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Rosetta
2020.50
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Selects residues that are involved in strand-strand pairings. More...
#include <PairedSheetResidueSelector.hh>
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... | |
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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_ |
Selects residues that are involved in strand-strand pairings.
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 |
protocols::denovo_design::residue_selectors::PairedSheetResidueSelector::PairedSheetResidueSelector | ( | ) |
Constructor.
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overridedefault |
Destructor.
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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().
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static |
Get the mover class name.
Referenced by get_name(), protocols::denovo_design::residue_selectors::PairedSheetResidueSelectorCreator::keyname(), and provide_xml_schema().
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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.
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overridevirtual |
Get the mover class name.
Implements core::select::residue_selector::ResidueSelector.
References class_name().
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private |
Gets secondary structure string to be used in computation.
[in] | pose | input pose |
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().
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private |
Gets sheet topology string to be used in computation.
[in] | pose | input pose |
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().
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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_.
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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().
void protocols::denovo_design::residue_selectors::PairedSheetResidueSelector::set_sheet_topology | ( | std::string const & | sheet_topology | ) |
Sets sheet topology to be filtered.
References sheet_topology_.
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private |
Referenced by get_secstruct(), parse_my_tag(), and set_secstruct().
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private |
Referenced by get_sheet_topology(), parse_my_tag(), and set_sheet_topology().
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private |
Referenced by get_secstruct(), and parse_my_tag().