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protocols::denovo_design::residue_selectors::PairedSheetResidueSelector Class Reference

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

#include <PairedSheetResidueSelector.hh>

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

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
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]poseinput 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]poseinput 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_, sheet_topology_, and use_dssp_.

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

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

Sets sheet topology to be filtered.

References sheet_topology_.

Member Data Documentation

std::string protocols::denovo_design::residue_selectors::PairedSheetResidueSelector::secstruct_
private
std::string protocols::denovo_design::residue_selectors::PairedSheetResidueSelector::sheet_topology_
private
bool protocols::denovo_design::residue_selectors::PairedSheetResidueSelector::use_dssp_
private

Referenced by get_secstruct(), and parse_my_tag().


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