The ResidueIndexSelector returns a ResidueSubset, i.e. a utility::vector1< bool > containing 'true' for residue positions which match the given residue index. The index is read as comma-separated list of either Rosetta indices (e.g. 10) or PDB numbers (e.g. 10A, residue 10 of chain A). It can also take range specifications (e.g. 10A-20A). Detection and mapping from PDB to Rosetta residue numbers is done internally. More...

#include <ResidueIndexSelector.hh>

Inheritance diagram for core::select::residue_selector::ResidueIndexSelector:

[legend]

Public Member Functions
	ResidueIndexSelector ()

	ResidueIndexSelector (std::string const &index_str)

	ResidueIndexSelector (core::Size index_in)
	Convenience constructor for a single residue index. More...

	ResidueIndexSelector (utility::vector1< core::Size > const &index_in)
	Convenience constructor for a vector of indexes. More...

	ResidueIndexSelector (ResidueIndexSelector const &src)
	Copy constructor. More...

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

	~ResidueIndexSelector () 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_index (std::string const &index_str)
	sets the string by which residues are selected More...

void	set_index (core::Size index)
	Set an index using a size. More...

void	set_index_range (core::Size start, core::Size end)
	Set a range of indexes. Includes start and end. More...

void	append_index (core::Size index_in)
	Append an additional index (in Rosetta numbering) to the list of indices. More...

void	append_index (utility::vector1< core::Size > const &index_in)
	Append additional indexes (in Rosetta numbering) to the list of indices. More...

bool	error_on_out_of_bounds_index () const
	Is this selector set to throw an error if an out-of-range index is selected (e.g. residue 56 of a 55-residue pose)? More...

void	set_error_on_out_of_bounds_index (bool const setting)
	Set whether this selector set to throws an error if an out-of-range index is selected (e.g. residue 56 of a 55-residue pose). More...

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
std::string	index_str_

bool	error_on_out_of_bounds_index_
	If false, then there is no error if an index that is not in the pose is selected. True by default, which means that you get an error if you try to select an index that's not in the pose. More...

bool	reverse_
	If true, will reverse the index selection from the end of the pose. More...

Detailed Description

The ResidueIndexSelector returns a ResidueSubset, i.e. a utility::vector1< bool > containing 'true' for residue positions which match the given residue index. The index is read as comma-separated list of either Rosetta indices (e.g. 10) or PDB numbers (e.g. 10A, residue 10 of chain A). It can also take range specifications (e.g. 10A-20A). Detection and mapping from PDB to Rosetta residue numbers is done internally.

Constructor & Destructor Documentation

◆ ResidueIndexSelector() [1/5]

core::select::residue_selector::ResidueIndexSelector::ResidueIndexSelector ( )

◆ ResidueIndexSelector() [2/5]

core::select::residue_selector::ResidueIndexSelector::ResidueIndexSelector ( std::string const & index_str )

◆ ResidueIndexSelector() [3/5]

core::select::residue_selector::ResidueIndexSelector::ResidueIndexSelector ( core::Size index_in )

Convenience constructor for a single residue index.

References append_index().

◆ ResidueIndexSelector() [4/5]

core::select::residue_selector::ResidueIndexSelector::ResidueIndexSelector ( utility::vector1< core::Size > const & index_in )

Convenience constructor for a vector of indexes.

References append_index().

◆ ResidueIndexSelector() [5/5]

core::select::residue_selector::ResidueIndexSelector::ResidueIndexSelector ( ResidueIndexSelector const & src )

default

Copy constructor.

◆ ~ResidueIndexSelector()

core::select::residue_selector::ResidueIndexSelector::~ResidueIndexSelector ( )

overridedefault

Member Function Documentation

◆ append_index() [1/2]

void core::select::residue_selector::ResidueIndexSelector::append_index ( core::Size index_in )

Append an additional index (in Rosetta numbering) to the list of indices.

Author: Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

References index_str_.

Referenced by protocols::fold_from_loops::utils::Nub::get_nub_pieces(), and ResidueIndexSelector().

◆ append_index() [2/2]

void core::select::residue_selector::ResidueIndexSelector::append_index ( utility::vector1< core::Size > const & index_in )

Append additional indexes (in Rosetta numbering) to the list of indices.

References index_str_.

◆ apply()

ResidueSubset core::select::residue_selector::ResidueIndexSelector::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 error_on_out_of_bounds_index(), core::pose::get_resnum_list(), index_str_, core::pose::symmetry::is_symmetric(), reverse_, core::pose::Pose::size(), core::pose::symmetry::symmetry_info(), and core::select::residue_selector::TR().

◆ class_name()

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

static

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

◆ clone()

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

overridevirtual

Clone operator.

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

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

◆ error_on_out_of_bounds_index()

bool core::select::residue_selector::ResidueIndexSelector::error_on_out_of_bounds_index ( ) const

inline

Is this selector set to throw an error if an out-of-range index is selected (e.g. residue 56 of a 55-residue pose)?

References error_on_out_of_bounds_index_.

Referenced by apply(), and parse_my_tag().

◆ get_name()

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

overridevirtual

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

References class_name().

◆ parse_my_tag()

void core::select::residue_selector::ResidueIndexSelector::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 error_on_out_of_bounds_index(), reverse_, set_error_on_out_of_bounds_index(), set_index(), and core::select::residue_selector::TR().

◆ provide_xml_schema()

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

static

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

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

◆ set_error_on_out_of_bounds_index()

void core::select::residue_selector::ResidueIndexSelector::set_error_on_out_of_bounds_index ( bool const setting )

inline

Set whether this selector set to throws an error if an out-of-range index is selected (e.g. residue 56 of a 55-residue pose).

References error_on_out_of_bounds_index_.

Referenced by parse_my_tag().

◆ set_index() [1/2]

void core::select::residue_selector::ResidueIndexSelector::set_index ( core::Size index )

Set an index using a size.

References set_index(), and core::id::to_string().

◆ set_index() [2/2]

void core::select::residue_selector::ResidueIndexSelector::set_index ( std::string const & index_str )

sets the string by which residues are selected

References index_str_.

Referenced by parse_my_tag(), set_index(), and set_index_range().

◆ set_index_range()

void core::select::residue_selector::ResidueIndexSelector::set_index_range	(	core::Size	start,
		core::Size	end
	)

Set a range of indexes. Includes start and end.

References core::sequence::end, protocols::sic_dock::range(), set_index(), protocols::loops::start, and core::id::to_string().

Member Data Documentation

◆ error_on_out_of_bounds_index_

bool core::select::residue_selector::ResidueIndexSelector::error_on_out_of_bounds_index_

private

If false, then there is no error if an index that is not in the pose is selected. True by default, which means that you get an error if you try to select an index that's not in the pose.

Referenced by error_on_out_of_bounds_index(), and set_error_on_out_of_bounds_index().

◆ index_str_

std::string core::select::residue_selector::ResidueIndexSelector::index_str_

private

Referenced by append_index(), apply(), and set_index().

◆ reverse_

bool core::select::residue_selector::ResidueIndexSelector::reverse_

private

If true, will reverse the index selection from the end of the pose.

Referenced by apply(), and parse_my_tag().

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

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

Public Member Functions

Static Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ ResidueIndexSelector() [1/5]

◆ ResidueIndexSelector() [2/5]

◆ ResidueIndexSelector() [3/5]

◆ ResidueIndexSelector() [4/5]

◆ ResidueIndexSelector() [5/5]

◆ ~ResidueIndexSelector()

Member Function Documentation

◆ append_index() [1/2]

◆ append_index() [2/2]

◆ apply()

◆ class_name()

◆ clone()

◆ error_on_out_of_bounds_index()

◆ get_name()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ set_error_on_out_of_bounds_index()

◆ set_index() [1/2]

◆ set_index() [2/2]

◆ set_index_range()

Member Data Documentation

◆ error_on_out_of_bounds_index_

◆ index_str_

◆ reverse_