The LayerSelector 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). Detection and mapping from PDB to Rosetta residue numbers is done internally. More...

#include <LayerSelector.hh>

Inheritance diagram for core::select::residue_selector::LayerSelector:

[legend]

Public Member Functions
	LayerSelector ()
	Default constructor. More...

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

	~LayerSelector () override
	Destructor. More...

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

ResidueSubset	apply (core::pose::Pose const &pose) const override
	Apply function: generate a ResidueSubset given a Pose. More...

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &) override
	Parse xml tag setting up this selector. More...

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

void	set_layers (bool pick_core, bool pick_boundary, bool pick_surface)
	Set the layers that this selector will choose. More...

void	set_ball_radius (core::Real radius)
	Set the radius for the rolling ball algorithm used to determine burial. More...

void	set_use_sc_neighbors (bool val)
	Set whether the sidechain neighbors algorithm is used to determine burial (as opposed to the rolling ball algorithm). More...

bool	use_sc_neighbors () const
	Get whether the sidechain neighbors algorithm is used to determine burial (as opposed to the rolling ball algorithm). More...

void	set_cache_selection (bool const val)
	Set whether to cache versus recompute the layer selection whenever it is accessed. More...

void	set_sc_neighbor_dist_midpoint (core::Real val)
	Set the midpoint of the distance falloff if the sidechain neighbors method is used to define layers. More...

void	set_sc_neighbor_denominator (core::Real val)
	Set the factor by which sidechain neighbor counts are divided if the sidechain neighbors method is used to define layers. More...

void	set_cutoffs (core::Real core, core::Real surf)
	Set the cutoffs for core and surface layers. More...

void	set_angle_shift_factor (core::Real val)
	Set the sidechain neighbor angle shift value. More...

void	set_angle_exponent (core::Real val)
	Set the sidechain neighbor angle exponent. More...

void	set_dist_exponent (core::Real val)
	Set the sidechain neighbor distance exponent. More...

void	set_asu_only (bool const asu_only)
	Set select only the asymmetric unit residues or not. More...

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...

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

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

Private Attributes
bool	cache_selection_
	Whether to cache the residue selection or recompute it when requested. More...

bool	asu_only_
	Select only the asymmetric unit residues or not. More...

core::select::util::SelectResiduesByLayerOP	srbl_
	Owning pointer to the calculator that determines what layer a residue is in. More...

Detailed Description

The LayerSelector 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). Detection and mapping from PDB to Rosetta residue numbers is done internally.

Constructor & Destructor Documentation

core::select::residue_selector::LayerSelector::LayerSelector ( )

Default constructor.

References set_cutoffs(), set_use_sc_neighbors(), and use_sc_neighbors().

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

Copy constructor.

core::select::residue_selector::LayerSelector::~LayerSelector ( )

overridedefault

Destructor.

Member Function Documentation

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

overridevirtual

Apply function: generate a ResidueSubset given a Pose.

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

References asu_only_, cache_selection_, core::pose::Pose::size(), srbl_, and core::select::residue_selector::TR().

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

static

Get the class name.

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

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

overridevirtual

Clone operator.

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

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

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

overridevirtual

Get the class name.

Calls class_name().

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

References class_name().

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

overridevirtual

Parse xml tag setting up this selector.

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

References cache_selection_, set_angle_exponent(), set_angle_shift_factor(), set_asu_only(), set_ball_radius(), set_cutoffs(), set_dist_exponent(), set_layers(), set_sc_neighbor_denominator(), set_sc_neighbor_dist_midpoint(), set_use_sc_neighbors(), and use_sc_neighbors().

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

overridevirtual

Provide the citation.

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

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

static

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

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

void core::select::residue_selector::LayerSelector::set_angle_exponent ( core::Real val )

Set the sidechain neighbor angle exponent.

See the core::select::util::SelectResiduesByLayer class for details of the math.

References srbl_, and core::select::residue_selector::TR().

Referenced by parse_my_tag().

void core::select::residue_selector::LayerSelector::set_angle_shift_factor ( core::Real val )

Set the sidechain neighbor angle shift value.

See the core::select::util::SelectResiduesByLayer class for details of the math.

References srbl_, and core::select::residue_selector::TR().

Referenced by parse_my_tag().

void core::select::residue_selector::LayerSelector::set_asu_only ( bool const asu_only )

Set select only the asymmetric unit residues or not.

References asu_only_.

Referenced by parse_my_tag().

void core::select::residue_selector::LayerSelector::set_ball_radius ( core::Real radius )

Set the radius for the rolling ball algorithm used to determine burial.

References srbl_, and core::select::residue_selector::TR().

Referenced by parse_my_tag().

void core::select::residue_selector::LayerSelector::set_cache_selection ( bool const val )

inline

Set whether to cache versus recompute the layer selection whenever it is accessed.

References cache_selection_, and protocols::hybridization::val.

void core::select::residue_selector::LayerSelector::set_cutoffs	(	core::Real	core,
		core::Real	surf
	)

Set the cutoffs for core and surface layers.

Boundary is defined implicitly. This can be a SASA cutoff or a neighbour count, depending on the algorithm.

References srbl_, and core::select::residue_selector::TR().

Referenced by LayerSelector(), and parse_my_tag().

void core::select::residue_selector::LayerSelector::set_dist_exponent ( core::Real val )

Set the sidechain neighbor distance exponent.

See the core::select::util::SelectResiduesByLayer class for details of the math.

References srbl_, and core::select::residue_selector::TR().

Referenced by parse_my_tag().

void core::select::residue_selector::LayerSelector::set_layers	(	bool	pick_core,
		bool	pick_boundary,
		bool	pick_surface
	)

Set the layers that this selector will choose.

References srbl_, and core::select::residue_selector::TR().

Referenced by parse_my_tag().

void core::select::residue_selector::LayerSelector::set_sc_neighbor_denominator ( core::Real val )

Set the factor by which sidechain neighbor counts are divided if the sidechain neighbors method is used to define layers.

References srbl_, and core::select::residue_selector::TR().

Referenced by parse_my_tag().

void core::select::residue_selector::LayerSelector::set_sc_neighbor_dist_midpoint ( core::Real val )

Set the midpoint of the distance falloff if the sidechain neighbors method is used to define layers.

References srbl_, and core::select::residue_selector::TR().

Referenced by parse_my_tag().

void core::select::residue_selector::LayerSelector::set_use_sc_neighbors ( bool val )

Set whether the sidechain neighbors algorithm is used to determine burial (as opposed to the rolling ball algorithm).

References srbl_, and core::select::residue_selector::TR().

Referenced by LayerSelector(), and parse_my_tag().

bool core::select::residue_selector::LayerSelector::use_sc_neighbors ( ) const

Get whether the sidechain neighbors algorithm is used to determine burial (as opposed to the rolling ball algorithm).

References srbl_.

Referenced by LayerSelector(), and parse_my_tag().

Member Data Documentation

bool core::select::residue_selector::LayerSelector::asu_only_

private

Select only the asymmetric unit residues or not.

Referenced by apply(), and set_asu_only().

bool core::select::residue_selector::LayerSelector::cache_selection_

private

Whether to cache the residue selection or recompute it when requested.

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

core::select::util::SelectResiduesByLayerOP core::select::residue_selector::LayerSelector::srbl_

private

Owning pointer to the calculator that determines what layer a residue is in.

Object created and destroyed with LayerSelector objects.

Referenced by apply(), set_angle_exponent(), set_angle_shift_factor(), set_ball_radius(), set_cutoffs(), set_dist_exponent(), set_layers(), set_sc_neighbor_denominator(), set_sc_neighbor_dist_midpoint(), set_use_sc_neighbors(), and use_sc_neighbors().

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

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

Public Member Functions

Static Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation