The NeighborhoodResidueSelector selects residues neighboring a defined set of residues (the focus). The focus residue set can be obtained from another ResidueSelector, from a set of positions. Focus is included in subset by default. Use include_focus_in_subset to change this! More...

#include <NeighborhoodResidueSelector.hh>

Inheritance diagram for core::select::residue_selector::NeighborhoodResidueSelector:

[legend]

Public Member Functions
	NeighborhoodResidueSelector ()

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

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

	NeighborhoodResidueSelector (utility::vector1< bool > const &focus, Real distance, bool include_focus_in_subset=true)

	NeighborhoodResidueSelector (ResidueSelectorCOP selector, Real distance, bool include_focus_in_subset=true)

	~NeighborhoodResidueSelector () override

void	set_focus (std::string const &focus_str)
	Set the focus, which is the residues for which we will be getting neighbors of. More...

void	set_focus (utility::vector1< bool > const &focus)
	Set the focus, which is the residues for which we will be getting neighbors of. More...

void	set_focus_selector (ResidueSelectorCOP rs)
	Set a Residue Selector for the focus. More...

void	set_distance (Real distance)
	Set the distance we will be measuring to get neighbors. More...

void	set_include_focus_in_subset (bool include_focus)
	Setting to include the focus in the resulting subset or not. Default is TRUE. More...

void	set_atom_names_for_distance_measure (utility::vector1< std::string > const &atom_names)
	@breif Set atom names to be used for selecting instead of using neighbor atoms. 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 &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	provide_citation_info (basic::citation_manager::CitationCollectionList &) const override
	Provide the citation. 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...

Static Public Member Functions
static std::string	class_name ()

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

Private Member Functions
void	get_focus (core::pose::Pose const &, ResidueSubset &, utility::vector1< bool > &) const

void	set_defaults ()

void	clear_focus ()

Private Attributes
utility::vector1< bool >	focus_

std::string	focus_str_

Real	distance_

ResidueSelectorCOP	focus_selector_

bool	include_focus_in_subset_

utility::vector1< std::string >	atom_names_for_distance_measure_

Detailed Description

The NeighborhoodResidueSelector selects residues neighboring a defined set of residues (the focus). The focus residue set can be obtained from another ResidueSelector, from a set of positions. Focus is included in subset by default. Use include_focus_in_subset to change this!

Note: Uses the 10 A neighbor graph by default. If neighbor distance is great than this, we use slow-style double for loop.

Constructor & Destructor Documentation

◆ NeighborhoodResidueSelector() [1/4]

core::select::residue_selector::NeighborhoodResidueSelector::NeighborhoodResidueSelector ( )

References set_defaults().

◆ NeighborhoodResidueSelector() [2/4]

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

Copy constructor.

References focus_selector_.

◆ NeighborhoodResidueSelector() [3/4]

core::select::residue_selector::NeighborhoodResidueSelector::NeighborhoodResidueSelector	(	utility::vector1< bool > const &	focus,
		Real	distance,
		bool	include_focus_in_subset = `true`
	)

References core::kinematics::distance(), set_defaults(), set_distance(), set_focus(), and set_include_focus_in_subset().

◆ NeighborhoodResidueSelector() [4/4]

core::select::residue_selector::NeighborhoodResidueSelector::NeighborhoodResidueSelector	(	ResidueSelectorCOP	selector,
		Real	distance,
		bool	include_focus_in_subset = `true`
	)

References core::kinematics::distance(), set_defaults(), set_distance(), and set_include_focus_in_subset().

◆ ~NeighborhoodResidueSelector()

core::select::residue_selector::NeighborhoodResidueSelector::~NeighborhoodResidueSelector ( )

overridedefault

Member Function Documentation

◆ apply()

ResidueSubset core::select::residue_selector::NeighborhoodResidueSelector::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 atom_names_for_distance_measure_, distance_, core::pose::Pose::energies(), core::select::fill_neighbor_residues(), get_focus(), core::select::get_neighbor_residues(), core::select::get_residues_from_subset(), include_focus_in_subset_, protocols::hybridization::r1, protocols::hybridization::r2, core::pose::Pose::residue(), core::scoring::Energies::residue_neighbors_updated(), core::pose::Pose::size(), core::select::residue_selector::TR(), and core::pose::Pose::update_residue_neighbors().

Referenced by protocols::antibody::design::MutateFrameworkForCluster::apply(), protocols::ligand_docking::ProtLigEnsemble::apply(), protocols::glycan_docking::calc_GlycanDock_intf_metrics(), protocols::calc_taskop_movers::CreateSequenceMotifMover::initialize_objects(), and core::select::residue_selector::RandomResidueSelector::subset_from_randomized_vector().

◆ class_name()

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

static

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

◆ clear_focus()

void core::select::residue_selector::NeighborhoodResidueSelector::clear_focus ( )

private

References focus_, focus_selector_, and focus_str_.

Referenced by set_focus().

◆ clone()

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

overridevirtual

Clone operator.

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

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

Referenced by protocols::simple_moves::CoupledMover::apply().

◆ get_focus()

void core::select::residue_selector::NeighborhoodResidueSelector::get_focus	(	core::pose::Pose const &	pose,
		ResidueSubset &	subset,
		utility::vector1< bool > &	focus
	)		const

private

References focus_, focus_selector_, focus_str_, core::pose::get_resnum_list(), include_focus_in_subset_, and core::pose::Pose::size().

Referenced by apply().

◆ get_name()

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

overridevirtual

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

References class_name().

◆ parse_my_tag()

void core::select::residue_selector::NeighborhoodResidueSelector::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 distance_, core::select::residue_selector::get_embedded_residue_selector(), core::select::residue_selector::get_residue_selector(), include_focus_in_subset_, set_atom_names_for_distance_measure(), set_distance(), set_focus(), set_focus_selector(), set_include_focus_in_subset(), and core::select::residue_selector::TR().

◆ provide_citation_info()

void core::select::residue_selector::NeighborhoodResidueSelector::provide_citation_info ( basic::citation_manager::CitationCollectionList & citations ) const

overridevirtual

Provide the citation.

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

References focus_selector_.

◆ provide_xml_schema()

void core::select::residue_selector::NeighborhoodResidueSelector::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::NeighborhoodResidueSelectorCreator::provide_xml_schema().

◆ set_atom_names_for_distance_measure()

void core::select::residue_selector::NeighborhoodResidueSelector::set_atom_names_for_distance_measure ( utility::vector1< std::string > const & atom_names )

@breif Set atom names to be used for selecting instead of using neighbor atoms.

setter for custom atom names

A list of atom names, for each focus residue, the positions of which will be used for measuring distance to find neighbors. Since focus residues will be known only during the apply time, a check to see if the number of given atom names is equal to the number of focus residues. If these are not equal, an error is thrown.

References atom_names_for_distance_measure_.

Referenced by parse_my_tag().