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core::select::residue_selector::PrimarySequenceNeighborhoodSelector Class Reference

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:
Inheritance graph
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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...
 
virtual bool residue_selector_provides_citation_info () const
 Does this residue selector provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool residue_selector_is_unpublished () const
 Does this residue selector indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. 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

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

Member Function Documentation

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_.

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

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

void core::select::residue_selector::PrimarySequenceNeighborhoodSelector::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void core::select::residue_selector::PrimarySequenceNeighborhoodSelector::set_cross_chain_boundaries ( bool  cross)

References cross_chain_boundaries_.

Referenced by parse_my_tag().

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

References lower_residues_.

Referenced by parse_my_tag().

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

References selector_.

Referenced by parse_my_tag().

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

References upper_residues_.

Referenced by parse_my_tag().

Member Data Documentation

bool core::select::residue_selector::PrimarySequenceNeighborhoodSelector::cross_chain_boundaries_
private
core::Size core::select::residue_selector::PrimarySequenceNeighborhoodSelector::lower_residues_
private

Referenced by apply(), and set_lower_residues().

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

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

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: