy_
bool	generous_hbonds_
bool	legacy_counting_
bool	vsasa_
bool	use_sc_neighbors_
bool	skip_surface_res_

Constructor & Destructor Documentation

protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::BuriedUnsatisfiedPolarsCalculator	(	std::string const &	sasa_calc,
		std::string const &	hbond_calc,
		core::Real const	burial_cutoff = -1.0,
		bool const	generous = true,
		bool const	legacy = false,
		bool const	vsasa = true
	)

default constructor ( keeping this for historical reasons and compatibility with other code that calls this )

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

protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::BuriedUnsatisfiedPolarsCalculator	(	std::string const &	sasa_calc,
		std::string const &	hbond_calc,
		std::set< core::Size > const &	special_region,
		core::Real const	burial_cutoff = -1.0,
		bool const	generous = true,
		bool const	legacy = false,
		bool const	vsasa = true
	)

default constructor with special_region ( keeping this for historical reasons and compatibility with other code that calls this )

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

protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::BuriedUnsatisfiedPolarsCalculator	(	std::string const &	sasa_calc,
		std::string const &	hbond_calc,
		core::id::AtomID_Map< bool > const &	special_region,
		core::Real const	burial_cutoff,
		core::Real const	probe_r,
		core::Real const	residue_surface_cutoff,
		core::Real const	max_hbond_energy,
		bool const	generous,
		bool const	legacy,
		bool const	vsasa,
		bool const	use_sc_neighbors,
		bool const	skip_surface_res
	)

constructor where all options must be defined, for calling from code

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

Member Function Documentation

void protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::assert_calculators ( )

private

References generous_hbonds_, max_hbond_energy_, name_of_hbond_calc_, name_of_sasa_calc_, probe_radius_, protocols::kinmatch::str(), and vsasa_.

Referenced by BuriedUnsatisfiedPolarsCalculator().

void protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::calculate_sasa ( core::pose::Pose const &  pose, core::id::AtomID_Map< core::Real > &  atom_sasa, utility::vector1< core::Real > &  residue_sasa  ) const

private

References core::scoring::calc_per_atom_sasa(), core::id::AtomID_Map< T >::clear(), core::scoring::packing::get_surf_vol(), core::pose::initialize_atomid_map(), core::pose::Pose::metric(), core::id::AtomID_Map< T >::n_atom(), name_of_sasa_calc_, probe_radius_, core::id::AtomID_Map< T >::resize(), core::id::AtomID_Map< T >::size(), and core::scoring::packing::SurfVol::surf.

Referenced by recompute().

core::pose::metrics::PoseMetricCalculatorOP protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::clone ( ) const

inlineoverridevirtual

copy constructor implicit in clone call

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

References burial_cutoff_, generous_hbonds_, legacy_counting_, max_hbond_energy_, name_of_hbond_calc_, name_of_sasa_calc_, probe_radius_, residue_surface_cutoff_, skip_surface_res_, special_region_, use_sc_neighbors_, and vsasa_.

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

overrideprotectedvirtual

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

References all_bur_unsat_polars_, all_heavy_unsats_, atom_bur_unsat_, bb_heavy_unsats_, countable_nonheavy_unsats_, and residue_bur_unsat_polars_.

std::string const& protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::name_of_hbond_calc ( ) const

inline

References name_of_hbond_calc_.

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

std::string const& protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::name_of_sasa_calc ( ) const

inline

References name_of_sasa_calc_.

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

std::string protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::print ( std::string const &  key ) const

overrideprotectedvirtual

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

References all_bur_unsat_polars_, all_heavy_unsats_, bb_heavy_unsats_, countable_nonheavy_unsats_, residue_bur_unsat_polars_, and core::id::to_string().

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

overrideprotectedvirtual

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.

References all_bur_unsat_polars_, all_heavy_unsats_, atom_bur_unsat_, core::conformation::Residue::atom_is_backbone(), core::conformation::Residue::atom_type(), core::chemical::ResidueType::atom_type(), core::chemical::AtomType::atom_type_name(), core::conformation::Residue::atomic_charge(), core::conformation::Residue::attached_H_begin(), core::conformation::Residue::attached_H_end(), bb_heavy_unsats_, burial_cutoff_, calculate_sasa(), core::pose::Pose::conformation(), countable_nonheavy_unsats_, core::id::AtomID_Map< T >::empty(), core::pose::initialize_atomid_map(), core::chemical::AtomType::is_acceptor(), core::chemical::AtomType::is_donor(), legacy_counting_, core::pose::Pose::metric(), core::conformation::Residue::n_bonded_neighbor_all_res(), core::chemical::AtomType::name(), core::conformation::Residue::name1(), name_of_hbond_calc_, core::conformation::Residue::nheavyatoms(), core::chemical::ResidueType::number_bonded_hydrogens(), core::pose::Pose::residue(), residue_bur_unsat_polars_, residue_surface_cutoff_, satisfaction_cutoff(), core::id::AtomID_Map< T >::set(), core::pose::Pose::size(), skip_surface_res_, special_region_, special_region_entire_residue_, core::conformation::Residue::type(), and use_sc_neighbors_.

core::Size protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::satisfaction_cutoff ( std::string  atom_type )

staticprivate

ONLY USED FOR LEGACY BEHAVIOR (legacy=true), cutoff to determine if unsat.

ONLY USED FOR LEGACY BEHAVIOR (legacy=true)

Referenced by recompute().

void protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::set_special_region ( std::set< core::Size > const &  special_region )

inline

References core::id::AtomID_Map< T >::clear(), core::pose::metrics::EnergyDependentCalculator::notify_energy_change(), core::id::AtomID_Map< T >::set(), special_region_, and special_region_entire_residue_.

Referenced by BuriedUnsatisfiedPolarsCalculator().

void protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::set_special_region ( core::id::AtomID_Map< bool > const &  special_region )

inline

References core::pose::metrics::EnergyDependentCalculator::notify_energy_change(), special_region_, and special_region_entire_residue_.

Member Data Documentation

core::Size protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::all_bur_unsat_polars_

private

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

core::Size protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::all_heavy_unsats_

private

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

core::id::AtomID_Map< bool > protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::atom_bur_unsat_

private

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

core::Size protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::bb_heavy_unsats_

private

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

core::Real protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::burial_cutoff_

private

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

core::Size protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::countable_nonheavy_unsats_

private

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

bool protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::generous_hbonds_

private

Referenced by assert_calculators(), and clone().

bool protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::legacy_counting_

private

Referenced by clone(), and recompute().

core::Real protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::max_hbond_energy_

private

Referenced by assert_calculators(), and clone().

std::string protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::name_of_hbond_calc_

private

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

std::string protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::name_of_sasa_calc_

private

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

core::Real protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::probe_radius_

private

Referenced by assert_calculators(), calculate_sasa(), and clone().

utility::vector1< core::Size > protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::residue_bur_unsat_polars_

private

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

core::Real protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::residue_surface_cutoff_

private

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

bool protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::skip_surface_res_

private

Referenced by clone(), and recompute().

core::id::AtomID_Map< bool > protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::special_region_

private

Referenced by BuriedUnsatisfiedPolarsCalculator(), clone(), recompute(), and set_special_region().

bool protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::special_region_entire_residue_

private

Referenced by recompute(), and set_special_region().

bool protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::use_sc_neighbors_

private

Referenced by clone(), and recompute().

bool protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::vsasa_

private

Referenced by assert_calculators(), BuriedUnsatisfiedPolarsCalculator(), and clone().

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

• src/protocols/simple_pose_metric_calculators/BuriedUnsatisfiedPolarsCalculator.hh
• src/protocols/simple_pose_metric_calculators/BuriedUnsatisfiedPolarsCalculator.cc