#include <BuriedUnsatisfiedPolarsCalculator2.hh>

Inheritance diagram for protocols::buns::BuriedUnsatisfiedPolarsCalculator2:

Public Member Functions
	BuriedUnsatisfiedPolarsCalculator2 (std::string const &weak_bunsat_calc_)

	BuriedUnsatisfiedPolarsCalculator2 (std::string const &weak_bunsat_calc, std::set< core::Size > const &special_region)

core::pose::metrics::PoseMetricCalculatorOP	clone () const override

std::string const &	name_of_weak_bunsat_calc () const

void	set_layered_sasa (bool val)

void	set_generous_hbonds (bool val)

void	set_sasa_burial_cutoff (core::Real const &val)

void	set_AHD_cutoff (core::Real const &val)

void	set_dist_cutoff (core::Real const &val)

void	set_hxl_dist_cutoff (core::Real const &val)

void	set_sulph_dist_cutoff (core::Real const &val)

void	set_metal_dist_cutoff (core::Real const &val)

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

Private Member Functions
virtual void	generous_hbond () const

virtual void	bunsats_thorough_check (core::pose::Pose const &pose, core::id::AtomID_Map< bool > &bunsat_thorough_atomid_map)

virtual bool	single_bunsat_thorough_check (core::pose::Pose const &pose, core::id::AtomID const &bunsat_candidate_atom_id)

virtual void	bunsat_donor_nbr_residue_check (core::pose::Pose const &pose, core::id::AtomID const &bunsat_candidate_atom_id, core::conformation::Residue const &bunsat_rsd, numeric::xyzVector< core::Real > const &bunsat_xyz, core::Size const test_resi, core::Size &num_hbonds)

virtual void	bunsat_acc_nbr_residue_check (core::pose::Pose const &pose, core::id::AtomID const &bunsat_candidate_atom_id, core::conformation::Residue const &bunsat_rsd, numeric::xyzVector< core::Real > const &bunsat_xyz, core::Size const &test_resi, core::Size &num_hbonds)

bool	metal_check (core::conformation::Residue const &test_rsd, numeric::xyzVector< core::Real > const &bunsat_xyz, numeric::xyzVector< core::Real > const &test_xyz) const

bool	adjacent_bbbb_check (core::Size const &bunsat_resi, std::string const &bunsat_atom_name, core::Size const &test_resi, std::string const &test_atom_name) const

bool	self_scsc (core::conformation::Residue const &bunsat_rsd, core::Size const &bunsat_resi, core::Size const &bunsat_atom_num, core::conformation::Residue const &test_rsd, core::Size const &test_resi, core::Size const &test_atom_num) const

bool	sulphur_bond_check (core::conformation::Residue const &test_rsd, core::Size const &test_atom_num, numeric::xyzVector< core::Real > const &bunsat_xyz, numeric::xyzVector< core::Real > const &test_xyz) const

bool	don_geom_check (core::pose::Pose const &pose, core::conformation::Residue const &bunsat_rsd, core::Size const &bunsat_atom_num, numeric::xyzVector< core::Real > const &bunsat_xyz, numeric::xyzVector< core::Real > const &test_xyz) const

bool	acc_geom_check (core::pose::Pose const &pose, numeric::xyzVector< core::Real > const &bunsat_xyz, core::conformation::Residue const &test_rsd, core::Size const &test_atom_num, numeric::xyzVector< core::Real > const &test_xyz) const
	return true if bunsat_atom_num in bunsat_rsd as an hbond acceptor to a donor at test_xyz has acceptable hbond geometry, otherwise return false More...

void	assert_calculators ()

void	show ()

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_weak_bunsat_calc_

std::set< core::Size >	special_region_

bool	layered_sasa_

bool	generous_hbonds_

core::Real	sasa_burial_cutoff_

core::Real	AHD_cutoff_

core::Real	dist_cutoff_

core::Real	hxl_dist_cutoff_

core::Real	sulph_dist_cutoff_

core::Real	metal_dist_cutoff_

Constructor & Destructor Documentation

protocols::buns::BuriedUnsatisfiedPolarsCalculator2::BuriedUnsatisfiedPolarsCalculator2 ( std::string const & weak_bunsat_calc_ )

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

protocols::buns::BuriedUnsatisfiedPolarsCalculator2::BuriedUnsatisfiedPolarsCalculator2	(	std::string const &	weak_bunsat_calc,
		std::set< core::Size > const &	special_region
	)

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

Member Function Documentation

bool protocols::buns::BuriedUnsatisfiedPolarsCalculator2::acc_geom_check	(	core::pose::Pose const &	pose,
		numeric::xyzVector< core::Real > const &	bunsat_xyz,
		core::conformation::Residue const &	test_rsd,
		core::Size const &	test_atom_num,
		numeric::xyzVector< core::Real > const &	test_xyz
	)		const

private

return true if bunsat_atom_num in bunsat_rsd as an hbond acceptor to a donor at test_xyz has acceptable hbond geometry, otherwise return false

References AHD_cutoff_, core::conformation::Residue::atom(), core::conformation::Residue::atom_base(), dist_cutoff_, core::conformation::Residue::first_sidechain_atom(), hxl_dist_cutoff_, core::conformation::Residue::name(), core::conformation::Residue::name3(), and core::conformation::Atom::xyz().

Referenced by bunsat_acc_nbr_residue_check().

bool protocols::buns::BuriedUnsatisfiedPolarsCalculator2::adjacent_bbbb_check	(	core::Size const &	bunsat_resi,
		std::string const &	bunsat_atom_name,
		core::Size const &	test_resi,
		std::string const &	test_atom_name
	)		const

private

Referenced by bunsat_acc_nbr_residue_check(), and bunsat_donor_nbr_residue_check().

void protocols::buns::BuriedUnsatisfiedPolarsCalculator2::assert_calculators ( )

private

References core::pose::metrics::CalculatorFactory::Instance(), layered_sasa_, name_of_weak_bunsat_calc_, core::pose::metrics::CalculatorFactory::register_calculator(), sasa_burial_cutoff_, and protocols::buns::TR().

Referenced by BuriedUnsatisfiedPolarsCalculator2().

void protocols::buns::BuriedUnsatisfiedPolarsCalculator2::bunsat_acc_nbr_residue_check	(	core::pose::Pose const &	pose,
		core::id::AtomID const &	bunsat_candidate_atom_id,
		core::conformation::Residue const &	bunsat_rsd,
		numeric::xyzVector< core::Real > const &	bunsat_xyz,
		core::Size const &	test_resi,
		core::Size &	num_hbonds
	)

privatevirtual

References acc_geom_check(), adjacent_bbbb_check(), core::conformation::Residue::atom_name(), core::id::AtomID::atomno(), core::conformation::Residue::Hpos_polar(), metal_check(), core::pose::Pose::residue(), core::id::AtomID::rsd(), self_scsc(), and protocols::buns::TR().

Referenced by single_bunsat_thorough_check().

void protocols::buns::BuriedUnsatisfiedPolarsCalculator2::bunsat_donor_nbr_residue_check	(	core::pose::Pose const &	pose,
		core::id::AtomID const &	bunsat_candidate_atom_id,
		core::conformation::Residue const &	bunsat_rsd,
		numeric::xyzVector< core::Real > const &	bunsat_xyz,
		core::Size const	test_resi,
		core::Size &	num_hbonds
	)

privatevirtual

References core::conformation::Residue::accpt_pos(), adjacent_bbbb_check(), core::conformation::Residue::atom_name(), core::id::AtomID::atomno(), don_geom_check(), core::pose::Pose::residue(), core::id::AtomID::rsd(), self_scsc(), sulphur_bond_check(), and protocols::buns::TR().

Referenced by single_bunsat_thorough_check().

void protocols::buns::BuriedUnsatisfiedPolarsCalculator2::bunsats_thorough_check	(	core::pose::Pose const &	pose,
		core::id::AtomID_Map< bool > &	bunsat_thorough_atomid_map
	)

privatevirtual

References core::id::AtomID_Map< T >::n_atom(), residue_bur_unsat_polars_, core::id::AtomID_Map< T >::set(), single_bunsat_thorough_check(), core::id::AtomID_Map< T >::size(), special_region_, special_region_bur_unsat_polars_, and protocols::buns::TR().

Referenced by recompute().

core::pose::metrics::PoseMetricCalculatorOP protocols::buns::BuriedUnsatisfiedPolarsCalculator2::clone ( ) const

inlineoverridevirtual

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

References name_of_weak_bunsat_calc_.

bool protocols::buns::BuriedUnsatisfiedPolarsCalculator2::don_geom_check	(	core::pose::Pose const &	pose,
		core::conformation::Residue const &	bunsat_rsd,
		core::Size const &	bunsat_atom_num,
		numeric::xyzVector< core::Real > const &	bunsat_xyz,
		numeric::xyzVector< core::Real > const &	test_xyz
	)		const

private

References AHD_cutoff_, core::conformation::Residue::atom(), core::conformation::Residue::attached_H_begin(), core::conformation::Residue::attached_H_end(), core::conformation::Residue::first_sidechain_atom(), hxl_dist_cutoff_, core::conformation::Residue::name(), core::conformation::Residue::name3(), and core::conformation::Atom::xyz().

Referenced by bunsat_donor_nbr_residue_check().

void protocols::buns::BuriedUnsatisfiedPolarsCalculator2::generous_hbond ( ) const

privatevirtual

References core::scoring::get_score_function(), and protocols::buns::TR().

Referenced by recompute().

void protocols::buns::BuriedUnsatisfiedPolarsCalculator2::lookup	(	std::string const &	key,
		basic::MetricValueBase *	valptr
	)		const

overrideprotectedvirtual

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

References all_bur_unsat_polars_, atom_bur_unsat_, residue_bur_unsat_polars_, and special_region_bur_unsat_polars_.

bool protocols::buns::BuriedUnsatisfiedPolarsCalculator2::metal_check	(	core::conformation::Residue const &	test_rsd,
		numeric::xyzVector< core::Real > const &	bunsat_xyz,
		numeric::xyzVector< core::Real > const &	test_xyz
	)		const

private

References metal_dist_cutoff_, and core::conformation::Residue::name().

Referenced by bunsat_acc_nbr_residue_check().

std::string const& protocols::buns::BuriedUnsatisfiedPolarsCalculator2::name_of_weak_bunsat_calc ( ) const

inline

References name_of_weak_bunsat_calc_.

std::string protocols::buns::BuriedUnsatisfiedPolarsCalculator2::print ( std::string const & key ) const

overrideprotectedvirtual

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

References all_bur_unsat_polars_, residue_bur_unsat_polars_, special_region_bur_unsat_polars_, and core::id::to_string().

void protocols::buns::BuriedUnsatisfiedPolarsCalculator2::recompute ( core::pose::Pose const & this_pose )

overrideprotectedvirtual

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

References all_bur_unsat_polars_, atom_bur_unsat_, bunsats_thorough_check(), generous_hbond(), generous_hbonds_, core::pose::Pose::metric(), name_of_weak_bunsat_calc_, residue_bur_unsat_polars_, core::id::AtomID_Map< T >::resize(), show(), core::pose::Pose::size(), special_region_bur_unsat_polars_, and protocols::buns::TR().

core::Size protocols::buns::BuriedUnsatisfiedPolarsCalculator2::satisfaction_cutoff ( std::string atom_type )

staticprivate

Referenced by single_bunsat_thorough_check().

bool protocols::buns::BuriedUnsatisfiedPolarsCalculator2::self_scsc	(	core::conformation::Residue const &	bunsat_rsd,
		core::Size const &	bunsat_resi,
		core::Size const &	bunsat_atom_num,
		core::conformation::Residue const &	test_rsd,
		core::Size const &	test_resi,
		core::Size const &	test_atom_num
	)		const

private

References core::conformation::Residue::first_sidechain_atom().

Referenced by bunsat_acc_nbr_residue_check(), and bunsat_donor_nbr_residue_check().

void protocols::buns::BuriedUnsatisfiedPolarsCalculator2::set_AHD_cutoff ( core::Real const & val )

inline

References AHD_cutoff_, core::pose::metrics::EnergyDependentCalculator::notify_energy_change(), and protocols::hybridization::val.

void protocols::buns::BuriedUnsatisfiedPolarsCalculator2::set_dist_cutoff ( core::Real const & val )

inline

References dist_cutoff_, core::pose::metrics::EnergyDependentCalculator::notify_energy_change(), and protocols::hybridization::val.

void protocols::buns::BuriedUnsatisfiedPolarsCalculator2::set_generous_hbonds ( bool val )

inline

References generous_hbonds_, core::pose::metrics::EnergyDependentCalculator::notify_energy_change(), and protocols::hybridization::val.

void protocols::buns::BuriedUnsatisfiedPolarsCalculator2::set_hxl_dist_cutoff ( core::Real const & val )

inline

References hxl_dist_cutoff_, core::pose::metrics::EnergyDependentCalculator::notify_energy_change(), and protocols::hybridization::val.

void protocols::buns::BuriedUnsatisfiedPolarsCalculator2::set_layered_sasa ( bool val )

inline

References layered_sasa_, core::pose::metrics::EnergyDependentCalculator::notify_energy_change(), and protocols::hybridization::val.

void protocols::buns::BuriedUnsatisfiedPolarsCalculator2::set_metal_dist_cutoff ( core::Real const & val )

inline

References metal_dist_cutoff_, core::pose::metrics::EnergyDependentCalculator::notify_energy_change(), and protocols::hybridization::val.

void protocols::buns::BuriedUnsatisfiedPolarsCalculator2::set_sasa_burial_cutoff ( core::Real const & val )

inline

References core::pose::metrics::EnergyDependentCalculator::notify_energy_change(), sasa_burial_cutoff_, and protocols::hybridization::val.

void protocols::buns::BuriedUnsatisfiedPolarsCalculator2::set_sulph_dist_cutoff ( core::Real const & val )

inline

References core::pose::metrics::EnergyDependentCalculator::notify_energy_change(), sulph_dist_cutoff_, and protocols::hybridization::val.

void protocols::buns::BuriedUnsatisfiedPolarsCalculator2::show ( )

private

References AHD_cutoff_, dist_cutoff_, generous_hbonds_, layered_sasa_, name_of_weak_bunsat_calc_, sasa_burial_cutoff_, and protocols::buns::TR().

Referenced by recompute().

bool protocols::buns::BuriedUnsatisfiedPolarsCalculator2::single_bunsat_thorough_check	(	core::pose::Pose const &	pose,
		core::id::AtomID const &	bunsat_candidate_atom_id
	)

privatevirtual

References all_bur_unsat_polars_, core::id::AtomID::atomno(), bunsat_acc_nbr_residue_check(), bunsat_donor_nbr_residue_check(), core::pose::metrics::StructureDependentCalculator::get(), core::pose::Pose::residue(), core::id::AtomID::rsd(), satisfaction_cutoff(), and protocols::buns::TR().

Referenced by bunsats_thorough_check().

bool protocols::buns::BuriedUnsatisfiedPolarsCalculator2::sulphur_bond_check	(	core::conformation::Residue const &	test_rsd,
		core::Size const &	test_atom_num,
		numeric::xyzVector< core::Real > const &	bunsat_xyz,
		numeric::xyzVector< core::Real > const &	test_xyz
	)		const

private

References core::conformation::Residue::atom_type(), core::chemical::AtomType::element(), and sulph_dist_cutoff_.

Referenced by bunsat_donor_nbr_residue_check().

Member Data Documentation

core::Real protocols::buns::BuriedUnsatisfiedPolarsCalculator2::AHD_cutoff_

private

Referenced by acc_geom_check(), don_geom_check(), set_AHD_cutoff(), and show().

core::Size protocols::buns::BuriedUnsatisfiedPolarsCalculator2::all_bur_unsat_polars_

private

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

core::id::AtomID_Map< bool > protocols::buns::BuriedUnsatisfiedPolarsCalculator2::atom_bur_unsat_

private

Referenced by BuriedUnsatisfiedPolarsCalculator2(), lookup(), and recompute().

core::Real protocols::buns::BuriedUnsatisfiedPolarsCalculator2::dist_cutoff_

private

Referenced by acc_geom_check(), set_dist_cutoff(), and show().

bool protocols::buns::BuriedUnsatisfiedPolarsCalculator2::generous_hbonds_

private

Referenced by recompute(), set_generous_hbonds(), and show().

core::Real protocols::buns::BuriedUnsatisfiedPolarsCalculator2::hxl_dist_cutoff_

private

Referenced by acc_geom_check(), don_geom_check(), and set_hxl_dist_cutoff().

bool protocols::buns::BuriedUnsatisfiedPolarsCalculator2::layered_sasa_

private

Referenced by assert_calculators(), set_layered_sasa(), and show().

core::Real protocols::buns::BuriedUnsatisfiedPolarsCalculator2::metal_dist_cutoff_

private

Referenced by metal_check(), and set_metal_dist_cutoff().

std::string protocols::buns::BuriedUnsatisfiedPolarsCalculator2::name_of_weak_bunsat_calc_

private

Referenced by assert_calculators(), clone(), name_of_weak_bunsat_calc(), recompute(), and show().

utility::vector1< core::Size > protocols::buns::BuriedUnsatisfiedPolarsCalculator2::residue_bur_unsat_polars_

private

Referenced by bunsats_thorough_check(), BuriedUnsatisfiedPolarsCalculator2(), lookup(), print(), and recompute().

core::Real protocols::buns::BuriedUnsatisfiedPolarsCalculator2::sasa_burial_cutoff_

private

Referenced by assert_calculators(), set_sasa_burial_cutoff(), and show().

std::set< core::Size > protocols::buns::BuriedUnsatisfiedPolarsCalculator2::special_region_

private

Referenced by bunsats_thorough_check(), and BuriedUnsatisfiedPolarsCalculator2().

core::Size protocols::buns::BuriedUnsatisfiedPolarsCalculator2::special_region_bur_unsat_polars_

private

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

core::Real protocols::buns::BuriedUnsatisfiedPolarsCalculator2::sulph_dist_cutoff_

private

Referenced by set_sulph_dist_cutoff(), and sulphur_bond_check().

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

src/protocols/buns/BuriedUnsatisfiedPolarsCalculator2.hh
src/protocols/buns/BuriedUnsatisfiedPolarsCalculator2.cc

Public Member Functions

Protected Member Functions

Private Member Functions

Static Private Member Functions

Private Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation