#include <NumberHBondsCalculator.hh>

Inheritance diagram for protocols::toolbox::pose_metric_calculators::NumberHBondsCalculator:

Public Member Functions
	NumberHBondsCalculator ()

	NumberHBondsCalculator (std::set< core::Size > special_region)

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

Static Public Member Functions
static core::Real	sum_Hbond_terms (core::scoring::EnergyMap const &emap)

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)

void	determine_res_to_recompute (core::pose::Pose const &pose, utility::vector1< bool > &res_to_recompute)
	function to figure out which residues to recompute the hydrogen bonds for More...

void	compute_Hbonds_for_residue (core::pose::Pose const &pose, core::Size i, utility::vector1< bool > const &res_to_recompute, core::scoring::hbonds::HBondSet &hb_set)

Private Attributes
core::scoring::hbonds::HBondDatabaseCOP	hb_database

core::Size	all_Hbonds_

core::Size	special_region_Hbonds_

core::id::AtomID_Map< core::Size >	atom_Hbonds_

utility::vector1< core::Size >	residue_Hbonds_

utility::vector1< core::Real >	ref_residue_total_energies_

std::set< core::Size >	special_region_

Constructor & Destructor Documentation

protocols::toolbox::pose_metric_calculators::NumberHBondsCalculator::NumberHBondsCalculator ( )

Referenced by clone().

protocols::toolbox::pose_metric_calculators::NumberHBondsCalculator::NumberHBondsCalculator ( std::set< core::Size > special_region )

Member Function Documentation

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

virtual

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

References NumberHBondsCalculator().

void protocols::toolbox::pose_metric_calculators::NumberHBondsCalculator::compute_Hbonds_for_residue	(	core::pose::Pose const &	pose,
		core::Size	i,
		utility::vector1< bool > const &	res_to_recompute,
		core::scoring::hbonds::HBondSet &	hb_set
	)

protected

References core::graph::Node::const_upper_edge_list_begin(), core::graph::Node::const_upper_edge_list_end(), core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), core::graph::Graph::get_node(), hb_database, core::scoring::hbonds::identify_hbonds_1way(), core::scoring::hbonds::HBondSet::nhbonds(), core::graph::Node::num_neighbors_counting_self(), core::pose::Pose::residue(), residue_Hbonds_, special_region_, special_region_Hbonds_, and core::scoring::Energies::tenA_neighbor_graph().

Referenced by recompute().

void protocols::toolbox::pose_metric_calculators::NumberHBondsCalculator::determine_res_to_recompute	(	core::pose::Pose const &	pose,
		utility::vector1< bool > &	res_to_recompute
	)

protected

function to figure out which residues to recompute the hydrogen bonds for

strategy: for each residue, we check whether the internally cached total energies correspond to the energies found in the pose for that residue. If they do, this means that the number of H-bonds hasn't changed.

References atom_Hbonds_, core::id::AtomID_Map< T >::clear(), core::pose::Pose::energies(), ref_residue_total_energies_, residue_Hbonds_, core::scoring::Energies::residue_total_energies(), core::id::AtomID_Map< T >::resize(), special_region_, core::pose::Pose::total_residue(), and core::scoring::total_score.

Referenced by recompute().

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

protectedvirtual

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

References all_Hbonds_, atom_Hbonds_, residue_Hbonds_, and special_region_Hbonds_.

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

protectedvirtual

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

References all_Hbonds_, residue_Hbonds_, special_region_Hbonds_, and core::id::to_string().

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

protectedvirtual

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

References all_Hbonds_, atom_Hbonds_, core::conformation::Residue::atom_type(), core::chemical::ResidueType::attached_H_begin(), core::chemical::ResidueType::attached_H_end(), compute_Hbonds_for_residue(), determine_res_to_recompute(), core::chemical::AtomType::is_acceptor(), core::chemical::AtomType::is_donor(), core::conformation::Residue::nheavyatoms(), core::pose::Pose::residue(), residue_Hbonds_, core::id::AtomID_Map< T >::set(), core::pose::Pose::total_residue(), and core::conformation::Residue::type().

core::Real protocols::toolbox::pose_metric_calculators::NumberHBondsCalculator::sum_Hbond_terms ( core::scoring::EnergyMap const & emap )

static

References core::scoring::hbond_bb_sc, core::scoring::hbond_lr_bb, core::scoring::hbond_sc, and core::scoring::hbond_sr_bb.

Member Data Documentation

core::Size protocols::toolbox::pose_metric_calculators::NumberHBondsCalculator::all_Hbonds_

private

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

core::id::AtomID_Map< core::Size > protocols::toolbox::pose_metric_calculators::NumberHBondsCalculator::atom_Hbonds_

private

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

core::scoring::hbonds::HBondDatabaseCOP protocols::toolbox::pose_metric_calculators::NumberHBondsCalculator::hb_database

private

Referenced by compute_Hbonds_for_residue().

utility::vector1< core::Real > protocols::toolbox::pose_metric_calculators::NumberHBondsCalculator::ref_residue_total_energies_

private

Referenced by determine_res_to_recompute().

utility::vector1< core::Size > protocols::toolbox::pose_metric_calculators::NumberHBondsCalculator::residue_Hbonds_

private

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

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

private

Referenced by compute_Hbonds_for_residue(), and determine_res_to_recompute().

core::Size protocols::toolbox::pose_metric_calculators::NumberHBondsCalculator::special_region_Hbonds_

private

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

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

src/protocols/toolbox/pose_metric_calculators/NumberHBondsCalculator.hh
src/protocols/toolbox/pose_metric_calculators/NumberHBondsCalculator.cc

Public Member Functions

Static Public Member Functions

Protected Member Functions

Private Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation