protocols::simple_pose_metric_calculators::NumberHBondsCalculator Class Reference

#include <NumberHBondsCalculator.hh>

Inheritance diagram for protocols::simple_pose_metric_calculators::NumberHBondsCalculator:

Public Member Functions
	NumberHBondsCalculator ()
	NumberHBondsCalculator (bool const generous, std::set< core::Size > special_region=std::set< core::Size >())
	~NumberHBondsCalculator () override
core::pose::metrics::PoseMetricCalculatorOP	clone () const override
void	set_generous (bool generous)
void	set_special_region (std::set< core::Size > selection)
core::Size	get_total_hbonds ()
std::set< core::Size >	get_special_region ()
utility::vector1< core::Size >	get_residue_hbonds ()
void	set_max_hb_energy (core::Real energy)
void	set_cumul_hbonds (bool cumul_hbonds)
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 ()

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

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
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
bool	use_generous_hbonds_
std::set< core::Size >	special_region_
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_
core::Real	max_hb_energy_
bool	cumul_hbonds_

Constructor & Destructor Documentation

NumberHBondsCalculator() [1/2]

protocols::simple_pose_metric_calculators::NumberHBondsCalculator::NumberHBondsCalculator

(

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NumberHBondsCalculator() [2/2]

protocols::simple_pose_metric_calculators::NumberHBondsCalculator::NumberHBondsCalculator	(	bool const	generous,
		std::set< core::Size >	special_region = std::set< core::Size >()
	)

~NumberHBondsCalculator()

protocols::simple_pose_metric_calculators::NumberHBondsCalculator::~NumberHBondsCalculator ( )

override

Member Function Documentation

clone()

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

inlineoverridevirtual

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

compute_Hbonds_for_residue()

void protocols::simple_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 protocols::simple_pose_metric_calculators::choose_hbond_parameter_set(), core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), core::scoring::hbonds::HBondDatabase::get_database(), core::scoring::hbonds::identify_hbonds_1way(), core::scoring::hbonds::identify_intra_res_hbonds(), core::scoring::hbonds::HBondSet::nhbonds(), core::pose::Pose::residue(), residue_Hbonds_, special_region_, special_region_Hbonds_, core::scoring::Energies::tenA_neighbor_graph(), and use_generous_hbonds_.

Referenced by recompute().

determine_res_to_recompute()

void protocols::simple_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(), core::pose::Pose::size(), special_region_, and core::scoring::total_score.

Referenced by recompute().

get_residue_hbonds()

utility::vector1< core::Size > protocols::simple_pose_metric_calculators::NumberHBondsCalculator::get_residue_hbonds ( )

inline

References residue_Hbonds_.

get_special_region()

std::set< core::Size > protocols::simple_pose_metric_calculators::NumberHBondsCalculator::get_special_region ( )

inline

References special_region_.

get_total_hbonds()

core::Size protocols::simple_pose_metric_calculators::NumberHBondsCalculator::get_total_hbonds ( )

inline

References all_Hbonds_.

lookup()

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

overrideprotectedvirtual

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

References all_Hbonds_, atom_Hbonds_, residue_Hbonds_, and special_region_Hbonds_.

print()

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

overrideprotectedvirtual

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

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

recompute()

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

overrideprotectedvirtual

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(), core::scoring::hbonds::HBondOptions::bb_donor_acceptor_check(), compute_Hbonds_for_residue(), cumul_hbonds_, core::scoring::hbonds::HBondOptions::decompose_bb_hb_into_pair_energies(), determine_res_to_recompute(), core::scoring::hbonds::HBondOptions::exclude_DNA_DNA(), core::scoring::hbonds::HBondOptions::exclude_intra_res_protein(), core::scoring::hbonds::HBondOptions::exclude_intra_res_RNA(), core::scoring::hbonds::HBondOptions::exclude_self_hbonds(), core::scoring::hbonds::HBondSet::hbond_options(), core::chemical::AtomType::is_acceptor(), core::chemical::AtomType::is_donor(), core::scoring::hbonds::HBondOptions::max_hb_energy(), max_hb_energy_, core::conformation::Residue::nheavyatoms(), core::pose::Pose::residue(), residue_Hbonds_, core::id::AtomID_Map< T >::set(), core::pose::Pose::size(), core::conformation::Residue::type(), use_generous_hbonds_, and core::scoring::hbonds::HBondOptions::use_hb_env_dep().

set_cumul_hbonds()

void protocols::simple_pose_metric_calculators::NumberHBondsCalculator::set_cumul_hbonds ( bool  cumul_hbonds )

inline

References cumul_hbonds_.

set_generous()

void protocols::simple_pose_metric_calculators::NumberHBondsCalculator::set_generous ( bool  generous )

inline

References use_generous_hbonds_.

set_max_hb_energy()

void protocols::simple_pose_metric_calculators::NumberHBondsCalculator::set_max_hb_energy ( core::Real  energy )

inline

References protocols::buns::energy, and max_hb_energy_.

set_special_region()

void protocols::simple_pose_metric_calculators::NumberHBondsCalculator::set_special_region ( std::set< core::Size >  selection )

inline

References special_region_.

sum_Hbond_terms()

core::Real protocols::simple_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

all_Hbonds_

core::Size protocols::simple_pose_metric_calculators::NumberHBondsCalculator::all_Hbonds_

private

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

atom_Hbonds_

core::id::AtomID_Map< core::Size > protocols::simple_pose_metric_calculators::NumberHBondsCalculator::atom_Hbonds_

private

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

cumul_hbonds_

bool protocols::simple_pose_metric_calculators::NumberHBondsCalculator::cumul_hbonds_

private

Referenced by recompute(), and set_cumul_hbonds().

max_hb_energy_

core::Real protocols::simple_pose_metric_calculators::NumberHBondsCalculator::max_hb_energy_

private

Referenced by recompute(), and set_max_hb_energy().

ref_residue_total_energies_

utility::vector1< core::Real > protocols::simple_pose_metric_calculators::NumberHBondsCalculator::ref_residue_total_energies_

private

Referenced by determine_res_to_recompute().

residue_Hbonds_

utility::vector1< core::Size > protocols::simple_pose_metric_calculators::NumberHBondsCalculator::residue_Hbonds_

private

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

special_region_

std::set< core::Size > protocols::simple_pose_metric_calculators::NumberHBondsCalculator::special_region_

private

Referenced by compute_Hbonds_for_residue(), determine_res_to_recompute(), get_special_region(), and set_special_region().

special_region_Hbonds_

core::Size protocols::simple_pose_metric_calculators::NumberHBondsCalculator::special_region_Hbonds_

private

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

use_generous_hbonds_

bool protocols::simple_pose_metric_calculators::NumberHBondsCalculator::use_generous_hbonds_

private

Referenced by compute_Hbonds_for_residue(), recompute(), and set_generous().

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

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