The BondedResidueSelector selects residues that are connected to some set of residues (input_set) by a chemical bond. The input_set can be directly set using a set of residue positions or by a ResidueSelector. More...

#include <BondedResidueSelector.hh>

Inheritance diagram for core::select::residue_selector::BondedResidueSelector:

[legend]

Public Member Functions
	BondedResidueSelector ()

	BondedResidueSelector (std::set< core::Size > const &input_set)

	BondedResidueSelector (BondedResidueSelector const &other)

	~BondedResidueSelector () override

ResidueSelectorOP	clone () const override
	Clone operator. More...

ResidueSubset	apply (core::pose::Pose const &pose) const override
	Return a ResidueSubset indicating a selection of Residues from the input Pose; the ResidueSubset is an array of booleans where a value of "true" for position i indicates that residue i is a part of the selected subset – and a value of "false" would indicate that it is not. More...

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &datacache) override
	Initialize any data members of this instance from an input tag and a DataMap object. More...

std::string	get_name () const override

void	set_input_set (std::set< core::Size > const &input_set)
	adds a ResidueSelector More...

void	set_input_set (std::string const &input_set_str)

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

std::set< core::Size >	input_set () const

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

std::string	input_set_string () const

bool	input_set_defined () const

bool	input_set_selector_defined () 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 ()

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

Private Member Functions
void	get_input_set (core::pose::Pose const &, ResidueSubset &, std::set< core::Size > &) const
	Sets subset to be true for values contained in input_set. More...

Private Attributes
std::set< core::Size >	input_set_

std::string	input_set_str_

core::select::residue_selector::ResidueSelectorCOP	input_set_selector_

bool	input_set_defined_

bool	use_input_set_selector_

Detailed Description

The BondedResidueSelector selects residues that are connected to some set of residues (input_set) by a chemical bond. The input_set can be directly set using a set of residue positions or by a ResidueSelector.

Residues in the input_set are included in the final selection.

Constructor & Destructor Documentation

◆ BondedResidueSelector() [1/3]

core::select::residue_selector::BondedResidueSelector::BondedResidueSelector ( )

Referenced by clone().

◆ BondedResidueSelector() [2/3]

core::select::residue_selector::BondedResidueSelector::BondedResidueSelector ( std::set< core::Size > const & input_set )

References input_set(), and set_input_set().

◆ BondedResidueSelector() [3/3]

core::select::residue_selector::BondedResidueSelector::BondedResidueSelector ( BondedResidueSelector const & other )

References input_set(), input_set_defined(), input_set_defined_, input_set_selector(), input_set_selector_, input_set_selector_defined(), input_set_str_, input_set_string(), set_input_set(), and use_input_set_selector_.

◆ ~BondedResidueSelector()

core::select::residue_selector::BondedResidueSelector::~BondedResidueSelector ( )

overridedefault

Member Function Documentation

◆ apply()

ResidueSubset core::select::residue_selector::BondedResidueSelector::apply ( core::pose::Pose const & pose ) const

overridevirtual

Return a ResidueSubset indicating a selection of Residues from the input Pose; the ResidueSubset is an array of booleans where a value of "true" for position i indicates that residue i is a part of the selected subset – and a value of "false" would indicate that it is not.

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

References core::conformation::Conformation::bonded_neighbor_all_res(), core::pose::Pose::conformation(), get_input_set(), input_set_defined_, core::pose::Pose::residue(), core::pose::Pose::total_residue(), and core::select::residue_selector::TR().

◆ class_name()

std::string core::select::residue_selector::BondedResidueSelector::class_name ( )

static

Referenced by get_name(), core::select::residue_selector::BondedResidueSelectorCreator::keyname(), and provide_xml_schema().

◆ clone()

ResidueSelectorOP core::select::residue_selector::BondedResidueSelector::clone ( ) const

overridevirtual

Clone operator.

All ResidueSelectors must implement a clone() operator. This must create a copy of the object and return a ResidueSelectorOP to the original object.

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

References BondedResidueSelector().

◆ get_input_set()

void core::select::residue_selector::BondedResidueSelector::get_input_set	(	core::pose::Pose const &	pose,
		ResidueSubset &	subset,
		std::set< core::Size > &	input_set
	)		const

private

Sets subset to be true for values contained in input_set.

References core::pose::get_resnum_list(), input_set(), input_set_, input_set_selector_, input_set_str_, and use_input_set_selector_.

Referenced by apply().

◆ get_name()

std::string core::select::residue_selector::BondedResidueSelector::get_name ( ) const

overridevirtual

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

References class_name().

◆ input_set()

std::set< core::Size > core::select::residue_selector::BondedResidueSelector::input_set ( ) const

References input_set_.

Referenced by BondedResidueSelector(), get_input_set(), and set_input_set().

◆ input_set_defined()

bool core::select::residue_selector::BondedResidueSelector::input_set_defined ( ) const

References input_set_defined_.

Referenced by BondedResidueSelector().

◆ input_set_selector()

core::select::residue_selector::ResidueSelectorCOP core::select::residue_selector::BondedResidueSelector::input_set_selector ( ) const

References input_set_selector_.

Referenced by BondedResidueSelector().

◆ input_set_selector_defined()

bool core::select::residue_selector::BondedResidueSelector::input_set_selector_defined ( ) const

References use_input_set_selector_.

Referenced by BondedResidueSelector().

◆ input_set_string()

std::string core::select::residue_selector::BondedResidueSelector::input_set_string ( ) const

References input_set_str_.

Referenced by BondedResidueSelector().

◆ parse_my_tag()

void core::select::residue_selector::BondedResidueSelector::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	datacache
	)

overridevirtual

Initialize any data members of this instance from an input tag and a DataMap object.

Noop implementation in the base class in the case that a derived class has no need to read data from an input tag

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

References core::select::residue_selector::get_residue_selector(), set_input_set(), and set_input_set_selector().

◆ provide_xml_schema()

void core::select::residue_selector::BondedResidueSelector::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

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

Referenced by core::select::residue_selector::BondedResidueSelectorCreator::provide_xml_schema().

◆ set_input_set() [1/2]

void core::select::residue_selector::BondedResidueSelector::set_input_set ( std::set< core::Size > const & input_set )

adds a ResidueSelector

References input_set(), input_set_, input_set_defined_, and use_input_set_selector_.

Referenced by BondedResidueSelector(), and parse_my_tag().

◆ set_input_set() [2/2]

void core::select::residue_selector::BondedResidueSelector::set_input_set ( std::string const & input_set_str )

References input_set_defined_, input_set_str_, and use_input_set_selector_.

◆ set_input_set_selector()

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

References input_set_defined_, input_set_selector_, and use_input_set_selector_.

Referenced by parse_my_tag().

Member Data Documentation

◆ input_set_

std::set< core::Size > core::select::residue_selector::BondedResidueSelector::input_set_

private

Referenced by get_input_set(), input_set(), and set_input_set().

◆ input_set_defined_

bool core::select::residue_selector::BondedResidueSelector::input_set_defined_

private

Referenced by apply(), BondedResidueSelector(), input_set_defined(), set_input_set(), and set_input_set_selector().

◆ input_set_selector_

core::select::residue_selector::ResidueSelectorCOP core::select::residue_selector::BondedResidueSelector::input_set_selector_

private

Referenced by BondedResidueSelector(), get_input_set(), input_set_selector(), and set_input_set_selector().

◆ input_set_str_

std::string core::select::residue_selector::BondedResidueSelector::input_set_str_

private

Referenced by BondedResidueSelector(), get_input_set(), input_set_string(), and set_input_set().

◆ use_input_set_selector_

bool core::select::residue_selector::BondedResidueSelector::use_input_set_selector_

private

Referenced by BondedResidueSelector(), get_input_set(), input_set_selector_defined(), set_input_set(), and set_input_set_selector().

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

src/core/select/residue_selector/BondedResidueSelector.hh
src/core/select/residue_selector/BondedResidueSelector.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ BondedResidueSelector() [1/3]

◆ BondedResidueSelector() [2/3]

◆ BondedResidueSelector() [3/3]

◆ ~BondedResidueSelector()

Member Function Documentation

◆ apply()

◆ class_name()

◆ clone()

◆ get_input_set()

◆ get_name()

◆ input_set()

◆ input_set_defined()

◆ input_set_selector()

◆ input_set_selector_defined()

◆ input_set_string()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ set_input_set() [1/2]

◆ set_input_set() [2/2]

◆ set_input_set_selector()

Member Data Documentation

◆ input_set_

◆ input_set_defined_

◆ input_set_selector_

◆ input_set_str_

◆ use_input_set_selector_