Rosetta
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core::select::residue_selector::ResidueSelector Class Referenceabstract

#include <ResidueSelector.hh>

Inherits utility::VirtualBase.

Inherited by core::pack::task::residue_selector::ClashBasedShellSelector, core::select::residue_selector::AndResidueSelector, core::select::residue_selector::AsymmetricUnitSelector, core::select::residue_selector::BFactorSelector, core::select::residue_selector::BinSelector, core::select::residue_selector::BlockSelector, core::select::residue_selector::BondedResidueSelector, core::select::residue_selector::ChainSelector, core::select::residue_selector::CloseContactResidueSelector, core::select::residue_selector::ConfluentSelector, core::select::residue_selector::DensityFitResidueSelector, core::select::residue_selector::FalseResidueSelector, core::select::residue_selector::FractionSelector, core::select::residue_selector::GlycanLayerSelector, core::select::residue_selector::GlycanPositionSelector, core::select::residue_selector::GlycanResidueSelector, core::select::residue_selector::InterGroupInterfaceByVectorSelector, core::select::residue_selector::JumpDownstreamSelector, core::select::residue_selector::JumpUpstreamSelector, core::select::residue_selector::LayerSelector, core::select::residue_selector::LogicResidueSelector, core::select::residue_selector::NeighborhoodResidueSelector, core::select::residue_selector::NotResidueSelector, core::select::residue_selector::NumNeighborsSelector, core::select::residue_selector::OrResidueSelector, core::select::residue_selector::PhiSelector, core::select::residue_selector::PrimarySequenceNeighborhoodSelector, core::select::residue_selector::RandomGlycanFoliageSelector, core::select::residue_selector::RandomResidueSelector, core::select::residue_selector::ResidueInMembraneSelector, core::select::residue_selector::ResidueInSequenceMotifSelector, core::select::residue_selector::ResidueIndexSelector, core::select::residue_selector::ResidueNameSelector, core::select::residue_selector::ResiduePDBInfoHasLabelSelector, core::select::residue_selector::ResiduePropertySelector, core::select::residue_selector::ResidueSpanSelector, core::select::residue_selector::ReturnResidueSubsetSelector, core::select::residue_selector::SSElementSelector, core::select::residue_selector::ScoreTermValueBasedSelector, core::select::residue_selector::SecondaryStructureSelector, core::select::residue_selector::SimpleMetricSelector, core::select::residue_selector::SliceResidueSelector, core::select::residue_selector::SymmetricalResidueSelector, core::select::residue_selector::TrueResidueSelector, core::select::residue_selector::VirtualResidueSelector, protocols::antibody::design::ResnumFromStringsWithRangesSelector, protocols::antibody::residue_selector::AntibodyRegionSelector, protocols::antibody::residue_selector::CDRResidueSelector, protocols::cyclic_peptide::RamaMutationSelector, protocols::denovo_design::residue_selectors::NamedSegmentSelector, protocols::denovo_design::residue_selectors::PairedSheetResidueSelector, protocols::environment::claims::EnvLabelSelector, protocols::fold_from_loops::selectors::ConstraintResidueSelector, protocols::fold_from_loops::selectors::CutpointResidueSelector, protocols::fold_from_loops::selectors::ProteinResidueSelector, protocols::hbnet::UnsatSelector, protocols::residue_selectors::HBondSelector, protocols::residue_selectors::LigandMetalContactSelector, protocols::residue_selectors::NativeSelector, protocols::residue_selectors::StoredResidueSubsetSelector, and protocols::residue_selectors::TaskSelector.

Public Member Functions

 ResidueSelector ()
 Constructor. More...
 
 ~ResidueSelector () override
 Destructor. More...
 
virtual ResidueSelectorOP clone () const =0
 Clone operator. More...
 
virtual ResidueSubset apply (core::pose::Pose const &pose) const =0
 Return a ResidueSubset indicating a selection of Residues from the input Pose; the ResidueSubset is an array of booleans where a value of "true" for position i indicates that residue i is a part of the selected subset – and a value of "false" would indicate that it is not. More...
 
virtual void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &datacache)
 Initialize any data members of this instance from an input tag and a DataMap object. More...
 
virtual std::string get_name () const =0
 
utility::vector1< core::Sizeselection_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...
 

Constructor & Destructor Documentation

◆ ResidueSelector()

core::select::residue_selector::ResidueSelector::ResidueSelector ( )
default

Constructor.

◆ ~ResidueSelector()

core::select::residue_selector::ResidueSelector::~ResidueSelector ( )
overridedefault

Destructor.

Member Function Documentation

◆ apply()

virtual ResidueSubset core::select::residue_selector::ResidueSelector::apply ( core::pose::Pose const &  pose) const
pure virtual

Return a ResidueSubset indicating a selection of Residues from the input Pose; the ResidueSubset is an array of booleans where a value of "true" for position i indicates that residue i is a part of the selected subset – and a value of "false" would indicate that it is not.

Implemented in protocols::residue_selectors::TaskSelector, protocols::residue_selectors::StoredResidueSubsetSelector, protocols::residue_selectors::NativeSelector, protocols::residue_selectors::LigandMetalContactSelector, protocols::residue_selectors::HBondSelector, protocols::hbnet::UnsatSelector, protocols::fold_from_loops::selectors::ProteinResidueSelector, protocols::fold_from_loops::selectors::CutpointResidueSelector, protocols::fold_from_loops::selectors::ConstraintResidueSelector, protocols::environment::claims::EnvLabelSelector, protocols::denovo_design::residue_selectors::PairedSheetResidueSelector, protocols::denovo_design::residue_selectors::NamedSegmentSelector, protocols::cyclic_peptide::RamaMutationSelector, protocols::antibody::residue_selector::CDRResidueSelector, protocols::antibody::residue_selector::AntibodyRegionSelector, protocols::antibody::design::ResnumFromStringsWithRangesSelector, core::select::residue_selector::VirtualResidueSelector, core::select::residue_selector::TrueResidueSelector, core::select::residue_selector::SymmetricalResidueSelector, core::select::residue_selector::SSElementSelector, core::select::residue_selector::SliceResidueSelector, core::select::residue_selector::SimpleMetricSelector, core::select::residue_selector::SecondaryStructureSelector, core::select::residue_selector::ScoreTermValueBasedSelector, core::select::residue_selector::ReturnResidueSubsetSelector, core::select::residue_selector::ResidueSpanSelector, core::select::residue_selector::ResiduePropertySelector, core::select::residue_selector::ResiduePDBInfoHasLabelSelector, core::select::residue_selector::ResidueNameSelector, core::select::residue_selector::ResidueInSequenceMotifSelector, core::select::residue_selector::ResidueInMembraneSelector, core::select::residue_selector::ResidueIndexSelector, core::select::residue_selector::RandomResidueSelector, core::select::residue_selector::RandomGlycanFoliageSelector, core::select::residue_selector::PrimarySequenceNeighborhoodSelector, core::select::residue_selector::PhiSelector, core::select::residue_selector::OrResidueSelector, core::select::residue_selector::NumNeighborsSelector, core::select::residue_selector::NotResidueSelector, core::select::residue_selector::NeighborhoodResidueSelector, core::select::residue_selector::LogicResidueSelector, core::select::residue_selector::LayerSelector, core::select::residue_selector::JumpUpstreamSelector, core::select::residue_selector::JumpDownstreamSelector, core::select::residue_selector::InterGroupInterfaceByVectorSelector, core::select::residue_selector::GlycanResidueSelector, core::select::residue_selector::GlycanPositionSelector, core::select::residue_selector::GlycanLayerSelector, core::select::residue_selector::FractionSelector, core::select::residue_selector::FalseResidueSelector, core::select::residue_selector::ConfluentSelector, core::select::residue_selector::CloseContactResidueSelector, core::select::residue_selector::ChainSelector, core::select::residue_selector::BondedResidueSelector, core::select::residue_selector::BlockSelector, core::select::residue_selector::BinSelector, core::select::residue_selector::BFactorSelector, core::select::residue_selector::AsymmetricUnitSelector, core::select::residue_selector::AndResidueSelector, core::pack::task::residue_selector::ClashBasedShellSelector, and core::select::residue_selector::DensityFitResidueSelector.

Referenced by protocols::contact_map::ContactMap::fill_contacts(), protocols::contact_map::ContactMap::fill_contacts_all_atom2(), selection_positions(), and core::select::residue_selector::InterGroupInterfaceByVectorSelector::set_from_residue_selector().

◆ clone()

virtual ResidueSelectorOP core::select::residue_selector::ResidueSelector::clone ( ) const
pure virtual

Clone operator.

All ResidueSelectors must implement a clone() operator. This must create a copy of the object and return a ResidueSelectorOP to the original object.

Implemented in protocols::residue_selectors::TaskSelector, protocols::residue_selectors::StoredResidueSubsetSelector, protocols::residue_selectors::NativeSelector, protocols::residue_selectors::LigandMetalContactSelector, protocols::residue_selectors::HBondSelector, protocols::hbnet::UnsatSelector, protocols::fold_from_loops::selectors::ProteinResidueSelector, protocols::fold_from_loops::selectors::CutpointResidueSelector, protocols::fold_from_loops::selectors::ConstraintResidueSelector, protocols::environment::claims::EnvLabelSelector, protocols::denovo_design::residue_selectors::PairedSheetResidueSelector, protocols::denovo_design::residue_selectors::NamedSegmentSelector, protocols::cyclic_peptide::RamaMutationSelector, protocols::antibody::residue_selector::CDRResidueSelector, protocols::antibody::residue_selector::AntibodyRegionSelector, protocols::antibody::design::ResnumFromStringsWithRangesSelector, core::select::residue_selector::VirtualResidueSelector, core::select::residue_selector::TrueResidueSelector, core::select::residue_selector::SymmetricalResidueSelector, core::select::residue_selector::SSElementSelector, core::select::residue_selector::SliceResidueSelector, core::select::residue_selector::SimpleMetricSelector, core::select::residue_selector::SecondaryStructureSelector, core::select::residue_selector::ScoreTermValueBasedSelector, core::select::residue_selector::ReturnResidueSubsetSelector, core::select::residue_selector::ResidueSpanSelector, core::select::residue_selector::ResiduePropertySelector, core::select::residue_selector::ResiduePDBInfoHasLabelSelector, core::select::residue_selector::ResidueNameSelector, core::select::residue_selector::ResidueInSequenceMotifSelector, core::select::residue_selector::ResidueInMembraneSelector, core::select::residue_selector::ResidueIndexSelector, core::select::residue_selector::RandomResidueSelector, core::select::residue_selector::RandomGlycanFoliageSelector, core::select::residue_selector::PrimarySequenceNeighborhoodSelector, core::select::residue_selector::PhiSelector, core::select::residue_selector::OrResidueSelector, core::select::residue_selector::NumNeighborsSelector, core::select::residue_selector::NotResidueSelector, core::select::residue_selector::NeighborhoodResidueSelector, core::select::residue_selector::LogicResidueSelector, core::select::residue_selector::LayerSelector, core::select::residue_selector::JumpUpstreamSelector, core::select::residue_selector::JumpDownstreamSelector, core::select::residue_selector::InterGroupInterfaceByVectorSelector, core::select::residue_selector::GlycanSequonsSelector, core::select::residue_selector::GlycanResidueSelector, core::select::residue_selector::GlycanPositionSelector, core::select::residue_selector::GlycanLayerSelector, core::select::residue_selector::FractionSelector, core::select::residue_selector::FalseResidueSelector, core::select::residue_selector::DensityFitResidueSelector, core::select::residue_selector::ConfluentSelector, core::select::residue_selector::CloseContactResidueSelector, core::select::residue_selector::ChainSelector, core::select::residue_selector::BondedResidueSelector, core::select::residue_selector::BlockSelector, core::select::residue_selector::BinSelector, core::select::residue_selector::BFactorSelector, core::select::residue_selector::AsymmetricUnitSelector, core::select::residue_selector::AndResidueSelector, and core::pack::task::residue_selector::ClashBasedShellSelector.

Referenced by protocols::denovo_design::movers::AlignResiduesMover::add_target_selector(), protocols::denovo_design::movers::AlignResiduesMover::add_template_selector(), protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter::query_selector(), protocols::fold_from_loops::movers::AlignByResidueSelectorMover::query_selector(), protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter::reference_selector(), protocols::fold_from_loops::movers::AlignByResidueSelectorMover::reference_selector(), protocols::fold_from_loops::filters::ScorePoseSegmentFromResidueSelectorFilter::residue_selector(), protocols::fold_from_loops::movers::LabelPoseFromResidueSelectorMover::residue_selector(), protocols::constraint_generator::AtomPairConstraintGenerator::set_residue_selector(), protocols::denovo_design::filters::SSShapeComplementarityFilter::set_residue_selector(), protocols::fldsgn::filters::SecondaryStructureFilter::set_residue_selector(), protocols::fold_from_loops::constraint_generator::SegmentedAtomPairConstraintGenerator::set_residue_selector(), protocols::fold_from_loops::movers::ReleaseConstraintFromResidueMover::set_residue_selector(), protocols::simple_filters::Worst9merFilter::set_residue_selector(), protocols::simple_moves::StructProfileMover::set_residue_selector(), protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::set_residue_selector(), and protocols::constraint_generator::AtomPairConstraintGenerator::set_secondary_residue_selector().

◆ get_name()

virtual std::string core::select::residue_selector::ResidueSelector::get_name ( ) const
pure virtual

Implemented in protocols::residue_selectors::TaskSelector, protocols::residue_selectors::StoredResidueSubsetSelector, protocols::residue_selectors::NativeSelector, protocols::residue_selectors::LigandMetalContactSelector, protocols::residue_selectors::HBondSelector, protocols::hbnet::UnsatSelector, protocols::fold_from_loops::selectors::ProteinResidueSelector, protocols::fold_from_loops::selectors::CutpointResidueSelector, protocols::fold_from_loops::selectors::ConstraintResidueSelector, protocols::environment::claims::EnvLabelSelector, protocols::denovo_design::residue_selectors::PairedSheetResidueSelector, protocols::denovo_design::residue_selectors::NamedSegmentSelector, protocols::cyclic_peptide::RamaMutationSelector, protocols::antibody::residue_selector::CDRResidueSelector, protocols::antibody::residue_selector::AntibodyRegionSelector, protocols::antibody::design::ResnumFromStringsWithRangesSelector, core::select::residue_selector::VirtualResidueSelector, core::select::residue_selector::TrueResidueSelector, core::select::residue_selector::SymmetricalResidueSelector, core::select::residue_selector::SSElementSelector, core::select::residue_selector::SliceResidueSelector, core::select::residue_selector::SimpleMetricSelector, core::select::residue_selector::SecondaryStructureSelector, core::select::residue_selector::ScoreTermValueBasedSelector, core::select::residue_selector::ReturnResidueSubsetSelector, core::select::residue_selector::ResidueSpanSelector, core::select::residue_selector::ResiduePropertySelector, core::select::residue_selector::ResiduePDBInfoHasLabelSelector, core::select::residue_selector::ResidueNameSelector, core::select::residue_selector::ResidueInSequenceMotifSelector, core::select::residue_selector::ResidueInMembraneSelector, core::select::residue_selector::ResidueIndexSelector, core::select::residue_selector::RandomResidueSelector, core::select::residue_selector::RandomGlycanFoliageSelector, core::select::residue_selector::PrimarySequenceNeighborhoodSelector, core::select::residue_selector::PhiSelector, core::select::residue_selector::OrResidueSelector, core::select::residue_selector::NumNeighborsSelector, core::select::residue_selector::NotResidueSelector, core::select::residue_selector::NeighborhoodResidueSelector, core::select::residue_selector::LogicResidueSelector, core::select::residue_selector::LayerSelector, core::select::residue_selector::JumpUpstreamSelector, core::select::residue_selector::JumpDownstreamSelector, core::select::residue_selector::InterGroupInterfaceByVectorSelector, core::select::residue_selector::GlycanSequonsSelector, core::select::residue_selector::GlycanResidueSelector, core::select::residue_selector::GlycanPositionSelector, core::select::residue_selector::GlycanLayerSelector, core::select::residue_selector::FractionSelector, core::select::residue_selector::FalseResidueSelector, core::select::residue_selector::DensityFitResidueSelector, core::select::residue_selector::ConfluentSelector, core::select::residue_selector::CloseContactResidueSelector, core::select::residue_selector::ChainSelector, core::select::residue_selector::BondedResidueSelector, core::select::residue_selector::BlockSelector, core::select::residue_selector::BinSelector, core::select::residue_selector::BFactorSelector, core::select::residue_selector::AsymmetricUnitSelector, core::select::residue_selector::AndResidueSelector, and core::pack::task::residue_selector::ClashBasedShellSelector.

◆ parse_my_tag()

void core::select::residue_selector::ResidueSelector::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap datacache 
)
virtual

Initialize any data members of this instance from an input tag and a DataMap object.

Noop implementation in the base class in the case that a derived class has no need to read data from an input tag

Reimplemented in protocols::residue_selectors::NativeSelector, protocols::residue_selectors::LigandMetalContactSelector, protocols::residue_selectors::HBondSelector, protocols::hbnet::UnsatSelector, protocols::fold_from_loops::selectors::ProteinResidueSelector, protocols::fold_from_loops::selectors::CutpointResidueSelector, protocols::fold_from_loops::selectors::ConstraintResidueSelector, protocols::environment::claims::EnvLabelSelector, protocols::denovo_design::residue_selectors::PairedSheetResidueSelector, protocols::denovo_design::residue_selectors::NamedSegmentSelector, protocols::cyclic_peptide::RamaMutationSelector, protocols::antibody::residue_selector::CDRResidueSelector, protocols::antibody::residue_selector::AntibodyRegionSelector, protocols::antibody::design::ResnumFromStringsWithRangesSelector, core::select::residue_selector::VirtualResidueSelector, core::select::residue_selector::TrueResidueSelector, core::select::residue_selector::SliceResidueSelector, core::select::residue_selector::SimpleMetricSelector, core::select::residue_selector::SecondaryStructureSelector, core::select::residue_selector::ReturnResidueSubsetSelector, core::select::residue_selector::ResiduePropertySelector, core::select::residue_selector::RandomGlycanFoliageSelector, core::select::residue_selector::PhiSelector, core::select::residue_selector::OrResidueSelector, core::select::residue_selector::NumNeighborsSelector, core::select::residue_selector::NotResidueSelector, core::select::residue_selector::NeighborhoodResidueSelector, core::select::residue_selector::LogicResidueSelector, core::select::residue_selector::InterGroupInterfaceByVectorSelector, core::select::residue_selector::GlycanResidueSelector, core::select::residue_selector::GlycanPositionSelector, core::select::residue_selector::GlycanLayerSelector, core::select::residue_selector::FractionSelector, core::select::residue_selector::FalseResidueSelector, core::select::residue_selector::DensityFitResidueSelector, core::select::residue_selector::ConfluentSelector, core::select::residue_selector::CloseContactResidueSelector, core::select::residue_selector::ChainSelector, core::select::residue_selector::BlockSelector, core::select::residue_selector::BinSelector, core::select::residue_selector::BFactorSelector, core::select::residue_selector::AsymmetricUnitSelector, core::select::residue_selector::AndResidueSelector, core::pack::task::residue_selector::ClashBasedShellSelector, core::select::residue_selector::ScoreTermValueBasedSelector, core::select::residue_selector::BondedResidueSelector, core::select::residue_selector::RandomResidueSelector, protocols::residue_selectors::TaskSelector, protocols::residue_selectors::StoredResidueSubsetSelector, core::select::residue_selector::SymmetricalResidueSelector, core::select::residue_selector::SSElementSelector, core::select::residue_selector::ResidueSpanSelector, core::select::residue_selector::ResiduePDBInfoHasLabelSelector, core::select::residue_selector::ResidueNameSelector, core::select::residue_selector::ResidueInSequenceMotifSelector, core::select::residue_selector::ResidueInMembraneSelector, core::select::residue_selector::ResidueIndexSelector, core::select::residue_selector::PrimarySequenceNeighborhoodSelector, core::select::residue_selector::LayerSelector, core::select::residue_selector::JumpUpstreamSelector, core::select::residue_selector::JumpDownstreamSelector, and core::select::residue_selector::GlycanSequonsSelector.

◆ provide_citation_info()

void core::select::residue_selector::ResidueSelector::provide_citation_info ( basic::citation_manager::CitationCollectionList &  ) const
virtual

Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by residue selectors wishing to provide citation information.

Reimplemented in core::select::residue_selector::SliceResidueSelector, core::select::residue_selector::OrResidueSelector, core::select::residue_selector::NotResidueSelector, core::select::residue_selector::NeighborhoodResidueSelector, core::select::residue_selector::LayerSelector, core::select::residue_selector::BFactorSelector, and core::select::residue_selector::AndResidueSelector.

◆ selection_positions()

utility::vector1< core::Size > core::select::residue_selector::ResidueSelector::selection_positions ( core::pose::Pose const &  pose) const

Calls apply and returns the Rosetta numbering corresponding to the selected residues.

References apply(), and core::select::residue_selector::selection_positions().


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