#include <HBondSelector.hh>

Inheritance diagram for protocols::residue_selectors::HBondSelector:

Public Member Functions
	HBondSelector ()
	Constructor. More...

	HBondSelector (HBondSelector const &src)

	~HBondSelector () override
	Destructor. More...

core::select::residue_selector::ResidueSelectorOP	clone () const override
	Clone function. More...

core::select::residue_selector::ResidueSubset	apply (core::pose::Pose const &pose) const override
	"Apply" function. More...

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &datamap) override
	XML parse. More...

std::string	get_name () const override
	Get the mover class name. More...

void	set_hbond_energy_cutoff (core::Real input_value)
	Set the threshold for considering something to be a hydrogen bond. More...

core::Real	get_hbond_energy_cutoff () const
	Get the threshold for considering something to be a hydrogen bond. More...

void	set_include_bb_bb (bool const input_setting)
	Set whether backbone-backbone hydrogen bonds are included. More...

bool	get_include_bb_bb () const
	Get whether backbone-backbone hydrogen bonds are included. More...

void	set_scorefxn (core::scoring::ScoreFunctionCOP sfxn_in)
	Set the scorefunction. More...

core::scoring::ScoreFunctionCOP	get_scorefxn () const
	Get the scorefunction. More...

std::string	get_input_set_str () const

void	set_input_set_str (std::string)

core::select::residue_selector::ResidueSelectorCOP	get_input_set_selector () const

void	set_input_set_selector (core::select::residue_selector::ResidueSelectorCOP)

bool	get_input_set_defined () const

bool	get_use_input_set_selector () const

Public Member Functions inherited from core::select::residue_selector::ResidueSelector
	ResidueSelector ()
	Constructor. More...

	~ResidueSelector () override
	Destructor. More...

utility::vector1< core::Size >	selection_positions (core::pose::Pose const &pose) const
	Calls apply and returns the Rosetta numbering corresponding to the selected residues. More...

virtual void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

Static Public Member Functions
static std::string	class_name ()
	Get the mover class name. More...

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
	Provide XSD information, allowing automatic evaluation of bad XML. More...

Private Member Functions
void	compute_input_set (core::pose::Pose const &, std::set< core::Size > &) const

Private Attributes
core::Real	hbond_energy_cutoff_
	The energy cutoff for considering something to be a hydrogen. More...

bool	include_bb_bb_
	Should backbone-backbone hydrogen bonds be included? Default false. More...

core::scoring::ScoreFunctionOP	scorefxn_
	The scorefunction to use for hydrogen bond scoring. More...

core::select::residue_selector::ResidueSelectorCOP	input_set_selector_
	Ways of specifying for which residues we'll be searching for hydrogen bond partners. More...

std::string	input_set_str_

bool	input_set_defined_

bool	use_input_set_selector_

Constructor & Destructor Documentation

◆ HBondSelector() [1/2]

protocols::residue_selectors::HBondSelector::HBondSelector ( )

Constructor.

References input_set_selector_.

◆ HBondSelector() [2/2]

protocols::residue_selectors::HBondSelector::HBondSelector ( HBondSelector const & src )

References get_hbond_energy_cutoff(), get_include_bb_bb(), get_input_set_defined(), get_input_set_selector(), get_input_set_str(), get_scorefxn(), get_use_input_set_selector(), input_set_defined_, set_hbond_energy_cutoff(), set_include_bb_bb(), set_input_set_selector(), set_input_set_str(), set_scorefxn(), and use_input_set_selector_.

◆ ~HBondSelector()

protocols::residue_selectors::HBondSelector::~HBondSelector ( )

overridedefault

Destructor.

Member Function Documentation

◆ apply()

core::select::residue_selector::ResidueSubset protocols::residue_selectors::HBondSelector::apply ( core::pose::Pose const & pose ) const

overridevirtual

"Apply" function.

Given the pose, generate a vector of bools with entries for every residue in the pose indicating whether each residue is selected ("true") or not ("false").

Implements core::select::residue_selector::ResidueSelector.

References core::pose::Pose::clone(), compute_input_set(), core::scoring::hbonds::HBondOptions::decompose_bb_hb_into_pair_energies(), core::scoring::get_score_function(), core::scoring::hbonds::HBondSet::hbond(), core::scoring::hbond, hbond_energy_cutoff_, core::scoring::methods::EnergyMethodOptions::hbond_options(), include_bb_bb_, core::scoring::hbonds::HBondSet::nhbonds(), scorefxn_, core::scoring::hbonds::HBondSet::setup_for_residue_pair_energies(), and core::pose::Pose::total_residue().

◆ class_name()

std::string protocols::residue_selectors::HBondSelector::class_name ( )

static

Get the mover class name.

Static function to return class name; anything else returning the class name should call this function to avoid discrepancies

Referenced by get_name(), protocols::residue_selectors::HBondSelectorCreator::keyname(), and provide_xml_schema().

◆ clone()

core::select::residue_selector::ResidueSelectorOP protocols::residue_selectors::HBondSelector::clone ( ) const

overridevirtual

Clone function.

Copy this object and return owning pointer to the copy (created on the heap).

Implements core::select::residue_selector::ResidueSelector.

◆ compute_input_set()

void protocols::residue_selectors::HBondSelector::compute_input_set	(	core::pose::Pose const &	pose,
		std::set< core::Size > &	input_set
	)		const

private

References core::pose::get_resnum_list(), input_set_selector_, input_set_str_, core::pose::Pose::total_residue(), and use_input_set_selector_.

Referenced by apply().

◆ get_hbond_energy_cutoff()

core::Real protocols::residue_selectors::HBondSelector::get_hbond_energy_cutoff ( ) const

Get the threshold for considering something to be a hydrogen bond.

References hbond_energy_cutoff_.

Referenced by HBondSelector().

◆ get_include_bb_bb()

bool protocols::residue_selectors::HBondSelector::get_include_bb_bb ( ) const

Get whether backbone-backbone hydrogen bonds are included.

References include_bb_bb_.

Referenced by HBondSelector().

◆ get_input_set_defined()

bool protocols::residue_selectors::HBondSelector::get_input_set_defined ( ) const

References input_set_defined_.

Referenced by HBondSelector().

◆ get_input_set_selector()

core::select::residue_selector::ResidueSelectorCOP protocols::residue_selectors::HBondSelector::get_input_set_selector ( ) const

References input_set_selector_.

Referenced by HBondSelector().

◆ get_input_set_str()

std::string protocols::residue_selectors::HBondSelector::get_input_set_str ( ) const

References input_set_str_.

Referenced by HBondSelector().

◆ get_name()

std::string protocols::residue_selectors::HBondSelector::get_name ( ) const

overridevirtual

Get the mover class name.

Non-static function to return class name

Implements core::select::residue_selector::ResidueSelector.

References class_name().

◆ get_scorefxn()

core::scoring::ScoreFunctionCOP protocols::residue_selectors::HBondSelector::get_scorefxn ( ) const

Get the scorefunction.

References scorefxn_.

Referenced by HBondSelector().

◆ get_use_input_set_selector()

bool protocols::residue_selectors::HBondSelector::get_use_input_set_selector ( ) const

References use_input_set_selector_.

Referenced by HBondSelector().

◆ parse_my_tag()

void protocols::residue_selectors::HBondSelector::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	datamap
	)

overridevirtual

XML parse.

Parse RosettaScripts tags and set up this mover.

Reimplemented from core::select::residue_selector::ResidueSelector.

References core::select::residue_selector::get_residue_selector(), hbond_energy_cutoff_, include_bb_bb_, input_set_defined_, input_set_selector_, core::scoring::parse_score_function(), set_input_set_selector(), set_input_set_str(), set_scorefxn(), and use_input_set_selector_.

◆ provide_xml_schema()

void protocols::residue_selectors::HBondSelector::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

Provide XSD information, allowing automatic evaluation of bad XML.

Static function allowing evaluation of XML before parsing

References core::pose::attributes_for_get_resnum_selector(), core::select::residue_selector::attributes_for_parse_residue_selector(), core::scoring::attributes_for_parse_score_function(), class_name(), and core::select::residue_selector::xsd_type_definition_w_attributes_and_optional_subselector().

Referenced by protocols::residue_selectors::HBondSelectorCreator::provide_xml_schema().

◆ set_hbond_energy_cutoff()

void protocols::residue_selectors::HBondSelector::set_hbond_energy_cutoff ( core::Real input_value )

Set the threshold for considering something to be a hydrogen bond.

References hbond_energy_cutoff_.

Referenced by HBondSelector().

◆ set_include_bb_bb()

void protocols::residue_selectors::HBondSelector::set_include_bb_bb ( bool const input_setting )

Set whether backbone-backbone hydrogen bonds are included.

References include_bb_bb_.

Referenced by HBondSelector().

◆ set_input_set_selector()

void protocols::residue_selectors::HBondSelector::set_input_set_selector ( core::select::residue_selector::ResidueSelectorCOP select )

References input_set_defined_, input_set_selector_, and use_input_set_selector_.

Referenced by HBondSelector(), and parse_my_tag().

◆ set_input_set_str()

void protocols::residue_selectors::HBondSelector::set_input_set_str ( std::string input )

References input_set_defined_, input_set_str_, and use_input_set_selector_.

Referenced by HBondSelector(), and parse_my_tag().

◆ set_scorefxn()

void protocols::residue_selectors::HBondSelector::set_scorefxn ( core::scoring::ScoreFunctionCOP sfxn_in )

Set the scorefunction.

Clones the input.

References core::scoring::hbonds::HBondOptions::decompose_bb_hb_into_pair_energies(), core::scoring::methods::EnergyMethodOptions::hbond_options(), and scorefxn_.

Referenced by HBondSelector(), and parse_my_tag().

Member Data Documentation

◆ hbond_energy_cutoff_

core::Real protocols::residue_selectors::HBondSelector::hbond_energy_cutoff_

private

The energy cutoff for considering something to be a hydrogen.

Defaults to -0.5.

Referenced by apply(), get_hbond_energy_cutoff(), parse_my_tag(), and set_hbond_energy_cutoff().

◆ include_bb_bb_

bool protocols::residue_selectors::HBondSelector::include_bb_bb_

private

Should backbone-backbone hydrogen bonds be included? Default false.

Referenced by apply(), get_include_bb_bb(), parse_my_tag(), and set_include_bb_bb().

◆ input_set_defined_

bool protocols::residue_selectors::HBondSelector::input_set_defined_

private

Referenced by get_input_set_defined(), HBondSelector(), parse_my_tag(), set_input_set_selector(), and set_input_set_str().

◆ input_set_selector_

core::select::residue_selector::ResidueSelectorCOP protocols::residue_selectors::HBondSelector::input_set_selector_

private

Ways of specifying for which residues we'll be searching for hydrogen bond partners.

If none are provided, all residues in the pose forming hydrogen bonds will be selected.

Referenced by compute_input_set(), get_input_set_selector(), HBondSelector(), parse_my_tag(), and set_input_set_selector().

◆ input_set_str_

std::string protocols::residue_selectors::HBondSelector::input_set_str_

private

Referenced by compute_input_set(), get_input_set_str(), and set_input_set_str().

◆ scorefxn_

core::scoring::ScoreFunctionOP protocols::residue_selectors::HBondSelector::scorefxn_

mutableprivate

The scorefunction to use for hydrogen bond scoring.

If no scorefunction is provided, then the default scorefunction is used.

Referenced by apply(), get_scorefxn(), and set_scorefxn().

◆ use_input_set_selector_

bool protocols::residue_selectors::HBondSelector::use_input_set_selector_

private

Referenced by compute_input_set(), get_use_input_set_selector(), HBondSelector(), parse_my_tag(), set_input_set_selector(), and set_input_set_str().

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

src/protocols/residue_selectors/HBondSelector.hh
src/protocols/residue_selectors/HBondSelector.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Constructor & Destructor Documentation

◆ HBondSelector() [1/2]

◆ HBondSelector() [2/2]

◆ ~HBondSelector()

Member Function Documentation

◆ apply()

◆ class_name()

◆ clone()

◆ compute_input_set()

◆ get_hbond_energy_cutoff()

◆ get_include_bb_bb()

◆ get_input_set_defined()

◆ get_input_set_selector()

◆ get_input_set_str()

◆ get_name()

◆ get_scorefxn()

◆ get_use_input_set_selector()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ set_hbond_energy_cutoff()

◆ set_include_bb_bb()

◆ set_input_set_selector()

◆ set_input_set_str()

◆ set_scorefxn()

Member Data Documentation

◆ hbond_energy_cutoff_

◆ include_bb_bb_

◆ input_set_defined_

◆ input_set_selector_

◆ input_set_str_

◆ scorefxn_

◆ use_input_set_selector_