Selects residues from a named segment generated by StructureArchitects. More...

#include <NamedSegmentSelector.hh>

Inheritance diagram for protocols::denovo_design::residue_selectors::NamedSegmentSelector:

Public Types
typedef components::SegmentResid	SignedResid

typedef std::set< SignedResid >	SignedResidSet

typedef core::select::residue_selector::ResidueRanges	ResidueRanges

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

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

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

	NamedSegmentSelector (SegmentName const &segment_name, std::string const &residues_str)

	~NamedSegmentSelector () 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_segment (SegmentName const &segment_name)

void	set_residues (std::string const &residues_str)

void	set_error_on_missing_segment (bool const error_on_missing)

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...

virtual void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. 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 Member Functions
SignedResidSet	resid_set () const

void	compute_residue_subset_for_segment (ResidueSubset &subset, components::Segment const &seg, SignedResidSet const &resids) const
	Computes residue subset from a Segment and list of resids. More...

ResidueSubset	compute_residue_subset (components::StructureData const &sd, SignedResidSet const &resids) const
	Computes residue subset from a StructureData and list of resids. More...

Private Attributes
SegmentName	segment_

std::string	residues_

bool	error_on_missing_segment_

Detailed Description

Selects residues from a named segment generated by StructureArchitects.

Member Typedef Documentation

◆ ResidueRanges

typedef core::select::residue_selector::ResidueRanges protocols::denovo_design::residue_selectors::NamedSegmentSelector::ResidueRanges

◆ ResidueSelectorOP

typedef core::select::residue_selector::ResidueSelectorOP protocols::denovo_design::residue_selectors::NamedSegmentSelector::ResidueSelectorOP

◆ ResidueSubset

typedef core::select::residue_selector::ResidueSubset protocols::denovo_design::residue_selectors::NamedSegmentSelector::ResidueSubset

◆ SignedResid

typedef components::SegmentResid protocols::denovo_design::residue_selectors::NamedSegmentSelector::SignedResid

◆ SignedResidSet

typedef std::set< SignedResid > protocols::denovo_design::residue_selectors::NamedSegmentSelector::SignedResidSet

Constructor & Destructor Documentation

◆ NamedSegmentSelector() [1/2]

protocols::denovo_design::residue_selectors::NamedSegmentSelector::NamedSegmentSelector ( )

Constructor.

◆ NamedSegmentSelector() [2/2]

protocols::denovo_design::residue_selectors::NamedSegmentSelector::NamedSegmentSelector	(	SegmentName const &	segment_name,
		std::string const &	residues_str
	)

◆ ~NamedSegmentSelector()

protocols::denovo_design::residue_selectors::NamedSegmentSelector::~NamedSegmentSelector ( )

overridedefault

Destructor.

Member Function Documentation

◆ apply()

NamedSegmentSelector::ResidueSubset protocols::denovo_design::residue_selectors::NamedSegmentSelector::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 core::pose::Pose::chain(), class_name(), compute_residue_subset(), protocols::denovo_design::components::StructureDataFactory::create_from_pose(), protocols::denovo_design::components::StructureDataFactory::get_from_const_pose(), protocols::denovo_design::components::StructureDataFactory::has_cached_data(), core::pose::symmetry::is_symmetric(), core::conformation::Residue::name(), resid_set(), core::select::resids(), core::pose::Pose::residue(), protocols::denovo_design::symmetric_residue_subset(), and protocols::TR().

◆ class_name()

std::string protocols::denovo_design::residue_selectors::NamedSegmentSelector::class_name ( )

static

Get the mover class name.

Referenced by apply(), compute_residue_subset(), get_name(), protocols::denovo_design::residue_selectors::NamedSegmentSelectorCreator::keyname(), and provide_xml_schema().

◆ clone()

NamedSegmentSelector::ResidueSelectorOP protocols::denovo_design::residue_selectors::NamedSegmentSelector::clone ( ) const

overridevirtual

Clone operator.

Clone function.

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

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

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

◆ compute_residue_subset()

NamedSegmentSelector::ResidueSubset protocols::denovo_design::residue_selectors::NamedSegmentSelector::compute_residue_subset	(	components::StructureData const &	sd,
		SignedResidSet const &	resids
	)		const

private

Computes residue subset from a StructureData and list of resids.

Parameters

[in]	sd	StructureData object
[in]	resids	List of signed residue number, can be empty if no residue numbers are specified

References protocols::denovo_design::components::StructureData::alias(), class_name(), compute_residue_subset_for_segment(), error_on_missing_segment_, protocols::denovo_design::components::StructureData::has_alias(), protocols::denovo_design::components::StructureData::has_segment(), protocols::denovo_design::components::StructureData::has_segment_group(), protocols::denovo_design::components::StructureData::pose_length(), core::select::resids(), protocols::denovo_design::components::StructureData::segment(), segment_, protocols::denovo_design::components::StructureData::segment_group(), and protocols::TR().

Referenced by apply().

◆ compute_residue_subset_for_segment()

void protocols::denovo_design::residue_selectors::NamedSegmentSelector::compute_residue_subset_for_segment	(	ResidueSubset &	subset,
		components::Segment const &	seg,
		SignedResidSet const &	resids
	)		const

private

Computes residue subset from a Segment and list of resids.

Parameters

[out]	subset	ResidueSubset to be modified
[in]	sd	StructureData object
[in]	resids	List of signed residue numbers, can be empty if the entire segment is being selected

References protocols::denovo_design::components::Segment::lower(), core::select::resids(), protocols::denovo_design::components::Segment::segment_to_pose(), and protocols::denovo_design::components::Segment::upper().

Referenced by compute_residue_subset().

◆ get_name()

std::string protocols::denovo_design::residue_selectors::NamedSegmentSelector::get_name ( ) const

overridevirtual

Get the mover class name.

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

References class_name().

◆ parse_my_tag()

void protocols::denovo_design::residue_selectors::NamedSegmentSelector::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 protocols::pack_daemon::error_message, error_on_missing_segment_, residues_, segment_, set_error_on_missing_segment(), set_residues(), and set_segment().

◆ provide_xml_schema()

void protocols::denovo_design::residue_selectors::NamedSegmentSelector::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

Provide XSD information, enabling mechanical validation of input XML.

References class_name(), and core::pack::palette::xsd_type_definition_w_attributes().

Referenced by protocols::denovo_design::residue_selectors::NamedSegmentSelectorCreator::provide_xml_schema().

◆ resid_set()

NamedSegmentSelector::SignedResidSet protocols::denovo_design::residue_selectors::NamedSegmentSelector::resid_set ( ) const

private

References residues_, protocols::loops::start, and protocols::loops::stop.

Referenced by apply().

◆ set_error_on_missing_segment()

void protocols::denovo_design::residue_selectors::NamedSegmentSelector::set_error_on_missing_segment ( bool const error_on_missing )

inline

References error_on_missing_segment_.

Referenced by parse_my_tag().

◆ set_residues()

void protocols::denovo_design::residue_selectors::NamedSegmentSelector::set_residues ( std::string const & residues_str )

References residues_.

Referenced by parse_my_tag().

◆ set_segment()

void protocols::denovo_design::residue_selectors::NamedSegmentSelector::set_segment ( SegmentName const & segment_name )

References segment_.

Referenced by parse_my_tag().

Member Data Documentation

◆ error_on_missing_segment_

bool protocols::denovo_design::residue_selectors::NamedSegmentSelector::error_on_missing_segment_

private

Referenced by compute_residue_subset(), parse_my_tag(), and set_error_on_missing_segment().

◆ residues_

std::string protocols::denovo_design::residue_selectors::NamedSegmentSelector::residues_

private

Referenced by parse_my_tag(), resid_set(), and set_residues().

◆ segment_

SegmentName protocols::denovo_design::residue_selectors::NamedSegmentSelector::segment_

private

Referenced by compute_residue_subset(), parse_my_tag(), and set_segment().

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

src/protocols/denovo_design/residue_selectors/NamedSegmentSelector.hh
src/protocols/denovo_design/residue_selectors/NamedSegmentSelector.cc

Public Types

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

◆ ResidueRanges

◆ ResidueSelectorOP

◆ ResidueSubset

◆ SignedResid

◆ SignedResidSet

Constructor & Destructor Documentation

◆ NamedSegmentSelector() [1/2]

◆ NamedSegmentSelector() [2/2]

◆ ~NamedSegmentSelector()

Member Function Documentation

◆ apply()

◆ class_name()

◆ clone()

◆ compute_residue_subset()

◆ compute_residue_subset_for_segment()

◆ get_name()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ resid_set()

◆ set_error_on_missing_segment()

◆ set_residues()

◆ set_segment()

Member Data Documentation

◆ error_on_missing_segment_

◆ residues_

◆ segment_