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core::select::residue_selector::LayerSelector Class Reference

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:
Inheritance graph
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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
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
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
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: