Selects residues that are involved in strand-strand pairings. More...

#include <PairedSheetResidueSelector.hh>

Inheritance diagram for protocols::denovo_design::residue_selectors::PairedSheetResidueSelector:

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

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

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

	~PairedSheetResidueSelector () 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_use_dssp (bool const use_dssp)

void	set_sheet_topology (std::string const &sheet_topology)
	Sets sheet topology to be filtered. More...

void	set_secstruct (std::string const &secstruct)
	Sets secondary structure to be used in calculations. More...

Public Member Functions inherited from core::select::residue_selector::ResidueSelector
	ResidueSelector ()
	Constructor. More...

	~ResidueSelector () override
	Destructor. 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
std::string	get_secstruct (core::pose::Pose const &pose) const
	Gets secondary structure string to be used in computation. More...

std::string	get_sheet_topology (core::pose::Pose const &pose) const
	Gets sheet topology string to be used in computation. More...

Private Attributes
std::string	secstruct_

std::string	sheet_topology_

bool	use_dssp_

Detailed Description

Selects residues that are involved in strand-strand pairings.

Member Typedef Documentation

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

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

Constructor & Destructor Documentation

protocols::denovo_design::residue_selectors::PairedSheetResidueSelector::PairedSheetResidueSelector ( )

Constructor.

protocols::denovo_design::residue_selectors::PairedSheetResidueSelector::~PairedSheetResidueSelector ( )

overridedefault

Destructor.

Member Function Documentation

PairedSheetResidueSelector::ResidueSubset protocols::denovo_design::residue_selectors::PairedSheetResidueSelector::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 get_secstruct(), get_sheet_topology(), core::scoring::pair, core::pose::Pose::size(), and protocols::TR().

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

static

Get the mover class name.

Referenced by get_name(), protocols::denovo_design::residue_selectors::PairedSheetResidueSelectorCreator::keyname(), and provide_xml_schema().

PairedSheetResidueSelector::ResidueSelectorOP protocols::denovo_design::residue_selectors::PairedSheetResidueSelector::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.

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

overridevirtual

Get the mover class name.

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

References class_name().

std::string protocols::denovo_design::residue_selectors::PairedSheetResidueSelector::get_secstruct ( core::pose::Pose const & pose ) const

private

Gets secondary structure string to be used in computation.

Parameters

[in] pose input pose

Returns: String representing secondary structure (e.g. "LEEEEELLEEEEEL")

If secstruct_ is given, that is returned. If use_dssp_ is true, DSSP secstruct is returned If use_dssp_ is false and secstruct_ is not given, return pose's secondary structure

References protocols::simple_filters::dssp(), core::scoring::dssp::Dssp::get_dssp_secstruct(), core::pose::Pose::secstruct(), secstruct_, protocols::TR(), and use_dssp_.

Referenced by apply().

std::string protocols::denovo_design::residue_selectors::PairedSheetResidueSelector::get_sheet_topology ( core::pose::Pose const & pose ) const

private

Gets sheet topology string to be used in computation.

Parameters

[in] pose input pose

Returns: String representing sheet topology (e.g. "1-2.A.0;2-3.P.1")

If sheet_topology_ is given, that is returned. If sheet_topology_ is not given, and the pose has a cached StructureData, the topology string is derived from that. If a sheet topology cannot be found by the above methods, an error is thrown

References protocols::denovo_design::components::StructureDataFactory::get_from_const_pose(), protocols::denovo_design::components::SegmentPairing::get_strand_pairings(), protocols::denovo_design::components::StructureDataFactory::has_cached_data(), sheet_topology_, and protocols::TR().

Referenced by apply().

void protocols::denovo_design::residue_selectors::PairedSheetResidueSelector::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 secstruct_, set_secstruct(), set_sheet_topology(), set_use_dssp(), sheet_topology_, and use_dssp_.

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

static

Provide XSD information, enabling mechanical validation of input XML.

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

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

void protocols::denovo_design::residue_selectors::PairedSheetResidueSelector::set_secstruct ( std::string const & secstruct )

Sets secondary structure to be used in calculations.

References secstruct_.

Referenced by protocols::fldsgn::filters::SecondaryStructureFilter::correct_for_incomplete_strand_pairings(), and parse_my_tag().

void protocols::denovo_design::residue_selectors::PairedSheetResidueSelector::set_sheet_topology ( std::string const & sheet_topology )

Sets sheet topology to be filtered.

References sheet_topology_.

Referenced by parse_my_tag().

void protocols::denovo_design::residue_selectors::PairedSheetResidueSelector::set_use_dssp ( bool const use_dssp )

inline

References use_dssp_.

Referenced by parse_my_tag().

Member Data Documentation

std::string protocols::denovo_design::residue_selectors::PairedSheetResidueSelector::secstruct_

private

Referenced by get_secstruct(), parse_my_tag(), and set_secstruct().

std::string protocols::denovo_design::residue_selectors::PairedSheetResidueSelector::sheet_topology_

private

Referenced by get_sheet_topology(), parse_my_tag(), and set_sheet_topology().

bool protocols::denovo_design::residue_selectors::PairedSheetResidueSelector::use_dssp_

private

Referenced by get_secstruct(), parse_my_tag(), and set_use_dssp().

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

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

Public Types

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation