The PrimarySequenceNeighborhoodSelector returns a ResidueSubset, i.e. a utility::vector1< bool > containing 'true' for residue positions which are located near the given selected residues in primary sequence space. More...

#include <PrimarySequenceNeighborhoodSelector.hh>

Inheritance diagram for core::select::residue_selector::PrimarySequenceNeighborhoodSelector:

[legend]

Public Member Functions
	PrimarySequenceNeighborhoodSelector ()

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

	PrimarySequenceNeighborhoodSelector (core::Size const lower_residues, core::Size const upper_residues, core::select::residue_selector::ResidueSelectorCOP const selector, bool cross_chain_boundaries=false)

	~PrimarySequenceNeighborhoodSelector () override

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 &) 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_lower_residues (core::Size const nres)

void	set_upper_residues (core::Size const nres)

void	set_selector (core::select::residue_selector::ResidueSelectorCOP const selector)

void	set_cross_chain_boundaries (bool cross)

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 Attributes
core::Size	lower_residues_

core::Size	upper_residues_

core::select::residue_selector::ResidueSelectorCOP	selector_

bool	cross_chain_boundaries_

Detailed Description

The PrimarySequenceNeighborhoodSelector returns a ResidueSubset, i.e. a utility::vector1< bool > containing 'true' for residue positions which are located near the given selected residues in primary sequence space.

Constructor & Destructor Documentation

◆ PrimarySequenceNeighborhoodSelector() [1/2]

core::select::residue_selector::PrimarySequenceNeighborhoodSelector::PrimarySequenceNeighborhoodSelector ( )

◆ PrimarySequenceNeighborhoodSelector() [2/2]

core::select::residue_selector::PrimarySequenceNeighborhoodSelector::PrimarySequenceNeighborhoodSelector	(	core::Size const	lower_residues,
		core::Size const	upper_residues,
		core::select::residue_selector::ResidueSelectorCOP const	selector,
		bool	cross_chain_boundaries = `false`
	)

◆ ~PrimarySequenceNeighborhoodSelector()

core::select::residue_selector::PrimarySequenceNeighborhoodSelector::~PrimarySequenceNeighborhoodSelector ( )

overridedefault

Member Function Documentation

◆ apply()

ResidueSubset core::select::residue_selector::PrimarySequenceNeighborhoodSelector::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 cross_chain_boundaries_, core::sequence::end, core::pose::is_lower_terminus(), core::pose::is_upper_terminus(), lower_residues_, protocols::sic_dock::range(), selector_, core::pose::Pose::size(), protocols::loops::start, core::select::residue_selector::TR(), and upper_residues_.

◆ class_name()

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

static

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

◆ clone()

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

overridevirtual

Clone operator.

Copy this object and return an owning pointer to the new object.

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

◆ get_name()

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

overridevirtual

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

References class_name().

◆ parse_my_tag()

void core::select::residue_selector::PrimarySequenceNeighborhoodSelector::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(), selector_, set_cross_chain_boundaries(), set_lower_residues(), set_selector(), set_upper_residues(), protocols::hybridization::t, and core::select::residue_selector::TR().

◆ provide_xml_schema()

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

static

References 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::PrimarySequenceNeighborhoodSelectorCreator::provide_xml_schema().

◆ set_cross_chain_boundaries()

void core::select::residue_selector::PrimarySequenceNeighborhoodSelector::set_cross_chain_boundaries ( bool cross )

References cross_chain_boundaries_.

Referenced by parse_my_tag().

◆ set_lower_residues()

void core::select::residue_selector::PrimarySequenceNeighborhoodSelector::set_lower_residues ( core::Size const nres )

References lower_residues_.

Referenced by parse_my_tag().

◆ set_selector()

void core::select::residue_selector::PrimarySequenceNeighborhoodSelector::set_selector ( core::select::residue_selector::ResidueSelectorCOP const selector )

References selector_.

Referenced by parse_my_tag().

◆ set_upper_residues()

void core::select::residue_selector::PrimarySequenceNeighborhoodSelector::set_upper_residues ( core::Size const nres )

References upper_residues_.

Referenced by parse_my_tag().

Member Data Documentation

◆ cross_chain_boundaries_

bool core::select::residue_selector::PrimarySequenceNeighborhoodSelector::cross_chain_boundaries_

private

Referenced by apply(), and set_cross_chain_boundaries().

◆ lower_residues_

core::Size core::select::residue_selector::PrimarySequenceNeighborhoodSelector::lower_residues_

private

Referenced by apply(), and set_lower_residues().

◆ selector_

core::select::residue_selector::ResidueSelectorCOP core::select::residue_selector::PrimarySequenceNeighborhoodSelector::selector_

private

Referenced by apply(), parse_my_tag(), and set_selector().

◆ upper_residues_

core::Size core::select::residue_selector::PrimarySequenceNeighborhoodSelector::upper_residues_

private

Referenced by apply(), and set_upper_residues().

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

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

Public Member Functions

Static Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ PrimarySequenceNeighborhoodSelector() [1/2]

◆ PrimarySequenceNeighborhoodSelector() [2/2]

◆ ~PrimarySequenceNeighborhoodSelector()

Member Function Documentation

◆ apply()

◆ class_name()

◆ clone()

◆ get_name()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ set_cross_chain_boundaries()

◆ set_lower_residues()

◆ set_selector()

◆ set_upper_residues()

Member Data Documentation

◆ cross_chain_boundaries_

◆ lower_residues_

◆ selector_

◆ upper_residues_