protocols::filters::Filter Class Reference

#include <Filter.hh>

Inherits ReferenceCount.

Inherited by protocols::calc_taskop_filters::ConservedPosMutationFilter, protocols::calc_taskop_filters::MultipleSigmoids, protocols::calc_taskop_filters::Operator, protocols::calc_taskop_filters::RelativePoseFilter, protocols::calc_taskop_filters::RotamerBoltzmannWeight, protocols::calc_taskop_filters::RotamerBoltzmannWeight2, protocols::calc_taskop_filters::Sigmoid, protocols::constraint_filters::ConstraintScoreCutoffFilter, protocols::constraint_filters::ConstraintScoreFilter, protocols::constraint_filters::SavePoseConstraintToFileFilter, protocols::constraint_filters::ShowConstraintsFilter, protocols::cyclic_peptide::CycpepSymmetryFilter, protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter, protocols::denovo_design::filters::ExposedHydrophobicsFilter, protocols::denovo_design::filters::PreProlineFilter, protocols::denovo_design::filters::SSPredictionFilter, protocols::denovo_design::filters::SSShapeComplementarityFilter, protocols::dna_dock::DNAClashCheckFilter, protocols::dna_dock::PropagateClashCheckFilter, protocols::docking::DockingHighResFilter, protocols::docking::DockingLowResFilter, protocols::enzdes::DiffAtomSasaFilter, protocols::enzdes::EnzdesScorefileFilter, protocols::enzdes::EnzScoreFilter, protocols::enzdes::LigBurialFilter, protocols::enzdes::LigDSasaFilter, protocols::enzdes::LigInterfaceEnergyFilter, protocols::enzdes::RemoveLigandFilter, protocols::enzdes::RepackWithoutLigandFilter, protocols::enzdes::ResidueConformerFilter, protocols::evolution::AASynthesisFitnessCost, protocols::evolution::AlignmentAAFinder, protocols::evolution::AlignmentGapInserter, protocols::filters::CalculatorFilter, protocols::filters::CombinedFilter, protocols::filters::CompoundFilter, protocols::filters::ContingentFilter, protocols::filters::FalseFilter, protocols::filters::IfThenFilter, protocols::filters::MoveBeforeFilter, protocols::filters::ReplicateFilter, protocols::filters::StochasticFilter, protocols::filters::TimeFilter, protocols::filters::TrueFilter, protocols::filters::VectorPoseFilter, protocols::fldsgn::filters::CoreDunbrackFilter, protocols::fldsgn::filters::FragQualFilter, protocols::fldsgn::filters::HelixBendFilter, protocols::fldsgn::filters::HelixKinkFilter, protocols::fldsgn::filters::HelixPairingFilter, protocols::fldsgn::filters::HSSTripletFilter, protocols::fldsgn::filters::InterlockingAromaFilter, protocols::fldsgn::filters::NcontactsFilter, protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter, protocols::fldsgn::filters::SecondaryStructureCountFilter, protocols::fldsgn::filters::SecondaryStructureFilter, protocols::fldsgn::filters::SecondaryStructureHasResidueFilter, protocols::fldsgn::filters::SheetTopologyFilter, protocols::fldsgn::filters::StrandCurvatureByLevels, protocols::fldsgn::filters::StrandHelixGeometryFilter, protocols::fold_from_loops::filters::ConstraintFulfilmentFilter, protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter, protocols::fold_from_loops::filters::ScorePoseSegmentFromResidueSelectorFilter, protocols::frag_picker::FragmentScoreFilter, protocols::hbnet::HBNetScore, protocols::helical_bundle::BundleReporterFilter, protocols::indexed_structure_store::filters::FragmentLookupFilter, protocols::ligand_docking::AtomCountFilter, protocols::ligand_docking::ChainExistsFilter, protocols::ligand_docking::CompleteConnectionsFilter, protocols::ligand_docking::HBondAcceptorFilter, protocols::ligand_docking::HBondDonorFilter, protocols::ligand_docking::HeavyAtomFilter, protocols::ligand_docking::MolarMassFilter, protocols::ligand_docking::MolecularMassFilter, protocols::loops::filters::LoopAnalyzerFilter, protocols::matdes::ClashCheckFilter, protocols::matdes::GetRBDOFValues, protocols::matdes::InterfacePackingFilter, protocols::matdes::OligomericAverageDegreeFilter, protocols::matdes::SymUnsatHbondFilter, protocols::peptide_deriver::PeptideDeriverFilter, protocols::protein_interface_design::filters::AtomicContactCountFilter, protocols::protein_interface_design::filters::AverageDegreeFilter, protocols::protein_interface_design::filters::BindingStrainFilter, protocols::protein_interface_design::filters::BoltzmannFilter, protocols::protein_interface_design::filters::ClashWithTargetFilter, protocols::protein_interface_design::filters::DesignableResiduesFilter, protocols::protein_interface_design::filters::DisulfideFilter, protocols::protein_interface_design::filters::FilterScanFilter, protocols::protein_interface_design::filters::FNatFilter, protocols::protein_interface_design::filters::HbondsToAtomFilter, protocols::protein_interface_design::filters::HbondsToResidueFilter, protocols::protein_interface_design::filters::InterfaceHolesFilter, protocols::protein_interface_design::filters::IRmsdFilter, protocols::protein_interface_design::filters::LRmsdFilter, protocols::protein_interface_design::filters::RelativeSegmentFilter, protocols::protein_interface_design::filters::RmsdFilter, protocols::protein_interface_design::filters::RmsdSimpleFilter, protocols::protein_interface_design::filters::SequenceRecoveryFilter, protocols::protein_interface_design::filters::SpecificResiduesNearInterfaceFilter, protocols::protein_interface_design::filters::SSamountFilter, protocols::protein_interface_design::filters::StubScoreFilter, protocols::protein_interface_design::filters::Torsion, protocols::score_filters::GeometryFilter, protocols::score_filters::ScoreCutoffFilter, protocols::score_filters::ScoreTypeFilter, protocols::simple_ddg::AlaScan, protocols::simple_ddg::DdgFilter, protocols::simple_ddg::DdGScan, protocols::simple_ddg::InterfaceBindingEnergyDensityFilter, protocols::simple_ddg::SSElementBisectddGFilter, protocols::simple_filters::AbinitioBaseFilter, protocols::simple_filters::AngleToVector, protocols::simple_filters::AtomicContactFilter, protocols::simple_filters::AtomicDistanceFilter, protocols::simple_filters::AveragePathLengthFilter, protocols::simple_filters::BuriedSurfaceAreaFilter, protocols::simple_filters::BuriedUnsatHbondFilter, protocols::simple_filters::ChainBreak, protocols::simple_filters::ChainCountFilter, protocols::simple_filters::ContactMolecularSurfaceFilter, protocols::simple_filters::DeltaFilter, protocols::simple_filters::DisulfideEntropyFilter, protocols::simple_filters::DomainInterfaceFilter, protocols::simple_filters::EnergyPerResidueFilter, protocols::simple_filters::ExpiryFilter, protocols::simple_filters::FileExistFilter, protocols::simple_filters::FileRemoveFilter, protocols::simple_filters::HelixHelixAngleFilter, protocols::simple_filters::HolesFilter, protocols::simple_filters::InterfaceHbondsFilter, protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter, protocols::simple_filters::InterfaceSasaFilter, protocols::simple_filters::InterRepeatContactFilter, protocols::simple_filters::IntraRepeatContactFilter, protocols::simple_filters::LeastNativeLike9merFilter, protocols::simple_filters::LongestContinuousPolarSegmentFilter, protocols::simple_filters::MembAccesResidueLipophilicityFilter, protocols::simple_filters::MotifScoreFilter, protocols::simple_filters::MPSpanAngleFilter, protocols::simple_filters::MutationsFilter, protocols::simple_filters::NeighborTypeFilter, protocols::simple_filters::NetChargeFilter, protocols::simple_filters::NMerPSSMEnergyFilter, protocols::simple_filters::NMerSVMEnergyFilter, protocols::simple_filters::NonSequentialNeighborsFilter, protocols::simple_filters::PackerNeighborGraphFilter, protocols::simple_filters::PackStatFilter, protocols::simple_filters::PDDFScoreFilter, protocols::simple_filters::PoseComment, protocols::simple_filters::PoseInfoFilter, protocols::simple_filters::RangeFilter, protocols::simple_filters::ReadPoseExtraScoreFilter, protocols::simple_filters::RepeatParameterFilter, protocols::simple_filters::ReportFilter, protocols::simple_filters::ResidueBurialFilter, protocols::simple_filters::ResidueChiralityFilter, protocols::simple_filters::ResidueCountFilter, protocols::simple_filters::ResidueDepthFilter, protocols::simple_filters::ResidueDistanceFilter, protocols::simple_filters::ResidueIEFilter, protocols::simple_filters::ResidueLipophilicityFilter, protocols::simple_filters::ResidueSelectionDistanceFilter, protocols::simple_filters::ResidueSetChainEnergyFilter, protocols::simple_filters::ResiduesInInterfaceFilter, protocols::simple_filters::SaveResfileToDiskFilter, protocols::simple_filters::SAXSScoreFilter, protocols::simple_filters::SecretionPredictionFilter, protocols::simple_filters::SequenceDistance, protocols::simple_filters::ShapeComplementarityFilter, protocols::simple_filters::SidechainRmsdFilter, protocols::simple_filters::SimpleHbondsToAtomFilter, protocols::simple_filters::SimpleMetricFilter, protocols::simple_filters::SpanTopologyMatchPoseFilter, protocols::simple_filters::SSElementLengthFilter, protocols::simple_filters::SSElementMotifContactFilter, protocols::simple_filters::SSMotifFinder, protocols::simple_filters::StemFinder, protocols::simple_filters::SymmetricMotifFilter, protocols::simple_filters::TaskAwareSASAFilter, protocols::simple_filters::TaskAwareScoreTypeFilter, protocols::simple_filters::TerminusDistanceFilter, protocols::simple_filters::TMsAACompFilter, protocols::simple_filters::TMsSpanMembraneFilter, and protocols::simple_filters::TotalSasaFilter.

Public Member Functions
	Filter ()
	Filter (std::string const &)
	Filter (Filter const &)
	~Filter () override
virtual void	report (std::ostream &, core::pose::Pose const &) const
virtual core::Real	report_sm (core::pose::Pose const &) const
	used to report filter internals through a score or silent file More...
virtual std::string	get_type () const
std::string	get_user_defined_name () const
void	set_user_defined_name (std::string const &name)
virtual void	clear ()
	used to clear internal variables if needed. Using fresh_instance is preferred since it's a pure virtual More...
virtual void	parse_my_tag (utility::tag::TagCOP, basic::datacache::DataMap &, Filters_map const &, moves::Movers_map const &, core::pose::Pose const &)
virtual FilterOP	clone () const =0
virtual FilterOP	fresh_instance () const =0
virtual bool	apply (core::pose::Pose const &pose) const =0
	Returns true if the given pose passes the filter, false otherwise. More...
virtual core::Real	score (core::pose::Pose &pose)
virtual std::string	name () const
virtual bool	filter_provides_citation_info () const
	Does this filter provide information about how to cite it? More...
virtual utility::vector1 < basic::citation_manager::CitationCollectionCOP >	provide_citation_info () const
	Provide the citation. More...
virtual bool	filter_is_unpublished () const
	Does this filter indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
virtual utility::vector1 < basic::citation_manager::UnpublishedModuleInfoCOP >	provide_authorship_info_for_unpublished () const
	Provide a list of authors and their e-mail addresses, as strings. More...

Protected Attributes
std::string	scorename_

Private Attributes
std::string const	type_
std::string	user_defined_name_

Constructor & Destructor Documentation

protocols::filters::Filter::Filter

(

)

protocols::filters::Filter::Filter

(

std::string const &

type

)

protocols::filters::Filter::Filter

(

Filter const &

init

)

protocols::filters::Filter::~Filter ( )

overridedefault

Member Function Documentation

virtual bool protocols::filters::Filter::apply ( core::pose::Pose const &  pose ) const

pure virtual

Returns true if the given pose passes the filter, false otherwise.

Implemented in protocols::enzdes::ResidueConformerFilter, protocols::enzdes::EnzdesScorefileFilter, protocols::enzdes::RepackWithoutLigandFilter, protocols::filters::IfThenFilter, protocols::enzdes::DiffAtomSasaFilter, protocols::filters::MoveBeforeFilter, protocols::filters::CombinedFilter, protocols::enzdes::EnzScoreFilter, protocols::simple_filters::ResidueDepthFilter, protocols::peptide_deriver::PeptideDeriverFilter, protocols::fldsgn::filters::HSSTripletFilter, protocols::fldsgn::filters::HelixPairingFilter, protocols::enzdes::LigInterfaceEnergyFilter, protocols::filters::CompoundFilter, protocols::fldsgn::filters::SheetTopologyFilter, protocols::simple_filters::SaveResfileToDiskFilter, protocols::indexed_structure_store::filters::FragmentLookupFilter, protocols::matdes::GetRBDOFValues, protocols::helical_bundle::BundleReporterFilter, protocols::matdes::OligomericAverageDegreeFilter, protocols::fldsgn::filters::InterlockingAromaFilter, protocols::fldsgn::filters::SecondaryStructureFilter, protocols::simple_filters::SecretionPredictionFilter, protocols::simple_filters::PackerNeighborGraphFilter, protocols::fldsgn::filters::CoreDunbrackFilter, protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter, protocols::simple_filters::TaskAwareSASAFilter, protocols::fldsgn::filters::FragQualFilter, protocols::fldsgn::filters::NcontactsFilter, protocols::matdes::ClashCheckFilter, protocols::dna_dock::PropagateClashCheckFilter, protocols::simple_filters::HolesFilter, protocols::simple_filters::IntraRepeatContactFilter, protocols::simple_filters::PackStatFilter, protocols::simple_filters::InterRepeatContactFilter, protocols::simple_filters::ShapeComplementarityFilter, protocols::dna_dock::DNAClashCheckFilter, protocols::fldsgn::filters::HelixKinkFilter, protocols::simple_filters::SSElementMotifContactFilter, protocols::simple_filters::RangeFilter, protocols::enzdes::LigBurialFilter, protocols::fldsgn::filters::SecondaryStructureCountFilter, protocols::matdes::SymUnsatHbondFilter, protocols::simple_ddg::SSElementBisectddGFilter, protocols::simple_filters::SSElementLengthFilter, protocols::fldsgn::filters::SecondaryStructureHasResidueFilter, protocols::simple_filters::SimpleMetricFilter, protocols::filters::StochasticFilter, protocols::simple_filters::ContactMolecularSurfaceFilter, protocols::simple_filters::DomainInterfaceFilter, protocols::simple_filters::LeastNativeLike9merFilter, protocols::simple_ddg::DdGScan, protocols::docking::DockingHighResFilter, protocols::fldsgn::filters::StrandHelixGeometryFilter, protocols::calc_taskop_filters::RotamerBoltzmannWeight2, protocols::denovo_design::filters::SSShapeComplementarityFilter, protocols::protein_interface_design::filters::HbondsToResidueFilter, protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter, protocols::protein_interface_design::filters::DisulfideFilter, protocols::constraint_filters::ConstraintScoreCutoffFilter, protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter, protocols::fldsgn::filters::StrandCurvatureByLevels, protocols::score_filters::ScoreCutoffFilter, protocols::calc_taskop_filters::ConservedPosMutationFilter, protocols::denovo_design::filters::ExposedHydrophobicsFilter, protocols::protein_interface_design::filters::HbondsToAtomFilter, protocols::denovo_design::filters::PreProlineFilter, protocols::filters::FalseFilter, protocols::simple_filters::BuriedUnsatHbondFilter, protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter, protocols::simple_filters::SheetFilter, protocols::fldsgn::filters::HelixBendFilter, protocols::fold_from_loops::filters::ConstraintFulfilmentFilter, protocols::fold_from_loops::filters::ScorePoseSegmentFromResidueSelectorFilter, protocols::protein_interface_design::filters::AtomicContactCountFilter, protocols::protein_interface_design::filters::SpecificResiduesNearInterfaceFilter, protocols::enzdes::LigDSasaFilter, protocols::simple_filters::COFilter, protocols::simple_filters::InterfaceHbondsFilter, protocols::simple_filters::RGFilter, protocols::enzdes::RemoveLigandFilter, protocols::hbnet::HBNetScore, protocols::ligand_docking::AtomCountFilter, protocols::ligand_docking::HBondAcceptorFilter, protocols::ligand_docking::HeavyAtomFilter, protocols::ligand_docking::MolarMassFilter, protocols::ligand_docking::MolecularMassFilter, protocols::simple_ddg::InterfaceBindingEnergyDensityFilter, protocols::simple_filters::AbinitioBaseFilter, protocols::simple_filters::BuriedSurfaceAreaFilter, protocols::simple_filters::SymmetricMotifFilter, protocols::ligand_docking::ChainExistsFilter, protocols::score_filters::ScoreTypeFilter, protocols::simple_filters::LongestContinuousPolarSegmentFilter, protocols::simple_filters::MotifScoreFilter, protocols::simple_filters::ResidueIEFilter, protocols::loops::filters::LoopAnalyzerFilter, protocols::docking::DockingLowResFilter, protocols::frag_picker::FragmentScoreFilter, protocols::ligand_docking::CompleteConnectionsFilter, protocols::evolution::AlignmentGapInserter, protocols::protein_interface_design::filters::SSamountFilter, protocols::simple_filters::AveragePathLengthFilter, protocols::simple_filters::DisulfideEntropyFilter, protocols::ligand_docking::HBondDonorFilter, protocols::protein_interface_design::filters::FilterScanFilter, protocols::protein_interface_design::filters::RmsdSimpleFilter, protocols::simple_filters::MembAccesResidueLipophilicityFilter, protocols::simple_filters::ReadPoseExtraScoreFilter, protocols::protein_interface_design::filters::StubScoreFilter, protocols::simple_filters::ResidueCountFilter, protocols::denovo_design::filters::SSPredictionFilter, protocols::evolution::AlignmentAAFinder, protocols::simple_filters::PDDFScoreFilter, protocols::simple_filters::SAXSScoreFilter, protocols::calc_taskop_filters::RotamerBoltzmannWeight, protocols::constraint_filters::ConstraintScoreFilter, protocols::filters::TrueFilter, protocols::filters::CalculatorFilter, protocols::filters::ContingentFilter, protocols::protein_interface_design::filters::FNatFilter, protocols::protein_interface_design::filters::IRmsdFilter, protocols::simple_filters::HelixHelixAngleFilter, protocols::simple_filters::NeighborTypeFilter, protocols::simple_filters::ResidueSetChainEnergyFilter, protocols::simple_filters::TaskAwareScoreTypeFilter, protocols::cyclic_peptide::CycpepSymmetryFilter, protocols::filters::VectorPoseFilter, protocols::protein_interface_design::filters::BindingStrainFilter, protocols::protein_interface_design::filters::DesignableResiduesFilter, protocols::protein_interface_design::filters::LRmsdFilter, protocols::protein_interface_design::filters::SequenceRecoveryFilter, protocols::simple_filters::AtomicContactFilter, protocols::simple_filters::SimpleHbondsToAtomFilter, protocols::simple_filters::TMsAACompFilter, protocols::calc_taskop_filters::MultipleSigmoids, protocols::calc_taskop_filters::Sigmoid, protocols::matdes::InterfacePackingFilter, protocols::protein_interface_design::filters::AverageDegreeFilter, protocols::protein_interface_design::filters::Torsion, protocols::recon_design::FitnessFilter, protocols::simple_filters::MutationsFilter, protocols::simple_filters::NMerSVMEnergyFilter, protocols::simple_filters::StemFinder, protocols::calc_taskop_filters::RelativePoseFilter, protocols::protein_interface_design::filters::RmsdFilter, protocols::simple_filters::AtomicDistanceFilter, protocols::simple_filters::MPSpanAngleFilter, protocols::simple_filters::NetChargeFilter, protocols::simple_filters::NMerPSSMEnergyFilter, protocols::simple_filters::ResidueChiralityFilter, protocols::simple_filters::ResidueLipophilicityFilter, protocols::simple_filters::SpanTopologyMatchPoseFilter, protocols::simple_filters::SSMotifFinder, protocols::simple_filters::TMsSpanMembraneFilter, protocols::calc_taskop_filters::Operator, protocols::constraint_filters::ShowConstraintsFilter, protocols::protein_interface_design::filters::BoltzmannFilter, protocols::score_filters::GeometryFilter, protocols::simple_ddg::AlaScan, protocols::simple_filters::ChainCountFilter, protocols::simple_filters::RepeatParameterFilter, protocols::simple_filters::TerminusDistanceFilter, protocols::evolution::AASynthesisFitnessCost, protocols::simple_filters::AngleToVector, protocols::simple_filters::ChainBreak, protocols::simple_filters::PoseComment, protocols::simple_filters::SequenceDistance, protocols::filters::TimeFilter, protocols::simple_ddg::DdgFilter, protocols::simple_filters::DeltaFilter, protocols::protein_interface_design::filters::InterfaceHolesFilter, protocols::simple_filters::EnergyPerResidueFilter, protocols::protein_interface_design::filters::RelativeSegmentFilter, protocols::simple_filters::ReportFilter, protocols::simple_filters::ExpiryFilter, protocols::simple_filters::FileExistFilter, protocols::simple_filters::FileRemoveFilter, protocols::simple_filters::InterfaceSasaFilter, protocols::simple_filters::ResiduesInInterfaceFilter, protocols::constraint_filters::SavePoseConstraintToFileFilter, protocols::filters::ReplicateFilter, protocols::protein_interface_design::filters::ClashWithTargetFilter, protocols::simple_filters::NonSequentialNeighborsFilter, protocols::simple_filters::PoseInfoFilter, protocols::simple_filters::ResidueDistanceFilter, protocols::simple_filters::TotalSasaFilter, protocols::simple_filters::ResidueSelectionDistanceFilter, protocols::simple_filters::SidechainRmsdFilter, and protocols::simple_filters::ResidueBurialFilter.

Referenced by protocols::rosetta_scripts::ParsedProtocol::apply_filter().

virtual void protocols::filters::Filter::clear ( )

inlinevirtual

used to clear internal variables if needed. Using fresh_instance is preferred since it's a pure virtual

Reimplemented in protocols::filters::CompoundFilter, protocols::hbnet::HBNetScore, and protocols::simple_filters::NeighborTypeFilter.

virtual FilterOP protocols::filters::Filter::clone ( ) const

pure virtual

Implemented in protocols::enzdes::ResidueConformerFilter, protocols::enzdes::EnzdesScorefileFilter, protocols::enzdes::RepackWithoutLigandFilter, protocols::filters::IfThenFilter, protocols::enzdes::DiffAtomSasaFilter, protocols::filters::MoveBeforeFilter, protocols::filters::CombinedFilter, protocols::enzdes::EnzScoreFilter, protocols::simple_filters::SimpleMetricFilter, protocols::simple_filters::ResidueDepthFilter, protocols::peptide_deriver::PeptideDeriverFilter, protocols::enzdes::LigInterfaceEnergyFilter, protocols::filters::CompoundFilter, protocols::simple_filters::LongestContinuousPolarSegmentFilter, protocols::indexed_structure_store::filters::FragmentLookupFilter, protocols::fldsgn::filters::StrandHelixGeometryFilter, protocols::cyclic_peptide::CycpepSymmetryFilter, protocols::simple_filters::PackerNeighborGraphFilter, protocols::fldsgn::filters::StrandCurvatureByLevels, protocols::calc_taskop_filters::RotamerBoltzmannWeight2, protocols::enzdes::LigBurialFilter, protocols::fldsgn::filters::HelixBendFilter, protocols::simple_filters::SecretionPredictionFilter, protocols::frag_picker::FragmentScoreFilter, protocols::fldsgn::filters::SheetTopologyFilter, protocols::simple_filters::SimpleHbondsToAtomFilter, protocols::fldsgn::filters::HelixPairingFilter, protocols::fldsgn::filters::HSSTripletFilter, protocols::filters::StochasticFilter, protocols::simple_filters::BuriedSurfaceAreaFilter, protocols::fldsgn::filters::NcontactsFilter, protocols::simple_filters::SaveResfileToDiskFilter, protocols::simple_filters::DomainInterfaceFilter, protocols::fldsgn::filters::CoreDunbrackFilter, protocols::fldsgn::filters::InterlockingAromaFilter, protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter, protocols::matdes::GetRBDOFValues, protocols::fldsgn::filters::FragQualFilter, protocols::matdes::OligomericAverageDegreeFilter, protocols::simple_filters::HolesFilter, protocols::simple_filters::TaskAwareSASAFilter, protocols::loops::filters::LoopAnalyzerFilter, protocols::docking::DockingHighResFilter, protocols::simple_filters::SSElementLengthFilter, protocols::fldsgn::filters::HelixKinkFilter, protocols::simple_ddg::SSElementBisectddGFilter, protocols::simple_filters::PackStatFilter, protocols::dna_dock::PropagateClashCheckFilter, protocols::protein_interface_design::filters::DisulfideFilter, protocols::simple_filters::SSElementMotifContactFilter, protocols::protein_interface_design::filters::HbondsToResidueFilter, protocols::fldsgn::filters::SecondaryStructureFilter, protocols::matdes::ClashCheckFilter, protocols::simple_filters::IntraRepeatContactFilter, protocols::simple_filters::LeastNativeLike9merFilter, protocols::simple_filters::RangeFilter, protocols::simple_filters::ShapeComplementarityFilter, protocols::constraint_filters::ConstraintScoreFilter, protocols::fldsgn::filters::SecondaryStructureCountFilter, protocols::simple_filters::ContactMolecularSurfaceFilter, protocols::simple_filters::InterRepeatContactFilter, protocols::simple_filters::SymmetricMotifFilter, protocols::dna_dock::DNAClashCheckFilter, protocols::fldsgn::filters::SecondaryStructureHasResidueFilter, protocols::denovo_design::filters::SSShapeComplementarityFilter, protocols::protein_interface_design::filters::HbondsToAtomFilter, protocols::filters::FalseFilter, protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter, protocols::denovo_design::filters::ExposedHydrophobicsFilter, protocols::enzdes::RemoveLigandFilter, protocols::helical_bundle::BundleReporterFilter, protocols::simple_filters::HelixHelixAngleFilter, protocols::simple_filters::BuriedUnsatHbondFilter, protocols::simple_filters::LongestContinuousApolarSegmentFilter, protocols::enzdes::LigDSasaFilter, protocols::protein_interface_design::filters::SpecificResiduesNearInterfaceFilter, protocols::denovo_design::filters::PreProlineFilter, protocols::matdes::SymUnsatHbondFilter, protocols::simple_ddg::InterfaceBindingEnergyDensityFilter, protocols::simple_filters::TMsAACompFilter, protocols::simple_ddg::DdGScan, protocols::simple_filters::InterfaceHbondsFilter, protocols::ligand_docking::AtomCountFilter, protocols::ligand_docking::HBondAcceptorFilter, protocols::ligand_docking::HeavyAtomFilter, protocols::ligand_docking::MolarMassFilter, protocols::ligand_docking::MolecularMassFilter, protocols::calc_taskop_filters::ConservedPosMutationFilter, protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter, protocols::score_filters::ScoreTypeFilter, protocols::simple_filters::AveragePathLengthFilter, protocols::simple_filters::DisulfideEntropyFilter, protocols::simple_filters::SheetFilter, protocols::docking::DockingLowResFilter, protocols::ligand_docking::ChainExistsFilter, protocols::simple_filters::ResidueIEFilter, protocols::constraint_filters::ConstraintScoreCutoffFilter, protocols::ligand_docking::CompleteConnectionsFilter, protocols::recon_design::FitnessFilter, protocols::score_filters::ScoreCutoffFilter, protocols::simple_filters::MembAccesResidueLipophilicityFilter, protocols::simple_filters::ResidueCountFilter, protocols::protein_interface_design::filters::FilterScanFilter, protocols::protein_interface_design::filters::StubScoreLoopsFilter, protocols::simple_filters::RepeatParameterFilter, protocols::filters::CalculatorFilter, protocols::protein_interface_design::filters::RmsdSimpleFilter, protocols::protein_interface_design::filters::SSamountFilter, protocols::protein_interface_design::filters::StubScoreFilter, protocols::simple_filters::ReadPoseExtraScoreFilter, protocols::constraint_filters::ShowConstraintsFilter, protocols::ligand_docking::HBondDonorFilter, protocols::simple_filters::NeighborTypeFilter, protocols::calc_taskop_filters::RotamerBoltzmannWeight, protocols::filters::ContingentFilter, protocols::simple_filters::AbinitioBaseFilter, protocols::simple_filters::AtomicContactFilter, protocols::simple_filters::TaskAwareScoreTypeFilter, protocols::denovo_design::filters::SSPredictionFilter, protocols::protein_interface_design::filters::BindingStrainFilter, protocols::protein_interface_design::filters::DesignableResiduesFilter, protocols::protein_interface_design::filters::SequenceRecoveryFilter, protocols::simple_filters::COFilter, protocols::simple_filters::RGFilter, protocols::filters::TrueFilter, protocols::matdes::InterfacePackingFilter, protocols::protein_interface_design::filters::AverageDegreeFilter, protocols::protein_interface_design::filters::FNatFilter, protocols::protein_interface_design::filters::IRmsdFilter, protocols::protein_interface_design::filters::Torsion, protocols::simple_filters::AtomicDistanceFilter, protocols::simple_filters::MPSpanAngleFilter, protocols::simple_filters::MutationsFilter, protocols::simple_filters::NetChargeFilter, protocols::simple_filters::ResidueChiralityFilter, protocols::simple_filters::ResidueLipophilicityFilter, protocols::simple_filters::ResidueSetChainEnergyFilter, protocols::simple_filters::SpanTopologyMatchPoseFilter, protocols::simple_filters::TMsSpanMembraneFilter, protocols::calc_taskop_filters::RelativePoseFilter, protocols::protein_interface_design::filters::LRmsdFilter, protocols::score_filters::GeometryFilter, protocols::simple_filters::ChainCountFilter, protocols::simple_filters::TerminusDistanceFilter, protocols::protein_interface_design::filters::BoltzmannFilter, protocols::simple_filters::NMerSVMEnergyFilter, protocols::filters::TimeFilter, protocols::protein_interface_design::filters::AtomicContactCountFilter, protocols::protein_interface_design::filters::RmsdFilter, protocols::simple_filters::NMerPSSMEnergyFilter, protocols::fold_from_loops::filters::ConstraintFulfilmentFilter, protocols::fold_from_loops::filters::ScorePoseSegmentFromResidueSelectorFilter, protocols::simple_ddg::AlaScan, protocols::simple_filters::DeltaFilter, protocols::simple_filters::MotifScoreFilter, protocols::simple_filters::TotalSasaFilter, protocols::calc_taskop_filters::MultipleSigmoids, protocols::evolution::AlignmentGapInserter, protocols::filters::ReplicateFilter, protocols::simple_ddg::DdgFilter, protocols::simple_filters::InterfaceSasaFilter, protocols::constraint_filters::SavePoseConstraintToFileFilter, protocols::evolution::AlignmentAAFinder, protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter, protocols::protein_interface_design::filters::InterfaceHolesFilter, protocols::simple_filters::EnergyPerResidueFilter, protocols::simple_filters::PoseInfoFilter, protocols::simple_filters::ResidueDistanceFilter, protocols::hbnet::HBNetScore, protocols::protein_interface_design::filters::RelativeSegmentFilter, protocols::simple_filters::ReportFilter, protocols::simple_filters::ResidueSelectionDistanceFilter, protocols::simple_filters::SidechainRmsdFilter, protocols::simple_filters::ExpiryFilter, protocols::simple_filters::FileExistFilter, protocols::simple_filters::FileRemoveFilter, protocols::simple_filters::ResidueBurialFilter, protocols::simple_filters::ResiduesInInterfaceFilter, protocols::calc_taskop_filters::Sigmoid, protocols::protein_interface_design::filters::ClashWithTargetFilter, protocols::simple_filters::NonSequentialNeighborsFilter, protocols::simple_filters::PDDFScoreFilter, protocols::simple_filters::SAXSScoreFilter, protocols::simple_filters::StemFinder, protocols::simple_filters::SSMotifFinder, protocols::calc_taskop_filters::Operator, protocols::evolution::AASynthesisFitnessCost, protocols::simple_filters::AngleToVector, protocols::simple_filters::ChainBreak, protocols::simple_filters::PoseComment, and protocols::simple_filters::SequenceDistance.

Referenced by protocols::denovo_design::movers::BuildDeNovoBackboneMover::set_score_filter().

bool protocols::filters::Filter::filter_is_unpublished ( ) const

virtual

Does this filter indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)?

Defaults to false. Derived classes may override this to provide authorship info. If set to true, the provide_authorship_info_for_unpublished() override should also be provided.

Author

Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org)

bool protocols::filters::Filter::filter_provides_citation_info ( ) const

virtual

Does this filter provide information about how to cite it?

Defaults to false. Derived classes may override this to provide citation info. If set to true, the provide_citation_info() override should also be provided.

Author

Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org)

Reimplemented in protocols::indexed_structure_store::filters::FragmentLookupFilter.

virtual FilterOP protocols::filters::Filter::fresh_instance ( ) const

pure virtual

Implemented in protocols::enzdes::ResidueConformerFilter, protocols::enzdes::EnzdesScorefileFilter, protocols::enzdes::RepackWithoutLigandFilter, protocols::filters::IfThenFilter, protocols::enzdes::DiffAtomSasaFilter, protocols::filters::MoveBeforeFilter, protocols::enzdes::EnzScoreFilter, protocols::filters::CombinedFilter, protocols::simple_filters::ResidueDepthFilter, protocols::simple_filters::SimpleMetricFilter, protocols::peptide_deriver::PeptideDeriverFilter, protocols::enzdes::LigInterfaceEnergyFilter, protocols::filters::CompoundFilter, protocols::indexed_structure_store::filters::FragmentLookupFilter, protocols::simple_filters::LongestContinuousPolarSegmentFilter, protocols::simple_filters::PackerNeighborGraphFilter, protocols::fldsgn::filters::StrandHelixGeometryFilter, protocols::cyclic_peptide::CycpepSymmetryFilter, protocols::enzdes::LigBurialFilter, protocols::simple_filters::SecretionPredictionFilter, protocols::fldsgn::filters::StrandCurvatureByLevels, protocols::calc_taskop_filters::RotamerBoltzmannWeight2, protocols::fldsgn::filters::HelixBendFilter, protocols::fldsgn::filters::SheetTopologyFilter, protocols::fldsgn::filters::HelixPairingFilter, protocols::fldsgn::filters::HSSTripletFilter, protocols::frag_picker::FragmentScoreFilter, protocols::filters::StochasticFilter, protocols::fldsgn::filters::NcontactsFilter, protocols::simple_filters::SaveResfileToDiskFilter, protocols::simple_filters::SimpleHbondsToAtomFilter, protocols::fldsgn::filters::CoreDunbrackFilter, protocols::fldsgn::filters::InterlockingAromaFilter, protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter, protocols::matdes::GetRBDOFValues, protocols::simple_filters::BuriedSurfaceAreaFilter, protocols::simple_filters::DomainInterfaceFilter, protocols::fldsgn::filters::FragQualFilter, protocols::matdes::OligomericAverageDegreeFilter, protocols::simple_filters::HolesFilter, protocols::simple_filters::TaskAwareSASAFilter, protocols::fldsgn::filters::HelixKinkFilter, protocols::simple_filters::PackStatFilter, protocols::simple_filters::SSElementLengthFilter, protocols::dna_dock::PropagateClashCheckFilter, protocols::docking::DockingHighResFilter, protocols::protein_interface_design::filters::DisulfideFilter, protocols::simple_ddg::SSElementBisectddGFilter, protocols::protein_interface_design::filters::HbondsToResidueFilter, protocols::simple_filters::IntraRepeatContactFilter, protocols::simple_filters::SSElementMotifContactFilter, protocols::fldsgn::filters::SecondaryStructureFilter, protocols::simple_filters::InterRepeatContactFilter, protocols::matdes::ClashCheckFilter, protocols::simple_filters::RangeFilter, protocols::simple_filters::ShapeComplementarityFilter, protocols::fldsgn::filters::SecondaryStructureCountFilter, protocols::simple_filters::ContactMolecularSurfaceFilter, protocols::simple_filters::LeastNativeLike9merFilter, protocols::loops::filters::LoopAnalyzerFilter, protocols::dna_dock::DNAClashCheckFilter, protocols::fldsgn::filters::SecondaryStructureHasResidueFilter, protocols::simple_filters::SymmetricMotifFilter, protocols::denovo_design::filters::SSShapeComplementarityFilter, protocols::protein_interface_design::filters::HbondsToAtomFilter, protocols::helical_bundle::BundleReporterFilter, protocols::constraint_filters::ConstraintScoreFilter, protocols::denovo_design::filters::ExposedHydrophobicsFilter, protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter, protocols::filters::FalseFilter, protocols::simple_filters::HelixHelixAngleFilter, protocols::enzdes::RemoveLigandFilter, protocols::enzdes::LigDSasaFilter, protocols::simple_filters::BuriedUnsatHbondFilter, protocols::ligand_docking::HeavyAtomFilter, protocols::protein_interface_design::filters::SpecificResiduesNearInterfaceFilter, protocols::simple_filters::TMsAACompFilter, protocols::matdes::SymUnsatHbondFilter, protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter, protocols::ligand_docking::AtomCountFilter, protocols::ligand_docking::HBondAcceptorFilter, protocols::ligand_docking::MolarMassFilter, protocols::ligand_docking::MolecularMassFilter, protocols::simple_filters::InterfaceHbondsFilter, protocols::denovo_design::filters::PreProlineFilter, protocols::simple_ddg::InterfaceBindingEnergyDensityFilter, protocols::simple_ddg::DdGScan, protocols::simple_filters::LongestContinuousApolarSegmentFilter, protocols::calc_taskop_filters::ConservedPosMutationFilter, protocols::ligand_docking::ChainExistsFilter, protocols::score_filters::ScoreTypeFilter, protocols::simple_filters::AveragePathLengthFilter, protocols::simple_filters::DisulfideEntropyFilter, protocols::simple_filters::SheetFilter, protocols::ligand_docking::CompleteConnectionsFilter, protocols::simple_filters::ResidueIEFilter, protocols::constraint_filters::ConstraintScoreCutoffFilter, protocols::score_filters::ScoreCutoffFilter, protocols::simple_filters::MembAccesResidueLipophilicityFilter, protocols::simple_filters::ResidueCountFilter, protocols::docking::DockingLowResFilter, protocols::simple_filters::ReadPoseExtraScoreFilter, protocols::simple_filters::RepeatParameterFilter, protocols::constraint_filters::ShowConstraintsFilter, protocols::filters::CalculatorFilter, protocols::ligand_docking::HBondDonorFilter, protocols::recon_design::FitnessFilter, protocols::protein_interface_design::filters::FilterScanFilter, protocols::protein_interface_design::filters::StubScoreLoopsFilter, protocols::simple_filters::NeighborTypeFilter, protocols::filters::ContingentFilter, protocols::protein_interface_design::filters::RmsdSimpleFilter, protocols::protein_interface_design::filters::SSamountFilter, protocols::protein_interface_design::filters::StubScoreFilter, protocols::simple_filters::AtomicContactFilter, protocols::simple_filters::AbinitioBaseFilter, protocols::simple_filters::COFilter, protocols::simple_filters::RGFilter, protocols::calc_taskop_filters::RotamerBoltzmannWeight, protocols::simple_filters::AtomicDistanceFilter, protocols::simple_filters::MPSpanAngleFilter, protocols::simple_filters::NetChargeFilter, protocols::simple_filters::ResidueChiralityFilter, protocols::simple_filters::ResidueLipophilicityFilter, protocols::simple_filters::ResidueSetChainEnergyFilter, protocols::simple_filters::SpanTopologyMatchPoseFilter, protocols::simple_filters::TaskAwareScoreTypeFilter, protocols::simple_filters::TMsSpanMembraneFilter, protocols::denovo_design::filters::SSPredictionFilter, protocols::protein_interface_design::filters::BindingStrainFilter, protocols::protein_interface_design::filters::DesignableResiduesFilter, protocols::protein_interface_design::filters::SequenceRecoveryFilter, protocols::score_filters::GeometryFilter, protocols::simple_filters::ChainCountFilter, protocols::simple_filters::TerminusDistanceFilter, protocols::filters::TrueFilter, protocols::matdes::InterfacePackingFilter, protocols::protein_interface_design::filters::AverageDegreeFilter, protocols::protein_interface_design::filters::FNatFilter, protocols::protein_interface_design::filters::IRmsdFilter, protocols::protein_interface_design::filters::Torsion, protocols::simple_filters::MutationsFilter, protocols::simple_filters::NMerSVMEnergyFilter, protocols::calc_taskop_filters::RelativePoseFilter, protocols::filters::TimeFilter, protocols::protein_interface_design::filters::LRmsdFilter, protocols::simple_filters::NMerPSSMEnergyFilter, protocols::fold_from_loops::filters::ConstraintFulfilmentFilter, protocols::fold_from_loops::filters::ScorePoseSegmentFromResidueSelectorFilter, protocols::protein_interface_design::filters::BoltzmannFilter, protocols::simple_ddg::AlaScan, protocols::simple_filters::MotifScoreFilter, protocols::protein_interface_design::filters::AtomicContactCountFilter, protocols::protein_interface_design::filters::RmsdFilter, protocols::evolution::AlignmentGapInserter, protocols::filters::ReplicateFilter, protocols::simple_filters::DeltaFilter, protocols::simple_filters::TotalSasaFilter, protocols::calc_taskop_filters::MultipleSigmoids, protocols::constraint_filters::SavePoseConstraintToFileFilter, protocols::evolution::AlignmentAAFinder, protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter, protocols::hbnet::HBNetScore, protocols::protein_interface_design::filters::InterfaceHolesFilter, protocols::simple_filters::EnergyPerResidueFilter, protocols::simple_filters::PoseInfoFilter, protocols::simple_filters::ResidueDistanceFilter, protocols::protein_interface_design::filters::RelativeSegmentFilter, protocols::simple_ddg::DdgFilter, protocols::simple_filters::InterfaceSasaFilter, protocols::simple_filters::ReportFilter, protocols::simple_filters::ResidueSelectionDistanceFilter, protocols::simple_filters::ExpiryFilter, protocols::simple_filters::FileExistFilter, protocols::simple_filters::FileRemoveFilter, protocols::simple_filters::ResiduesInInterfaceFilter, protocols::calc_taskop_filters::Sigmoid, protocols::simple_filters::NonSequentialNeighborsFilter, protocols::simple_filters::PDDFScoreFilter, protocols::simple_filters::SAXSScoreFilter, protocols::simple_filters::SidechainRmsdFilter, protocols::simple_filters::StemFinder, protocols::simple_filters::ResidueBurialFilter, protocols::simple_filters::SSMotifFinder, protocols::calc_taskop_filters::Operator, protocols::protein_interface_design::filters::ClashWithTargetFilter, protocols::evolution::AASynthesisFitnessCost, protocols::simple_filters::AngleToVector, protocols::simple_filters::ChainBreak, protocols::simple_filters::PoseComment, and protocols::simple_filters::SequenceDistance.

virtual std::string protocols::filters::Filter::get_type ( ) const

inlinevirtual

Reimplemented in protocols::simple_filters::DomainInterfaceFilter.

References type_.

std::string protocols::filters::Filter::get_user_defined_name ( ) const

inline

References user_defined_name_.

Referenced by protocols::constraint_filters::ConstraintScoreCutoffFilter::apply(), protocols::simple_filters::TaskAwareScoreTypeFilter::compute(), protocols::frag_picker::FragmentScoreFilter::compute(), protocols::simple_filters::BuriedUnsatHbondFilter::compute(), protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter::compute(), protocols::rosetta_scripts::ParsedProtocol::report_filters_to_pose(), protocols::simple_filters::ShapeComplementarityFilter::write_area(), protocols::simple_filters::LeastNativeLike9merFilter::write_mean_median(), protocols::simple_filters::ShapeComplementarityFilter::write_median_distance(), protocols::matdes::SymUnsatHbondFilter::write_pymol_string_to_pdb(), protocols::matdes::ClashCheckFilter::write_pymol_string_to_pdb(), protocols::simple_filters::MutationsFilter::write_to_pdb(), protocols::protein_interface_design::filters::SequenceRecoveryFilter::write_to_pdb(), protocols::simple_filters::TaskAwareScoreTypeFilter::write_to_pdb(), protocols::calc_taskop_filters::RotamerBoltzmannWeight::write_to_pdb(), protocols::simple_ddg::DdGScan::write_to_pdb(), protocols::matdes::SymUnsatHbondFilter::write_to_pdb(), protocols::matdes::ClashCheckFilter::write_to_pdb(), and protocols::matdes::OligomericAverageDegreeFilter::write_to_pdb().

virtual std::string protocols::filters::Filter::name ( ) const

inlinevirtual

Reimplemented in protocols::enzdes::ResidueConformerFilter, protocols::enzdes::EnzdesScorefileFilter, protocols::enzdes::RepackWithoutLigandFilter, protocols::filters::IfThenFilter, protocols::enzdes::DiffAtomSasaFilter, protocols::filters::MoveBeforeFilter, protocols::peptide_deriver::PeptideDeriverFilter, protocols::filters::CombinedFilter, protocols::simple_filters::ResidueDepthFilter, protocols::enzdes::EnzScoreFilter, protocols::protein_interface_design::filters::HbondsToResidueFilter, protocols::simple_filters::SimpleMetricFilter, protocols::simple_filters::ResidueCountFilter, protocols::filters::CompoundFilter, protocols::helical_bundle::BundleReporterFilter, protocols::enzdes::LigInterfaceEnergyFilter, protocols::fldsgn::filters::HSSTripletFilter, protocols::indexed_structure_store::filters::FragmentLookupFilter, protocols::fldsgn::filters::HelixPairingFilter, protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter, protocols::fldsgn::filters::SheetTopologyFilter, protocols::simple_filters::SaveResfileToDiskFilter, protocols::fldsgn::filters::InterlockingAromaFilter, protocols::matdes::GetRBDOFValues, protocols::matdes::OligomericAverageDegreeFilter, protocols::simple_filters::SecretionPredictionFilter, protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter, protocols::fldsgn::filters::CoreDunbrackFilter, protocols::fldsgn::filters::NcontactsFilter, protocols::simple_filters::TaskAwareSASAFilter, protocols::fldsgn::filters::FragQualFilter, protocols::matdes::ClashCheckFilter, protocols::fldsgn::filters::SecondaryStructureFilter, protocols::simple_filters::HolesFilter, protocols::simple_filters::ShapeComplementarityFilter, protocols::calc_taskop_filters::RotamerBoltzmannWeight2, protocols::simple_filters::IntraRepeatContactFilter, protocols::simple_filters::PackerNeighborGraphFilter, protocols::simple_filters::InterRepeatContactFilter, protocols::simple_filters::PackStatFilter, protocols::simple_filters::SSElementMotifContactFilter, protocols::enzdes::LigBurialFilter, protocols::filters::StochasticFilter, protocols::simple_ddg::DdGScan, protocols::simple_filters::ContactMolecularSurfaceFilter, protocols::matdes::SymUnsatHbondFilter, protocols::simple_ddg::SSElementBisectddGFilter, protocols::simple_filters::RangeFilter, protocols::simple_filters::SSElementLengthFilter, protocols::fldsgn::filters::HelixKinkFilter, protocols::simple_filters::SymmetricMotifFilter, protocols::simple_filters::DisulfideEntropyFilter, protocols::fldsgn::filters::SecondaryStructureCountFilter, protocols::fldsgn::filters::SecondaryStructureHasResidueFilter, protocols::protein_interface_design::filters::FilterScanFilter, protocols::simple_filters::AveragePathLengthFilter, protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter, protocols::score_filters::ScoreCutoffFilter, protocols::simple_filters::LongestContinuousPolarSegmentFilter, protocols::calc_taskop_filters::RotamerBoltzmannWeight, protocols::loops::filters::LoopAnalyzerFilter, protocols::constraint_filters::ConstraintScoreCutoffFilter, protocols::simple_filters::InterfaceHbondsFilter, protocols::denovo_design::filters::SSShapeComplementarityFilter, protocols::protein_interface_design::filters::DisulfideFilter, protocols::simple_filters::DomainInterfaceFilter, protocols::calc_taskop_filters::RelativePoseFilter, protocols::simple_filters::LeastNativeLike9merFilter, protocols::fldsgn::filters::StrandHelixGeometryFilter, protocols::dna_dock::PropagateClashCheckFilter, protocols::evolution::AlignmentGapInserter, protocols::simple_filters::ReadPoseExtraScoreFilter, protocols::protein_interface_design::filters::HbondsToAtomFilter, protocols::simple_filters::TaskAwareScoreTypeFilter, protocols::fldsgn::filters::StrandCurvatureByLevels, protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter, protocols::denovo_design::filters::PreProlineFilter, protocols::dna_dock::DNAClashCheckFilter, protocols::score_filters::ScoreTypeFilter, protocols::fldsgn::filters::HelixBendFilter, protocols::simple_filters::MutationsFilter, protocols::protein_interface_design::filters::SequenceRecoveryFilter, protocols::calc_taskop_filters::ConservedPosMutationFilter, protocols::constraint_filters::ConstraintScoreFilter, protocols::evolution::AlignmentAAFinder, protocols::simple_filters::BuriedUnsatHbondFilter, protocols::simple_filters::DeltaFilter, protocols::denovo_design::filters::ExposedHydrophobicsFilter, protocols::simple_ddg::DdgFilter, protocols::simple_filters::HelixHelixAngleFilter, protocols::simple_filters::ResidueIEFilter, protocols::frag_picker::FragmentScoreFilter, protocols::enzdes::LigDSasaFilter, protocols::filters::CalculatorFilter, protocols::matdes::InterfacePackingFilter, protocols::simple_filters::TMsAACompFilter, protocols::filters::FalseFilter, protocols::protein_interface_design::filters::Torsion, protocols::simple_ddg::AlaScan, protocols::simple_ddg::InterfaceBindingEnergyDensityFilter, protocols::simple_filters::StemFinder, protocols::enzdes::RemoveLigandFilter, protocols::ligand_docking::HeavyAtomFilter, protocols::protein_interface_design::filters::BoltzmannFilter, protocols::protein_interface_design::filters::DesignableResiduesFilter, protocols::simple_filters::SSMotifFinder, protocols::protein_interface_design::filters::BindingStrainFilter, protocols::simple_filters::SimpleHbondsToAtomFilter, protocols::calc_taskop_filters::Operator, protocols::fold_from_loops::filters::ConstraintFulfilmentFilter, protocols::ligand_docking::AtomCountFilter, protocols::ligand_docking::HBondAcceptorFilter, protocols::ligand_docking::MolarMassFilter, protocols::ligand_docking::MolecularMassFilter, protocols::protein_interface_design::filters::AtomicContactCountFilter, protocols::protein_interface_design::filters::RmsdSimpleFilter, protocols::simple_filters::SheetFilter, protocols::fold_from_loops::filters::ScorePoseSegmentFromResidueSelectorFilter, protocols::simple_filters::AngleToVector, protocols::filters::ContingentFilter, protocols::hbnet::HBNetScore, protocols::protein_interface_design::filters::RmsdFilter, protocols::protein_interface_design::filters::SpecificResiduesNearInterfaceFilter, protocols::protein_interface_design::filters::SSamountFilter, protocols::simple_filters::BuriedSurfaceAreaFilter, protocols::ligand_docking::ChainExistsFilter, protocols::simple_filters::EnergyPerResidueFilter, protocols::calc_taskop_filters::Sigmoid, protocols::ligand_docking::CompleteConnectionsFilter, protocols::protein_interface_design::filters::AverageDegreeFilter, protocols::simple_filters::AtomicContactFilter, protocols::simple_filters::ChainCountFilter, protocols::simple_filters::MembAccesResidueLipophilicityFilter, protocols::simple_filters::MotifScoreFilter, protocols::simple_filters::RepeatParameterFilter, protocols::constraint_filters::ShowConstraintsFilter, protocols::protein_interface_design::filters::StubScoreFilter, protocols::simple_filters::NonSequentialNeighborsFilter, protocols::simple_filters::ReportFilter, protocols::denovo_design::filters::SSPredictionFilter, protocols::protein_interface_design::filters::StubScoreLoopsFilter, protocols::simple_filters::AtomicDistanceFilter, protocols::ligand_docking::HBondDonorFilter, protocols::simple_filters::NeighborTypeFilter, protocols::simple_filters::NetChargeFilter, protocols::simple_filters::ResidueSetChainEnergyFilter, protocols::calc_taskop_filters::MultipleSigmoids, protocols::protein_interface_design::filters::InterfaceHolesFilter, protocols::simple_filters::AbinitioBaseFilter, protocols::simple_filters::COFilter, protocols::simple_filters::NMerSVMEnergyFilter, protocols::filters::ReplicateFilter, protocols::filters::TimeFilter, protocols::protein_interface_design::filters::FNatFilter, protocols::protein_interface_design::filters::IRmsdFilter, protocols::simple_filters::NMerPSSMEnergyFilter, protocols::simple_filters::RGFilter, protocols::protein_interface_design::filters::LRmsdFilter, protocols::protein_interface_design::filters::RelativeSegmentFilter, protocols::simple_filters::ChainBreak, protocols::simple_filters::MPSpanAngleFilter, protocols::simple_filters::ResidueBurialFilter, protocols::simple_filters::ResidueChiralityFilter, protocols::simple_filters::ResidueLipophilicityFilter, protocols::simple_filters::SpanTopologyMatchPoseFilter, protocols::simple_filters::TMsSpanMembraneFilter, protocols::cyclic_peptide::CycpepSymmetryFilter, protocols::score_filters::GeometryFilter, protocols::simple_filters::FileExistFilter, protocols::simple_filters::PoseComment, protocols::simple_filters::ResiduesInInterfaceFilter, protocols::simple_filters::SequenceDistance, protocols::simple_filters::TerminusDistanceFilter, protocols::simple_filters::ExpiryFilter, protocols::simple_filters::FileRemoveFilter, protocols::simple_filters::InterfaceSasaFilter, protocols::constraint_filters::SavePoseConstraintToFileFilter, protocols::simple_filters::PoseInfoFilter, protocols::evolution::AASynthesisFitnessCost, protocols::filters::TrueFilter, protocols::simple_filters::ResidueDistanceFilter, protocols::simple_filters::TotalSasaFilter, protocols::simple_filters::ResidueSelectionDistanceFilter, protocols::simple_filters::PDDFScoreFilter, protocols::simple_filters::SAXSScoreFilter, protocols::protein_interface_design::filters::ClashWithTargetFilter, protocols::simple_filters::LongestContinuousApolarSegmentFilter, and protocols::simple_filters::SidechainRmsdFilter.

Referenced by protocols::rosetta_scripts::ParsedProtocol::report_filters_to_pose(), and set_user_defined_name().

void protocols::filters::Filter::parse_my_tag ( utility::tag::TagCOP  , basic::datacache::DataMap &  , Filters_map const &  , moves::Movers_map const &  , core::pose::Pose const &    )

virtual

Reimplemented in protocols::enzdes::ResidueConformerFilter, protocols::enzdes::EnzdesScorefileFilter, protocols::enzdes::RepackWithoutLigandFilter, protocols::filters::IfThenFilter, protocols::enzdes::DiffAtomSasaFilter, protocols::filters::MoveBeforeFilter, protocols::filters::CombinedFilter, protocols::peptide_deriver::PeptideDeriverFilter, protocols::enzdes::EnzScoreFilter, protocols::simple_filters::ResidueDepthFilter, protocols::simple_filters::SimpleMetricFilter, protocols::enzdes::LigInterfaceEnergyFilter, protocols::filters::CompoundFilter, protocols::helical_bundle::BundleReporterFilter, protocols::fldsgn::filters::HSSTripletFilter, protocols::indexed_structure_store::filters::FragmentLookupFilter, protocols::fldsgn::filters::HelixPairingFilter, protocols::simple_filters::SecretionPredictionFilter, protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter, protocols::fldsgn::filters::NcontactsFilter, protocols::simple_filters::SaveResfileToDiskFilter, protocols::fldsgn::filters::SheetTopologyFilter, protocols::matdes::GetRBDOFValues, protocols::matdes::OligomericAverageDegreeFilter, protocols::enzdes::LigBurialFilter, protocols::fldsgn::filters::InterlockingAromaFilter, protocols::fldsgn::filters::SecondaryStructureFilter, protocols::simple_filters::SSElementMotifContactFilter, protocols::simple_filters::LongestContinuousPolarSegmentFilter, protocols::simple_filters::TaskAwareSASAFilter, protocols::fldsgn::filters::CoreDunbrackFilter, protocols::matdes::ClashCheckFilter, protocols::dna_dock::PropagateClashCheckFilter, protocols::fldsgn::filters::FragQualFilter, protocols::simple_ddg::SSElementBisectddGFilter, protocols::simple_filters::SSElementLengthFilter, protocols::filters::StochasticFilter, protocols::simple_filters::HolesFilter, protocols::simple_filters::ShapeComplementarityFilter, protocols::fldsgn::filters::StrandHelixGeometryFilter, protocols::simple_filters::SymmetricMotifFilter, protocols::simple_filters::IntraRepeatContactFilter, protocols::simple_filters::PackStatFilter, protocols::simple_filters::InterRepeatContactFilter, protocols::dna_dock::DNAClashCheckFilter, protocols::fldsgn::filters::HelixKinkFilter, protocols::fldsgn::filters::StrandCurvatureByLevels, protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter, protocols::calc_taskop_filters::RotamerBoltzmannWeight2, protocols::simple_filters::RangeFilter, protocols::protein_interface_design::filters::HbondsToResidueFilter, protocols::fldsgn::filters::HelixBendFilter, protocols::matdes::SymUnsatHbondFilter, protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter, protocols::fldsgn::filters::SecondaryStructureCountFilter, protocols::simple_filters::ContactMolecularSurfaceFilter, protocols::fldsgn::filters::SecondaryStructureHasResidueFilter, protocols::protein_interface_design::filters::DisulfideFilter, protocols::simple_filters::InterfaceHbondsFilter, protocols::frag_picker::FragmentScoreFilter, protocols::simple_ddg::DdGScan, protocols::simple_filters::LeastNativeLike9merFilter, protocols::simple_filters::ResidueCountFilter, protocols::protein_interface_design::filters::HbondsToAtomFilter, protocols::simple_filters::DisulfideEntropyFilter, protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter, protocols::simple_filters::SimpleHbondsToAtomFilter, protocols::hbnet::HBNetScore, protocols::score_filters::ScoreTypeFilter, protocols::simple_filters::AveragePathLengthFilter, protocols::simple_filters::BuriedSurfaceAreaFilter, protocols::simple_filters::DomainInterfaceFilter, protocols::simple_filters::ReadPoseExtraScoreFilter, protocols::simple_filters::HelixHelixAngleFilter, protocols::protein_interface_design::filters::FilterScanFilter, protocols::simple_filters::BuriedUnsatHbondFilter, protocols::simple_filters::MutationsFilter, protocols::protein_interface_design::filters::SequenceRecoveryFilter, protocols::enzdes::LigDSasaFilter, protocols::simple_filters::TMsAACompFilter, protocols::cyclic_peptide::CycpepSymmetryFilter, protocols::simple_ddg::AlaScan, protocols::loops::filters::LoopAnalyzerFilter, protocols::ligand_docking::HeavyAtomFilter, protocols::simple_ddg::DdgFilter, protocols::fold_from_loops::filters::ConstraintFulfilmentFilter, protocols::ligand_docking::AtomCountFilter, protocols::ligand_docking::HBondAcceptorFilter, protocols::ligand_docking::MolarMassFilter, protocols::ligand_docking::MolecularMassFilter, protocols::simple_filters::ResidueIEFilter, protocols::enzdes::RemoveLigandFilter, protocols::fold_from_loops::filters::ScorePoseSegmentFromResidueSelectorFilter, protocols::ligand_docking::ChainExistsFilter, protocols::simple_ddg::InterfaceBindingEnergyDensityFilter, protocols::constraint_filters::ConstraintScoreFilter, protocols::ligand_docking::CompleteConnectionsFilter, protocols::score_filters::ScoreCutoffFilter, protocols::simple_filters::MembAccesResidueLipophilicityFilter, protocols::simple_filters::MotifScoreFilter, protocols::simple_filters::RepeatParameterFilter, protocols::calc_taskop_filters::ConservedPosMutationFilter, protocols::constraint_filters::ConstraintScoreCutoffFilter, protocols::constraint_filters::ShowConstraintsFilter, protocols::denovo_design::filters::SSShapeComplementarityFilter, protocols::protein_interface_design::filters::RmsdSimpleFilter, protocols::protein_interface_design::filters::RmsdFilter, protocols::protein_interface_design::filters::SSamountFilter, protocols::filters::CalculatorFilter, protocols::ligand_docking::HBondDonorFilter, protocols::simple_filters::NeighborTypeFilter, protocols::simple_filters::NetChargeFilter, protocols::simple_filters::ResidueSetChainEnergyFilter, protocols::filters::ContingentFilter, protocols::protein_interface_design::filters::InterfaceHolesFilter, protocols::simple_filters::AtomicContactFilter, protocols::simple_filters::ChainCountFilter, protocols::simple_filters::NMerSVMEnergyFilter, protocols::evolution::AlignmentGapInserter, protocols::protein_interface_design::filters::AtomicContactCountFilter, protocols::protein_interface_design::filters::FNatFilter, protocols::protein_interface_design::filters::IRmsdFilter, protocols::protein_interface_design::filters::StubScoreFilter, protocols::recon_design::FitnessFilter, protocols::simple_filters::NMerPSSMEnergyFilter, protocols::calc_taskop_filters::RotamerBoltzmannWeight, protocols::protein_interface_design::filters::LRmsdFilter, protocols::protein_interface_design::filters::StubScoreLoopsFilter, protocols::simple_filters::AtomicDistanceFilter, protocols::simple_filters::MPSpanAngleFilter, protocols::simple_filters::ResidueChiralityFilter, protocols::simple_filters::ResidueLipophilicityFilter, protocols::simple_filters::SpanTopologyMatchPoseFilter, protocols::simple_filters::TMsSpanMembraneFilter, protocols::denovo_design::filters::ExposedHydrophobicsFilter, protocols::denovo_design::filters::SSPredictionFilter, protocols::protein_interface_design::filters::DesignableResiduesFilter, protocols::score_filters::GeometryFilter, protocols::simple_filters::ResiduesInInterfaceFilter, protocols::simple_filters::TerminusDistanceFilter, protocols::evolution::AlignmentAAFinder, protocols::protein_interface_design::filters::AverageDegreeFilter, protocols::simple_filters::InterfaceSasaFilter, protocols::simple_filters::TaskAwareScoreTypeFilter, protocols::filters::TimeFilter, protocols::protein_interface_design::filters::BindingStrainFilter, protocols::simple_filters::EnergyPerResidueFilter, protocols::matdes::InterfacePackingFilter, protocols::protein_interface_design::filters::Torsion, protocols::calc_taskop_filters::RelativePoseFilter, protocols::simple_filters::ReportFilter, protocols::filters::ReplicateFilter, protocols::protein_interface_design::filters::BoltzmannFilter, protocols::protein_interface_design::filters::RelativeSegmentFilter, protocols::protein_interface_design::filters::SpecificResiduesNearInterfaceFilter, protocols::simple_filters::ExpiryFilter, protocols::simple_filters::FileExistFilter, protocols::simple_filters::FileRemoveFilter, protocols::constraint_filters::SavePoseConstraintToFileFilter, protocols::denovo_design::filters::PreProlineFilter, protocols::simple_filters::NonSequentialNeighborsFilter, protocols::simple_filters::PoseInfoFilter, protocols::simple_filters::ResidueDistanceFilter, protocols::simple_filters::TotalSasaFilter, protocols::calc_taskop_filters::MultipleSigmoids, protocols::calc_taskop_filters::Sigmoid, protocols::simple_filters::DeltaFilter, protocols::simple_filters::ResidueSelectionDistanceFilter, protocols::simple_filters::StemFinder, protocols::simple_filters::SSMotifFinder, protocols::calc_taskop_filters::Operator, protocols::protein_interface_design::filters::ClashWithTargetFilter, protocols::simple_filters::AngleToVector, protocols::evolution::AASynthesisFitnessCost, protocols::simple_filters::ChainBreak, protocols::simple_filters::PoseComment, protocols::simple_filters::ResidueBurialFilter, protocols::simple_filters::SequenceDistance, and protocols::simple_filters::SidechainRmsdFilter.

utility::vector1< basic::citation_manager::UnpublishedModuleInfoCOP > protocols::filters::Filter::provide_authorship_info_for_unpublished ( ) const

virtual

Provide a list of authors and their e-mail addresses, as strings.

The citation should be in MLA format. Only the citation needs to be in the output string. No newlines should be included.

Returns

A list of pairs of (author, e-mail address). Empty list if not unpublished.

Author

Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org)

utility::vector1< basic::citation_manager::CitationCollectionCOP > protocols::filters::Filter::provide_citation_info ( ) const

virtual

Provide the citation.

Returns

A vector of citation collections. This allows the filter to provide citations for itself and for any modules that it invokes.

The default implementation of this function provides an empty vector. It may be overriden by filters wishing to provide citation information.

Author

Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org)

Reimplemented in protocols::indexed_structure_store::filters::FragmentLookupFilter.

virtual void protocols::filters::Filter::report ( std::ostream &  , core::pose::Pose const &    ) const

inlinevirtual

Reimplemented in protocols::enzdes::ResidueConformerFilter, protocols::enzdes::RepackWithoutLigandFilter, protocols::filters::IfThenFilter, protocols::enzdes::DiffAtomSasaFilter, protocols::filters::MoveBeforeFilter, protocols::enzdes::EnzScoreFilter, protocols::filters::CombinedFilter, protocols::peptide_deriver::PeptideDeriverFilter, protocols::enzdes::LigInterfaceEnergyFilter, protocols::filters::CompoundFilter, protocols::indexed_structure_store::filters::FragmentLookupFilter, protocols::matdes::GetRBDOFValues, protocols::fldsgn::filters::InterlockingAromaFilter, protocols::helical_bundle::BundleReporterFilter, protocols::matdes::OligomericAverageDegreeFilter, protocols::fldsgn::filters::CoreDunbrackFilter, protocols::simple_filters::TaskAwareSASAFilter, protocols::fldsgn::filters::FragQualFilter, protocols::simple_filters::SecretionPredictionFilter, protocols::matdes::ClashCheckFilter, protocols::simple_filters::HolesFilter, protocols::simple_filters::IntraRepeatContactFilter, protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter, protocols::simple_filters::InterRepeatContactFilter, protocols::fldsgn::filters::NcontactsFilter, protocols::simple_ddg::DdGScan, protocols::simple_filters::RangeFilter, protocols::matdes::SymUnsatHbondFilter, protocols::fldsgn::filters::SecondaryStructureCountFilter, protocols::enzdes::LigBurialFilter, protocols::filters::StochasticFilter, protocols::simple_filters::SSElementMotifContactFilter, protocols::fldsgn::filters::SecondaryStructureHasResidueFilter, protocols::simple_filters::SSElementLengthFilter, protocols::simple_ddg::SSElementBisectddGFilter, protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter, protocols::fldsgn::filters::StrandHelixGeometryFilter, protocols::calc_taskop_filters::RotamerBoltzmannWeight2, protocols::protein_interface_design::filters::HbondsToResidueFilter, protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter, protocols::simple_filters::InterfaceHbondsFilter, protocols::simple_filters::LeastNativeLike9merFilter, protocols::fldsgn::filters::StrandCurvatureByLevels, protocols::protein_interface_design::filters::HbondsToAtomFilter, protocols::simple_filters::SymmetricMotifFilter, protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter, protocols::protein_interface_design::filters::DisulfideFilter, protocols::denovo_design::filters::SSShapeComplementarityFilter, protocols::fldsgn::filters::HelixBendFilter, protocols::score_filters::ScoreTypeFilter, protocols::denovo_design::filters::ExposedHydrophobicsFilter, protocols::frag_picker::FragmentScoreFilter, protocols::simple_filters::ReadPoseExtraScoreFilter, protocols::simple_filters::BuriedUnsatHbondFilter, protocols::denovo_design::filters::PreProlineFilter, protocols::simple_ddg::DdgFilter, protocols::simple_filters::BuriedSurfaceAreaFilter, protocols::fold_from_loops::filters::ConstraintFulfilmentFilter, protocols::simple_filters::AveragePathLengthFilter, protocols::simple_filters::DisulfideEntropyFilter, protocols::simple_filters::LongestContinuousPolarSegmentFilter, protocols::simple_filters::ResidueIEFilter, protocols::loops::filters::LoopAnalyzerFilter, protocols::fold_from_loops::filters::ScorePoseSegmentFromResidueSelectorFilter, protocols::protein_interface_design::filters::SpecificResiduesNearInterfaceFilter, protocols::constraint_filters::ConstraintScoreCutoffFilter, protocols::enzdes::LigDSasaFilter, protocols::score_filters::ScoreCutoffFilter, protocols::simple_filters::ResidueCountFilter, protocols::simple_ddg::InterfaceBindingEnergyDensityFilter, protocols::protein_interface_design::filters::SSamountFilter, protocols::simple_filters::MotifScoreFilter, protocols::constraint_filters::ConstraintScoreFilter, protocols::protein_interface_design::filters::RmsdSimpleFilter, protocols::simple_filters::ResidueSetChainEnergyFilter, protocols::cyclic_peptide::CycpepSymmetryFilter, protocols::docking::DockingLowResFilter, protocols::protein_interface_design::filters::InterfaceHolesFilter, protocols::simple_filters::SimpleHbondsToAtomFilter, protocols::evolution::AlignmentGapInserter, protocols::simple_filters::NMerSVMEnergyFilter, protocols::protein_interface_design::filters::FNatFilter, protocols::protein_interface_design::filters::IRmsdFilter, protocols::simple_filters::NMerPSSMEnergyFilter, protocols::denovo_design::filters::SSPredictionFilter, protocols::protein_interface_design::filters::FilterScanFilter, protocols::protein_interface_design::filters::LRmsdFilter, protocols::simple_ddg::AlaScan, protocols::simple_filters::MembAccesResidueLipophilicityFilter, protocols::simple_filters::ResiduesInInterfaceFilter, protocols::evolution::AlignmentAAFinder, protocols::protein_interface_design::filters::StubScoreFilter, protocols::hbnet::HBNetScore, protocols::protein_interface_design::filters::RmsdFilter, protocols::calc_taskop_filters::RotamerBoltzmannWeight, protocols::filters::CalculatorFilter, protocols::filters::ContingentFilter, protocols::recon_design::FitnessFilter, protocols::simple_filters::AtomicContactFilter, protocols::simple_filters::EnergyPerResidueFilter, protocols::simple_filters::HelixHelixAngleFilter, protocols::simple_filters::NeighborTypeFilter, protocols::simple_filters::TaskAwareScoreTypeFilter, protocols::simple_filters::TMsAACompFilter, protocols::protein_interface_design::filters::BindingStrainFilter, protocols::protein_interface_design::filters::DesignableResiduesFilter, protocols::protein_interface_design::filters::RelativeSegmentFilter, protocols::protein_interface_design::filters::SequenceRecoveryFilter, protocols::simple_filters::ReportFilter, protocols::calc_taskop_filters::MultipleSigmoids, protocols::calc_taskop_filters::Sigmoid, protocols::matdes::InterfacePackingFilter, protocols::protein_interface_design::filters::AverageDegreeFilter, protocols::protein_interface_design::filters::Torsion, protocols::simple_filters::AtomicDistanceFilter, protocols::simple_filters::ExpiryFilter, protocols::simple_filters::FileExistFilter, protocols::simple_filters::FileRemoveFilter, protocols::simple_filters::MutationsFilter, protocols::simple_filters::RepeatParameterFilter, protocols::simple_filters::StemFinder, protocols::calc_taskop_filters::RelativePoseFilter, protocols::constraint_filters::ShowConstraintsFilter, protocols::simple_filters::ChainCountFilter, protocols::simple_filters::MPSpanAngleFilter, protocols::simple_filters::NetChargeFilter, protocols::simple_filters::NonSequentialNeighborsFilter, protocols::simple_filters::ResidueChiralityFilter, protocols::simple_filters::ResidueLipophilicityFilter, protocols::simple_filters::SpanTopologyMatchPoseFilter, protocols::simple_filters::SSMotifFinder, protocols::simple_filters::TMsSpanMembraneFilter, protocols::calc_taskop_filters::Operator, protocols::protein_interface_design::filters::BoltzmannFilter, protocols::score_filters::GeometryFilter, protocols::simple_filters::AngleToVector, protocols::simple_filters::TerminusDistanceFilter, protocols::evolution::AASynthesisFitnessCost, protocols::filters::TimeFilter, protocols::simple_filters::ChainBreak, protocols::simple_filters::PoseComment, protocols::simple_filters::SequenceDistance, protocols::protein_interface_design::filters::ClashWithTargetFilter, protocols::simple_filters::DeltaFilter, protocols::constraint_filters::SavePoseConstraintToFileFilter, protocols::simple_filters::InterfaceSasaFilter, protocols::simple_filters::PoseInfoFilter, protocols::filters::ReplicateFilter, protocols::simple_filters::ResidueDistanceFilter, protocols::simple_filters::TotalSasaFilter, protocols::simple_filters::ResidueSelectionDistanceFilter, protocols::simple_filters::SidechainRmsdFilter, and protocols::simple_filters::ResidueBurialFilter.

Referenced by protocols::rosetta_scripts::ParsedProtocol::apply_filter().

virtual core::Real protocols::filters::Filter::report_sm ( core::pose::Pose const &  ) const

inlinevirtual

used to report filter internals through a score or silent file

Reimplemented in protocols::enzdes::ResidueConformerFilter, protocols::enzdes::RepackWithoutLigandFilter, protocols::filters::IfThenFilter, protocols::enzdes::DiffAtomSasaFilter, protocols::filters::MoveBeforeFilter, protocols::enzdes::EnzScoreFilter, protocols::filters::CombinedFilter, protocols::enzdes::LigInterfaceEnergyFilter, protocols::filters::CompoundFilter, protocols::fldsgn::filters::HSSTripletFilter, protocols::indexed_structure_store::filters::FragmentLookupFilter, protocols::fldsgn::filters::HelixPairingFilter, protocols::fldsgn::filters::SheetTopologyFilter, protocols::helical_bundle::BundleReporterFilter, protocols::matdes::GetRBDOFValues, protocols::matdes::OligomericAverageDegreeFilter, protocols::fldsgn::filters::InterlockingAromaFilter, protocols::fldsgn::filters::SecondaryStructureFilter, protocols::fldsgn::filters::CoreDunbrackFilter, protocols::simple_filters::TaskAwareSASAFilter, protocols::fldsgn::filters::FragQualFilter, protocols::simple_filters::SecretionPredictionFilter, protocols::matdes::ClashCheckFilter, protocols::simple_filters::HolesFilter, protocols::simple_filters::IntraRepeatContactFilter, protocols::simple_filters::PackStatFilter, protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter, protocols::simple_filters::InterRepeatContactFilter, protocols::simple_filters::ShapeComplementarityFilter, protocols::fldsgn::filters::NcontactsFilter, protocols::enzdes::LigBurialFilter, protocols::matdes::SymUnsatHbondFilter, protocols::simple_filters::SimpleMetricFilter, protocols::fldsgn::filters::SecondaryStructureCountFilter, protocols::simple_filters::ContactMolecularSurfaceFilter, protocols::simple_filters::SSElementMotifContactFilter, protocols::filters::StochasticFilter, protocols::fldsgn::filters::SecondaryStructureHasResidueFilter, protocols::simple_filters::SymmetricMotifFilter, protocols::simple_filters::SSElementLengthFilter, protocols::simple_ddg::SSElementBisectddGFilter, protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter, protocols::protein_interface_design::filters::HbondsToResidueFilter, protocols::simple_filters::InterfaceHbondsFilter, protocols::fldsgn::filters::StrandHelixGeometryFilter, protocols::calc_taskop_filters::RotamerBoltzmannWeight2, protocols::simple_filters::LeastNativeLike9merFilter, protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter, protocols::protein_interface_design::filters::HbondsToAtomFilter, protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter, protocols::protein_interface_design::filters::DisulfideFilter, protocols::denovo_design::filters::SSShapeComplementarityFilter, protocols::score_filters::ScoreTypeFilter, protocols::fldsgn::filters::StrandCurvatureByLevels, protocols::denovo_design::filters::ExposedHydrophobicsFilter, protocols::simple_filters::ReadPoseExtraScoreFilter, protocols::fldsgn::filters::HelixBendFilter, protocols::simple_filters::BuriedUnsatHbondFilter, protocols::simple_filters::AveragePathLengthFilter, protocols::simple_filters::DisulfideEntropyFilter, protocols::frag_picker::FragmentScoreFilter, protocols::simple_filters::ResidueCountFilter, protocols::denovo_design::filters::PreProlineFilter, protocols::protein_interface_design::filters::AtomicContactCountFilter, protocols::simple_ddg::DdgFilter, protocols::enzdes::RemoveLigandFilter, protocols::fold_from_loops::filters::ConstraintFulfilmentFilter, protocols::simple_filters::ResidueIEFilter, protocols::fold_from_loops::filters::ScorePoseSegmentFromResidueSelectorFilter, protocols::ligand_docking::HeavyAtomFilter, protocols::protein_interface_design::filters::SpecificResiduesNearInterfaceFilter, protocols::enzdes::LigDSasaFilter, protocols::simple_filters::BuriedSurfaceAreaFilter, protocols::simple_ddg::InterfaceBindingEnergyDensityFilter, protocols::simple_filters::LongestContinuousPolarSegmentFilter, protocols::simple_filters::MotifScoreFilter, protocols::loops::filters::LoopAnalyzerFilter, protocols::protein_interface_design::filters::RmsdFilter, protocols::protein_interface_design::filters::SSamountFilter, protocols::protein_interface_design::filters::RmsdSimpleFilter, protocols::simple_filters::ResidueSetChainEnergyFilter, protocols::evolution::AlignmentGapInserter, protocols::protein_interface_design::filters::InterfaceHolesFilter, protocols::simple_filters::NMerSVMEnergyFilter, protocols::protein_interface_design::filters::FNatFilter, protocols::protein_interface_design::filters::IRmsdFilter, protocols::simple_ddg::AlaScan, protocols::simple_filters::NMerPSSMEnergyFilter, protocols::denovo_design::filters::SSPredictionFilter, protocols::evolution::AlignmentAAFinder, protocols::hbnet::HBNetScore, protocols::protein_interface_design::filters::FilterScanFilter, protocols::protein_interface_design::filters::LRmsdFilter, protocols::simple_filters::MembAccesResidueLipophilicityFilter, protocols::simple_filters::ResiduesInInterfaceFilter, protocols::constraint_filters::ConstraintScoreFilter, protocols::protein_interface_design::filters::StubScoreFilter, protocols::cyclic_peptide::CycpepSymmetryFilter, protocols::recon_design::FitnessFilter, protocols::simple_filters::SimpleHbondsToAtomFilter, protocols::simple_filters::TMsAACompFilter, protocols::calc_taskop_filters::RotamerBoltzmannWeight, protocols::filters::CalculatorFilter, protocols::filters::ContingentFilter, protocols::simple_filters::AtomicContactFilter, protocols::simple_filters::EnergyPerResidueFilter, protocols::simple_filters::HelixHelixAngleFilter, protocols::simple_filters::NeighborTypeFilter, protocols::simple_filters::TaskAwareScoreTypeFilter, protocols::protein_interface_design::filters::BindingStrainFilter, protocols::protein_interface_design::filters::DesignableResiduesFilter, protocols::protein_interface_design::filters::RelativeSegmentFilter, protocols::protein_interface_design::filters::SequenceRecoveryFilter, protocols::simple_filters::ReportFilter, protocols::calc_taskop_filters::MultipleSigmoids, protocols::calc_taskop_filters::Sigmoid, protocols::constraint_filters::ShowConstraintsFilter, protocols::matdes::InterfacePackingFilter, protocols::protein_interface_design::filters::AverageDegreeFilter, protocols::protein_interface_design::filters::Torsion, protocols::simple_filters::AtomicDistanceFilter, protocols::simple_filters::ExpiryFilter, protocols::simple_filters::FileExistFilter, protocols::simple_filters::FileRemoveFilter, protocols::simple_filters::MutationsFilter, protocols::simple_filters::StemFinder, protocols::calc_taskop_filters::RelativePoseFilter, protocols::simple_filters::ChainCountFilter, protocols::simple_filters::MPSpanAngleFilter, protocols::simple_filters::NetChargeFilter, protocols::simple_filters::NonSequentialNeighborsFilter, protocols::simple_filters::ResidueChiralityFilter, protocols::simple_filters::ResidueLipophilicityFilter, protocols::simple_filters::SpanTopologyMatchPoseFilter, protocols::simple_filters::SSMotifFinder, protocols::simple_filters::TMsSpanMembraneFilter, protocols::calc_taskop_filters::Operator, protocols::protein_interface_design::filters::BoltzmannFilter, protocols::score_filters::GeometryFilter, protocols::simple_filters::AngleToVector, protocols::simple_filters::RepeatParameterFilter, protocols::simple_filters::TerminusDistanceFilter, protocols::evolution::AASynthesisFitnessCost, protocols::filters::TimeFilter, protocols::simple_filters::ChainBreak, protocols::simple_filters::PoseComment, protocols::simple_filters::SequenceDistance, protocols::protein_interface_design::filters::ClashWithTargetFilter, protocols::simple_filters::DeltaFilter, protocols::constraint_filters::SavePoseConstraintToFileFilter, protocols::simple_filters::InterfaceSasaFilter, protocols::simple_filters::PoseInfoFilter, protocols::filters::ReplicateFilter, protocols::simple_filters::ResidueDistanceFilter, protocols::simple_filters::TotalSasaFilter, protocols::simple_filters::ResidueSelectionDistanceFilter, protocols::simple_filters::SidechainRmsdFilter, and protocols::simple_filters::ResidueBurialFilter.

Referenced by protocols::rosetta_scripts::ParsedProtocol::apply_filter(), protocols::rosetta_scripts::ParsedProtocol::report_filters_to_pose(), protocols::filters::StochasticFilter::report_sm(), and score().

core::Real protocols::filters::Filter::score ( core::pose::Pose &  pose )

virtual

Reimplemented in protocols::hbnet::HBNetScore.

References report_sm(), scorename_, and core::pose::setPoseExtraScore().

Referenced by protocols::simple_filters::NMerPSSMEnergyFilter::apply(), protocols::simple_filters::NMerSVMEnergyFilter::apply(), protocols::simple_filters::ResidueSetChainEnergyFilter::apply(), protocols::simple_filters::TaskAwareScoreTypeFilter::apply(), protocols::simple_filters::ReadPoseExtraScoreFilter::apply(), protocols::score_filters::ScoreTypeFilter::apply(), protocols::fold_from_loops::filters::ScorePoseSegmentFromResidueSelectorFilter::apply(), protocols::fold_from_loops::filters::ConstraintFulfilmentFilter::apply(), protocols::simple_filters::PackStatFilter::apply(), protocols::fldsgn::filters::NcontactsFilter::apply(), protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter::apply(), protocols::fldsgn::filters::SecondaryStructureFilter::apply(), protocols::helical_bundle::BundleReporterFilter::apply(), protocols::protein_interface_design::filters::ClashWithTargetFilter::compute(), protocols::score_filters::GeometryFilter::compute(), protocols::simple_filters::SpanTopologyMatchPoseFilter::compute(), protocols::simple_filters::EnergyPerResidueFilter::compute(), protocols::simple_filters::NMerPSSMEnergyFilter::compute(), protocols::simple_filters::NMerSVMEnergyFilter::compute(), protocols::simple_filters::ResidueSetChainEnergyFilter::compute(), protocols::frag_picker::FragmentScoreFilter::compute(), protocols::fold_from_loops::filters::ScorePoseSegmentFromResidueSelectorFilter::compute(), protocols::score_filters::ScoreTypeFilter::compute(), protocols::simple_ddg::SSElementBisectddGFilter::compute(), protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter::compute(), protocols::simple_filters::SSElementMotifContactFilter::compute(), protocols::fldsgn::filters::FragQualFilter::compute(), protocols::helical_bundle::BundleReporterFilter::compute(), protocols::enzdes::EnzScoreFilter::compute(), protocols::calc_taskop_filters::RotamerBoltzmannWeight::compute_Boltzmann_weight(), protocols::denovo_design::filters::SSShapeComplementarityFilter::compute_from_selector(), protocols::simple_filters::PackStatFilter::filtered_score(), protocols::score_filters::ScoreCutoffFilter::output_residue_pair_energies(), protocols::fold_from_loops::filters::ScorePoseSegmentFromResidueSelectorFilter::report(), protocols::fold_from_loops::filters::ConstraintFulfilmentFilter::report(), protocols::simple_filters::TaskAwareScoreTypeFilter::report_sm(), protocols::fold_from_loops::filters::ScorePoseSegmentFromResidueSelectorFilter::report_sm(), and protocols::fold_from_loops::filters::ConstraintFulfilmentFilter::report_sm().

void protocols::filters::Filter::set_user_defined_name ( std::string const &  name )

inline

References name(), and user_defined_name_.

Referenced by protocols::constraint_filters::ConstraintScoreCutoffFilter::parse_my_tag(), and protocols::simple_filters::RepeatParameterFilter::parse_my_tag().

Member Data Documentation

std::string protocols::filters::Filter::scorename_

protected

Referenced by protocols::simple_ddg::DdgFilter::DdgFilter(), protocols::hbnet::HBNetScore::HBNetScore(), and score().

std::string const protocols::filters::Filter::type_

private

Referenced by get_type().

std::string protocols::filters::Filter::user_defined_name_

private

Referenced by get_user_defined_name(), and set_user_defined_name().

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

• src/protocols/filters/Filter.hh
• src/protocols/filters/Filter.cc