A residue selector dependent on b-factor values. More...

#include <BFactorSelector.hh>

Inheritance diagram for core::select::residue_selector::BFactorSelector:

Public Types
typedef core::select::residue_selector::ResidueSelectorOP	ResidueSelectorOP

typedef core::select::residue_selector::ResidueSubset	ResidueSubset

Public Member Functions
	BFactorSelector ()
	Constructor. More...

	BFactorSelector (core::Size const lower_res, core::Size const upper_res, core::select::residue_selector::ResidueSelectorCOP const residue_selector, bool cross_chain_boundaries=false)
	Copy Constructor. Usually not necessary unless you need deep copying (e.g. OPs) More...

	~BFactorSelector () override
	Destructor. More...

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

ResidueSubset	apply (core::pose::Pose const &pose) const override
	"Apply" function. More...

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &datamap) override
	XML parse. More...

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

void	set_lower_residues (core::Size const nres)

void	set_upper_residues (core::Size const nres)

void	set_min_contiguous_res (core::Size const nres)

void	set_lower_bfactor_threshold (core::Real const lower_thresh)

void	set_upper_bfactor_threshold (core::Real const upper_thresh)

void	set_cross_chain_boundaries (bool cross)

void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const override
	This residue selector is unpublished. It returns AmeyaHarmalkar as its author. 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 ()
	Get the mover class name. More...

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
	Provide XSD information, enabling mechanical validation of input XML. More...

Private Attributes
core::Real	lower_threshold_ = 0.0

core::Real	upper_threshold_ = 100.0

core::Size	contiguous_res_ = 1

core::Size	lower_res_

core::Size	upper_res_

ResidueSelectorCOP	residue_selector_

bool	cross_chain_boundaries_

Detailed Description

A residue selector dependent on b-factor values.

Member Typedef Documentation

◆ ResidueSelectorOP

typedef core::select::residue_selector::ResidueSelectorOP core::select::residue_selector::BFactorSelector::ResidueSelectorOP

◆ ResidueSubset

typedef core::select::residue_selector::ResidueSubset core::select::residue_selector::BFactorSelector::ResidueSubset

Constructor & Destructor Documentation

◆ BFactorSelector() [1/2]

core::select::residue_selector::BFactorSelector::BFactorSelector ( )

Constructor.

◆ BFactorSelector() [2/2]

core::select::residue_selector::BFactorSelector::BFactorSelector	(	core::Size const	lower_res,
		core::Size const	upper_res,
		core::select::residue_selector::ResidueSelectorCOP const	residue_selector,
		bool	cross_chain_boundaries = `false`
	)

Copy Constructor. Usually not necessary unless you need deep copying (e.g. OPs)

◆ ~BFactorSelector()

core::select::residue_selector::BFactorSelector::~BFactorSelector ( )

override

Destructor.

Member Function Documentation

◆ apply()

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

overridevirtual

"Apply" function.

Given the pose, generate a vector of bools with entries for every residue in the pose indicating whether each residue is selected ("true") or not ("false").

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

References contiguous_res_, cross_chain_boundaries_, core::sequence::end, core::pose::is_lower_terminus(), core::pose::is_upper_terminus(), lower_res_, lower_threshold_, core::conformation::Residue::name3(), core::pose::Pose::pdb_info(), protocols::sic_dock::range(), core::pose::Pose::residue(), residue_selector_, core::pose::Pose::size(), protocols::loops::start, core::pose::Pose::total_residue(), core::select::residue_selector::TR(), upper_res_, and upper_threshold_.

◆ class_name()

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

static

Get the mover class name.

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

◆ clone()

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

overridevirtual

Clone operator.

Copy Constructor. Usually not necessary unless you need deep copying (e.g. OPs)

Copy the current object (creating the copy on the heap) and return an owning pointer to the copy. All ResidueSelectors must implement this.

Clone function.

Copy this object and return owning pointer to the copy (created on the heap).

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

◆ get_name()

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

overridevirtual

Get the mover class name.

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

References class_name().

◆ parse_my_tag()

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

overridevirtual

XML parse.

Parse RosettaScripts tags and set up this mover.

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

References core::select::residue_selector::get_residue_selector(), lower_threshold_, residue_selector_, set_cross_chain_boundaries(), set_lower_bfactor_threshold(), set_lower_residues(), set_min_contiguous_res(), set_upper_bfactor_threshold(), set_upper_residues(), core::select::residue_selector::TR(), and upper_threshold_.

◆ provide_citation_info()

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

overridevirtual

This residue selector is unpublished. It returns AmeyaHarmalkar as its author.

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

◆ provide_xml_schema()

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

static

Provide XSD information, enabling mechanical validation of input XML.

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

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

◆ set_cross_chain_boundaries()

void core::select::residue_selector::BFactorSelector::set_cross_chain_boundaries ( bool cross )

References cross_chain_boundaries_.

Referenced by parse_my_tag().

◆ set_lower_bfactor_threshold()

void core::select::residue_selector::BFactorSelector::set_lower_bfactor_threshold ( core::Real const lower_thresh )

References lower_threshold_.

Referenced by parse_my_tag().

◆ set_lower_residues()

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

References lower_res_.

Referenced by parse_my_tag().

◆ set_min_contiguous_res()

void core::select::residue_selector::BFactorSelector::set_min_contiguous_res ( core::Size const nres )

References contiguous_res_.

Referenced by parse_my_tag().

◆ set_upper_bfactor_threshold()

void core::select::residue_selector::BFactorSelector::set_upper_bfactor_threshold ( core::Real const upper_thresh )

References upper_threshold_.

Referenced by parse_my_tag().

◆ set_upper_residues()

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

References upper_res_.

Referenced by parse_my_tag().

Member Data Documentation

◆ contiguous_res_

core::Size core::select::residue_selector::BFactorSelector::contiguous_res_ = 1

private

Referenced by apply(), and set_min_contiguous_res().

◆ cross_chain_boundaries_

bool core::select::residue_selector::BFactorSelector::cross_chain_boundaries_

private

Referenced by apply(), and set_cross_chain_boundaries().

◆ lower_res_

core::Size core::select::residue_selector::BFactorSelector::lower_res_

private

Referenced by apply(), and set_lower_residues().

◆ lower_threshold_

core::Real core::select::residue_selector::BFactorSelector::lower_threshold_ = 0.0

private

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

◆ residue_selector_

ResidueSelectorCOP core::select::residue_selector::BFactorSelector::residue_selector_

private

Referenced by apply(), and parse_my_tag().

◆ upper_res_

core::Size core::select::residue_selector::BFactorSelector::upper_res_

private

Referenced by apply(), and set_upper_residues().

◆ upper_threshold_

core::Real core::select::residue_selector::BFactorSelector::upper_threshold_ = 100.0

private

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

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

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

Public Types

Public Member Functions

Static Public Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

◆ ResidueSelectorOP

◆ ResidueSubset

Constructor & Destructor Documentation

◆ BFactorSelector() [1/2]

◆ BFactorSelector() [2/2]

◆ ~BFactorSelector()

Member Function Documentation

◆ apply()

◆ class_name()

◆ clone()

◆ get_name()

◆ parse_my_tag()

◆ provide_citation_info()

◆ provide_xml_schema()

◆ set_cross_chain_boundaries()

◆ set_lower_bfactor_threshold()

◆ set_lower_residues()

◆ set_min_contiguous_res()

◆ set_upper_bfactor_threshold()

◆ set_upper_residues()

Member Data Documentation

◆ contiguous_res_

◆ cross_chain_boundaries_

◆ lower_res_

◆ lower_threshold_

◆ residue_selector_

◆ upper_res_

◆ upper_threshold_