protocols::filters::Filter Class Reference

#include <Filter.hh>

Public Member Functions
	Filter ()
	Filter (std::string const &)
	Filter (Filter const &)
virtual	~Filter ()
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 void	apply (core::io::serialization::PipeMap &pmap)
virtual void	score (core::io::serialization::PipeMap &pmap)
virtual core::Real	score (core::pose::Pose &pose)
virtual void	parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks)
virtual std::string	name () const

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 ( )

virtual

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::enzdes::DiffAtomSasaFilter, protocols::filters::IfThenFilter, protocols::enzdes::EnzScoreFilter, protocols::filters::MoveBeforeFilter, protocols::fldsgn::filters::HSSTripletFilter, protocols::fldsgn::filters::HelixPairingFilter, protocols::filters::CombinedFilter, protocols::fldsgn::filters::SheetTopologyFilter, protocols::fldsgn::filters::InterlockingAromaFilter, protocols::simple_filters::PackerNeighborGraphFilter, protocols::enzdes::LigInterfaceEnergyFilter, protocols::fldsgn::filters::CoreDunbrackFilter, protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter, protocols::fldsgn::filters::FragQualFilter, protocols::fldsgn::filters::NcontactsFilter, protocols::fldsgn::filters::SecondaryStructureFilter, protocols::simple_filters::HolesFilter, protocols::simple_filters::PackStatFilter, protocols::simple_filters::RangeFilter, protocols::simple_filters::ShapeComplementarityFilter, protocols::fldsgn::filters::HelixKinkFilter, protocols::fldsgn::filters::SecondaryStructureCountFilter, protocols::filters::CompoundFilter, protocols::simple_filters::DomainInterfaceFilter, protocols::enzdes::LigBurialFilter, protocols::simple_filters::BuriedRegionsFilter, protocols::docking::DockingHighResFilter, protocols::simple_filters::ConstraintScoreCutoffFilter, protocols::protein_interface_design::filters::DisulfideFilter, protocols::simple_filters::ScoreCutoffFilter, protocols::simple_filters::SheetFilter, protocols::denovo_design::filters::ExposedHydrophobicsFilter, protocols::simple_filters::ConservedPosMutationFilter, protocols::filters::StochasticFilter, protocols::protein_interface_design::filters::HbondsToAtomFilter, protocols::protein_interface_design::filters::HbondsToResidueFilter, protocols::protein_interface_design::filters::AtomicContactCountFilter, protocols::protein_interface_design::filters::SpecificResiduesNearInterfaceFilter, protocols::simple_filters::COFilter, protocols::simple_filters::RGFilter, protocols::enzdes::LigDSasaFilter, protocols::ligand_docking::AtomCountFilter, protocols::ligand_docking::HBondAcceptorFilter, protocols::ligand_docking::HeavyAtomFilter, protocols::ligand_docking::MolarMassFilter, protocols::ligand_docking::MolecularMassFilter, protocols::enzdes::RemoveLigandFilter, protocols::ligand_docking::HBondDonorFilter, protocols::simple_filters::AbinitioBaseFilter, protocols::simple_filters::InterfaceBindingEnergyDensityFilter, protocols::filters::FalseFilter, protocols::ligand_docking::ChainExistsFilter, protocols::simple_filters::SymmetricMotifFilter, protocols::docking::DockingLowResFilter, protocols::ligand_docking::CompleteConnectionsFilter, protocols::simple_filters::AveragePathLengthFilter, protocols::simple_filters::DisulfideEntropyFilter, protocols::protein_interface_design::filters::FilterScanFilter, protocols::simple_filters::DdgFilter, protocols::filters::HeavyAtomFilter, protocols::protein_interface_design::filters::StubScoreFilter, protocols::protein_interface_design::filters::StubScoreFilter, protocols::simple_filters::PDDFScoreFilter, protocols::simple_filters::SAXSScoreFilter, protocols::filters::TrueFilter, protocols::filters::ContingentFilter, protocols::protein_interface_design::filters::FNatFilter, protocols::protein_interface_design::filters::IRmsdFilter, protocols::simple_filters::ResidueCountFilter, protocols::simple_filters::ResidueSetChainEnergyFilter, protocols::simple_filters::RotamerBoltzmannWeight, protocols::protein_interface_design::filters::BindingStrainFilter, protocols::protein_interface_design::filters::DesignableResiduesFilter, protocols::protein_interface_design::filters::LRmsdFilter, protocols::protein_interface_design::filters::AverageDegreeFilter, protocols::protein_interface_design::filters::SequenceRecoveryFilter, protocols::simple_filters::AtomicContactFilter, protocols::simple_filters::MultipleSigmoids, protocols::simple_filters::Sigmoid, protocols::filters::CalculatorFilter, protocols::protein_interface_design::filters::Torsion, protocols::simple_filters::AtomicDistanceFilter, protocols::simple_filters::NMerPSSMEnergyFilter, protocols::simple_filters::NMerSVMEnergyFilter, protocols::simple_filters::RelativePoseFilter, protocols::simple_filters::ScoreTypeFilter, protocols::protein_interface_design::filters::BoltzmannFilter, protocols::protein_interface_design::filters::RelativeSegmentFilter, protocols::protein_interface_design::filters::RmsdFilter, protocols::simple_filters::AlaScan, protocols::simple_filters::NetChargeFilter, protocols::simple_filters::Operator, protocols::simple_filters::ResidueIEFilter, protocols::simple_filters::TerminusDistanceFilter, protocols::simple_filters::GeometryFilter, protocols::simple_filters::PoseComment, protocols::filters::TimeFilter, protocols::simple_filters::DeltaFilter, protocols::simple_filters::NeighborTypeFilter, protocols::protein_interface_design::filters::InterfaceHolesFilter, protocols::simple_filters::BuriedUnsatHbondFilter, protocols::simple_filters::EnergyPerResidueFilter, 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::filters::ReplicateFilter, protocols::protein_interface_design::filters::ClashWithTargetFilter, protocols::simple_filters::NonSequentialNeighborsFilter, protocols::simple_filters::PoseInfoFilter, protocols::simple_filters::ResidueDistanceFilter, protocols::simple_filters::SavePoseConstraintToFileFilter, protocols::simple_filters::TotalSasaFilter, protocols::simple_filters::SidechainRmsdFilter, and protocols::simple_filters::ResidueBurialFilter.

Referenced by protocols::loophash::LoopHashMoverWrapper::apply(), protocols::protein_interface_design::filters::SequenceRecoveryFilter::apply(), protocols::protein_interface_design::movers::LoopOver::apply(), protocols::protein_interface_design::filters::FilterScanFilter::apply(), protocols::moves::IfMover::apply(), protocols::moves::FilterMover::apply(), protocols::loophash::LoopHashDiversifier::apply(), protocols::protein_interface_design::movers::TryRotamers::apply(), apply(), and protocols::simple_filters::RangeFilter::report().

void protocols::filters::Filter::apply ( core::io::serialization::PipeMap &  pmap )

virtual

Reimplemented in protocols::protein_interface_design::filters::SequenceRecoveryFilter.

References apply(), clear(), and end.

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, and protocols::simple_filters::NeighborTypeFilter.

Referenced by apply(), and score().

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

pure virtual

Implemented in protocols::enzdes::ResidueConformerFilter, protocols::enzdes::EnzdesScorefileFilter, protocols::enzdes::RepackWithoutLigandFilter, protocols::enzdes::DiffAtomSasaFilter, protocols::filters::IfThenFilter, protocols::enzdes::EnzScoreFilter, protocols::filters::MoveBeforeFilter, protocols::filters::CombinedFilter, protocols::enzdes::LigInterfaceEnergyFilter, protocols::simple_filters::PackerNeighborGraphFilter, protocols::filters::CompoundFilter, protocols::fldsgn::filters::HelixPairingFilter, protocols::fldsgn::filters::HSSTripletFilter, protocols::enzdes::LigBurialFilter, protocols::fldsgn::filters::SheetTopologyFilter, protocols::fldsgn::filters::NcontactsFilter, protocols::simple_filters::DomainInterfaceFilter, protocols::fldsgn::filters::CoreDunbrackFilter, protocols::fldsgn::filters::InterlockingAromaFilter, protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter, protocols::fldsgn::filters::HelixKinkFilter, protocols::docking::DockingHighResFilter, protocols::fldsgn::filters::FragQualFilter, protocols::simple_filters::HolesFilter, protocols::simple_filters::RangeFilter, protocols::simple_filters::PackStatFilter, protocols::fldsgn::filters::SecondaryStructureFilter, protocols::protein_interface_design::filters::DisulfideFilter, protocols::simple_filters::BuriedRegionsFilter, protocols::simple_filters::ShapeComplementarityFilter, protocols::simple_filters::SymmetricMotifFilter, protocols::fldsgn::filters::SecondaryStructureCountFilter, protocols::denovo_design::filters::ExposedHydrophobicsFilter, protocols::enzdes::RemoveLigandFilter, protocols::filters::StochasticFilter, protocols::protein_interface_design::filters::HbondsToAtomFilter, protocols::protein_interface_design::filters::HbondsToResidueFilter, protocols::protein_interface_design::filters::SpecificResiduesNearInterfaceFilter, protocols::simple_filters::SheetFilter, protocols::enzdes::LigDSasaFilter, protocols::simple_filters::InterfaceBindingEnergyDensityFilter, protocols::ligand_docking::AtomCountFilter, protocols::ligand_docking::HBondAcceptorFilter, protocols::ligand_docking::HeavyAtomFilter, protocols::ligand_docking::MolarMassFilter, protocols::ligand_docking::MolecularMassFilter, protocols::ligand_docking::HBondDonorFilter, protocols::simple_filters::ConservedPosMutationFilter, protocols::filters::FalseFilter, protocols::ligand_docking::ChainExistsFilter, protocols::simple_filters::AveragePathLengthFilter, protocols::simple_filters::ConstraintScoreCutoffFilter, protocols::simple_filters::DisulfideEntropyFilter, protocols::simple_filters::ScoreCutoffFilter, protocols::docking::DockingLowResFilter, protocols::ligand_docking::CompleteConnectionsFilter, protocols::protein_interface_design::filters::FilterScanFilter, protocols::protein_interface_design::filters::StubScoreLoopsFilter, protocols::protein_interface_design::filters::StubScoreFilter, protocols::protein_interface_design::filters::StubScoreFilter, protocols::simple_filters::ResidueCountFilter, protocols::simple_filters::DdgFilter, protocols::filters::ContingentFilter, protocols::filters::HeavyAtomFilter, protocols::simple_filters::AbinitioBaseFilter, protocols::simple_filters::COFilter, protocols::simple_filters::RGFilter, protocols::simple_filters::RotamerBoltzmannWeight, protocols::filters::CalculatorFilter, protocols::protein_interface_design::filters::BindingStrainFilter, protocols::protein_interface_design::filters::DesignableResiduesFilter, protocols::protein_interface_design::filters::SequenceRecoveryFilter, protocols::simple_filters::AtomicContactFilter, protocols::filters::TrueFilter, protocols::protein_interface_design::filters::AverageDegreeFilter, protocols::protein_interface_design::filters::FNatFilter, protocols::protein_interface_design::filters::IRmsdFilter, protocols::simple_filters::AtomicDistanceFilter, protocols::simple_filters::ResidueSetChainEnergyFilter, protocols::protein_interface_design::filters::LRmsdFilter, protocols::protein_interface_design::filters::Torsion, protocols::simple_filters::NetChargeFilter, protocols::simple_filters::RelativePoseFilter, protocols::simple_filters::TerminusDistanceFilter, protocols::protein_interface_design::filters::BoltzmannFilter, protocols::simple_filters::GeometryFilter, protocols::filters::TimeFilter, protocols::protein_interface_design::filters::AtomicContactCountFilter, protocols::simple_filters::NeighborTypeFilter, protocols::simple_filters::NMerPSSMEnergyFilter, protocols::simple_filters::NMerSVMEnergyFilter, protocols::simple_filters::ScoreTypeFilter, protocols::protein_interface_design::filters::RelativeSegmentFilter, protocols::protein_interface_design::filters::RmsdFilter, protocols::simple_filters::AlaScan, protocols::simple_filters::DeltaFilter, protocols::simple_filters::ResidueIEFilter, protocols::simple_filters::TotalSasaFilter, protocols::simple_filters::BuriedUnsatHbondFilter, protocols::simple_filters::MultipleSigmoids, protocols::filters::ReplicateFilter, protocols::simple_filters::InterfaceSasaFilter, protocols::protein_interface_design::filters::InterfaceHolesFilter, protocols::simple_filters::PoseInfoFilter, protocols::simple_filters::ResidueDistanceFilter, protocols::simple_filters::SavePoseConstraintToFileFilter, protocols::simple_filters::EnergyPerResidueFilter, protocols::simple_filters::ReportFilter, protocols::simple_filters::SidechainRmsdFilter, protocols::simple_filters::ExpiryFilter, protocols::simple_filters::FileExistFilter, protocols::simple_filters::FileRemoveFilter, protocols::simple_filters::PDDFScoreFilter, protocols::simple_filters::ResidueBurialFilter, protocols::simple_filters::ResiduesInInterfaceFilter, protocols::simple_filters::SAXSScoreFilter, protocols::protein_interface_design::filters::ClashWithTargetFilter, protocols::simple_filters::NonSequentialNeighborsFilter, protocols::simple_filters::Sigmoid, protocols::simple_filters::Operator, and protocols::simple_filters::PoseComment.

Referenced by protocols::protein_interface_design::movers::PlaceStubMover::apply(), protocols::filters::FilterFactory::newFilter(), protocols::seeded_abinitio::PlaceFragments::parse_my_tag(), protocols::protein_interface_design::movers::HotspotHasherMover::parse_my_tag(), protocols::protein_interface_design::movers::LoopOver::parse_my_tag(), protocols::protein_interface_design::movers::TryRotamers::parse_my_tag(), protocols::protein_interface_design::movers::PlaceStubMover::parse_my_tag(), protocols::filters::CombinedFilter::parse_my_tag(), and protocols::protein_interface_design::movers::PlaceStubMover::PlaceStubMover().

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

pure virtual

Implemented in protocols::enzdes::ResidueConformerFilter, protocols::enzdes::EnzdesScorefileFilter, protocols::enzdes::RepackWithoutLigandFilter, protocols::enzdes::DiffAtomSasaFilter, protocols::filters::IfThenFilter, protocols::enzdes::EnzScoreFilter, protocols::filters::MoveBeforeFilter, protocols::filters::CombinedFilter, protocols::enzdes::LigInterfaceEnergyFilter, protocols::simple_filters::PackerNeighborGraphFilter, protocols::filters::CompoundFilter, protocols::fldsgn::filters::HelixPairingFilter, protocols::fldsgn::filters::HSSTripletFilter, protocols::enzdes::LigBurialFilter, protocols::fldsgn::filters::SheetTopologyFilter, protocols::fldsgn::filters::NcontactsFilter, protocols::fldsgn::filters::CoreDunbrackFilter, protocols::fldsgn::filters::InterlockingAromaFilter, protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter, protocols::simple_filters::DomainInterfaceFilter, protocols::fldsgn::filters::HelixKinkFilter, protocols::fldsgn::filters::FragQualFilter, protocols::simple_filters::HolesFilter, protocols::simple_filters::RangeFilter, protocols::docking::DockingHighResFilter, protocols::simple_filters::PackStatFilter, protocols::fldsgn::filters::SecondaryStructureFilter, protocols::protein_interface_design::filters::DisulfideFilter, protocols::simple_filters::BuriedRegionsFilter, protocols::simple_filters::ShapeComplementarityFilter, protocols::simple_filters::SymmetricMotifFilter, protocols::fldsgn::filters::SecondaryStructureCountFilter, protocols::denovo_design::filters::ExposedHydrophobicsFilter, protocols::enzdes::RemoveLigandFilter, protocols::filters::StochasticFilter, protocols::protein_interface_design::filters::HbondsToAtomFilter, protocols::protein_interface_design::filters::HbondsToResidueFilter, protocols::simple_filters::SheetFilter, protocols::enzdes::LigDSasaFilter, protocols::protein_interface_design::filters::SpecificResiduesNearInterfaceFilter, protocols::ligand_docking::AtomCountFilter, protocols::ligand_docking::HBondAcceptorFilter, protocols::ligand_docking::HeavyAtomFilter, protocols::ligand_docking::MolarMassFilter, protocols::ligand_docking::MolecularMassFilter, protocols::ligand_docking::HBondDonorFilter, protocols::simple_filters::InterfaceBindingEnergyDensityFilter, protocols::ligand_docking::ChainExistsFilter, protocols::simple_filters::AveragePathLengthFilter, protocols::simple_filters::ConservedPosMutationFilter, protocols::simple_filters::ConstraintScoreCutoffFilter, protocols::simple_filters::DisulfideEntropyFilter, protocols::simple_filters::ScoreCutoffFilter, protocols::ligand_docking::CompleteConnectionsFilter, protocols::filters::FalseFilter, protocols::docking::DockingLowResFilter, protocols::simple_filters::ResidueCountFilter, protocols::filters::HeavyAtomFilter, protocols::protein_interface_design::filters::FilterScanFilter, protocols::protein_interface_design::filters::StubScoreLoopsFilter, protocols::filters::ContingentFilter, protocols::protein_interface_design::filters::StubScoreFilter, protocols::protein_interface_design::filters::StubScoreFilter, protocols::simple_filters::COFilter, protocols::simple_filters::RGFilter, protocols::filters::CalculatorFilter, protocols::simple_filters::AbinitioBaseFilter, protocols::simple_filters::AtomicContactFilter, protocols::simple_filters::DdgFilter, protocols::simple_filters::AtomicDistanceFilter, protocols::simple_filters::ResidueSetChainEnergyFilter, protocols::simple_filters::RotamerBoltzmannWeight, protocols::protein_interface_design::filters::BindingStrainFilter, protocols::protein_interface_design::filters::DesignableResiduesFilter, protocols::protein_interface_design::filters::SequenceRecoveryFilter, protocols::simple_filters::NetChargeFilter, protocols::simple_filters::TerminusDistanceFilter, protocols::filters::TrueFilter, protocols::protein_interface_design::filters::AverageDegreeFilter, protocols::protein_interface_design::filters::FNatFilter, protocols::protein_interface_design::filters::IRmsdFilter, protocols::simple_filters::GeometryFilter, protocols::filters::TimeFilter, protocols::protein_interface_design::filters::LRmsdFilter, protocols::protein_interface_design::filters::Torsion, protocols::simple_filters::NeighborTypeFilter, protocols::simple_filters::NMerPSSMEnergyFilter, protocols::simple_filters::NMerSVMEnergyFilter, protocols::simple_filters::RelativePoseFilter, protocols::simple_filters::ScoreTypeFilter, protocols::protein_interface_design::filters::BoltzmannFilter, protocols::protein_interface_design::filters::RelativeSegmentFilter, protocols::simple_filters::AlaScan, protocols::simple_filters::ResidueIEFilter, protocols::protein_interface_design::filters::AtomicContactCountFilter, protocols::filters::ReplicateFilter, protocols::protein_interface_design::filters::RmsdFilter, protocols::simple_filters::DeltaFilter, protocols::simple_filters::TotalSasaFilter, protocols::protein_interface_design::filters::InterfaceHolesFilter, protocols::simple_filters::BuriedUnsatHbondFilter, protocols::simple_filters::MultipleSigmoids, protocols::simple_filters::PoseInfoFilter, protocols::simple_filters::ResidueDistanceFilter, protocols::simple_filters::SavePoseConstraintToFileFilter, protocols::simple_filters::EnergyPerResidueFilter, protocols::simple_filters::InterfaceSasaFilter, protocols::simple_filters::ReportFilter, protocols::simple_filters::ExpiryFilter, protocols::simple_filters::FileExistFilter, protocols::simple_filters::FileRemoveFilter, protocols::simple_filters::PDDFScoreFilter, protocols::simple_filters::ResiduesInInterfaceFilter, protocols::simple_filters::SAXSScoreFilter, protocols::simple_filters::NonSequentialNeighborsFilter, protocols::simple_filters::SidechainRmsdFilter, protocols::simple_filters::Sigmoid, protocols::simple_filters::ResidueBurialFilter, protocols::protein_interface_design::filters::ClashWithTargetFilter, protocols::simple_filters::Operator, and protocols::simple_filters::PoseComment.

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

inlinevirtual

Reimplemented in protocols::simple_filters::DomainInterfaceFilter, and protocols::simple_filters::BuriedRegionsFilter.

References type_.

Referenced by protocols::protein_interface_design::DockDesignFilterFactory::add_type(), protocols::simple_filters::Operator::compute(), protocols::simple_moves::GenericMonteCarloMover::load_trial_number_from_checkpoint(), protocols::simple_filters::Operator::modify_relative_filters_pdb_names(), protocols::enzdes::RemoveLigandFilter::report_sm(), and protocols::simple_filters::Operator::reset_baseline().

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

inline

References user_defined_name_.

Referenced by protocols::simple_filters::ConstraintScoreCutoffFilter::apply(), protocols::simple_filters::DeltaFilter::compute(), protocols::simple_moves::GenericMonteCarloMover::parse_my_tag(), protocols::simple_filters::Operator::report_sm(), protocols::simple_filters::ShapeComplementarityFilter::report_sm(), protocols::protein_interface_design::filters::SequenceRecoveryFilter::write_to_pdb(), and protocols::simple_filters::RotamerBoltzmannWeight::write_to_pdb().

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

inlinevirtual

Reimplemented in protocols::fldsgn::filters::HSSTripletFilter, protocols::simple_filters::PackerNeighborGraphFilter, protocols::fldsgn::filters::HelixPairingFilter, protocols::fldsgn::filters::SheetTopologyFilter, protocols::fldsgn::filters::InterlockingAromaFilter, protocols::fldsgn::filters::CoreDunbrackFilter, protocols::fldsgn::filters::FragQualFilter, protocols::fldsgn::filters::SecondaryStructureFilter, protocols::simple_filters::ScoreCutoffFilter, protocols::fldsgn::filters::NcontactsFilter, protocols::simple_filters::HolesFilter, protocols::simple_filters::ConstraintScoreCutoffFilter, protocols::simple_filters::PackStatFilter, protocols::simple_filters::RangeFilter, protocols::fldsgn::filters::HelixKinkFilter, protocols::simple_filters::DomainInterfaceFilter, protocols::simple_filters::BuriedRegionsFilter, protocols::simple_filters::ShapeComplementarityFilter, protocols::fldsgn::filters::SecondaryStructureCountFilter, protocols::simple_filters::ConservedPosMutationFilter, protocols::simple_filters::SheetFilter, protocols::simple_filters::COFilter, protocols::simple_filters::AbinitioBaseFilter, protocols::simple_filters::RGFilter, protocols::simple_filters::PDDFScoreFilter, protocols::simple_filters::SAXSScoreFilter, and protocols::protein_interface_design::filters::AtomicContactCountFilter.

Referenced by protocols::filters::CalculatorFilter::add_constant(), protocols::filters::CalculatorFilter::add_filter(), and set_user_defined_name().

void protocols::filters::Filter::parse_def ( utility::lua::LuaObject const &  def, utility::lua::LuaObject const &  score_fxns, utility::lua::LuaObject const &  tasks  )

virtual

Reimplemented in protocols::enzdes::LigInterfaceEnergyFilter, protocols::simple_filters::ShapeComplementarityFilter, protocols::protein_interface_design::filters::SequenceRecoveryFilter, protocols::simple_filters::DdgFilter, protocols::simple_filters::RotamerBoltzmannWeight, protocols::protein_interface_design::filters::DesignableResiduesFilter, protocols::simple_filters::ScoreTypeFilter, and protocols::simple_filters::InterfaceSasaFilter.

References utility_exit_with_message.

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::enzdes::DiffAtomSasaFilter, protocols::filters::IfThenFilter, protocols::enzdes::EnzScoreFilter, protocols::filters::MoveBeforeFilter, protocols::filters::CombinedFilter, protocols::enzdes::LigInterfaceEnergyFilter, protocols::fldsgn::filters::HSSTripletFilter, protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter, protocols::fldsgn::filters::NcontactsFilter, protocols::fldsgn::filters::HelixPairingFilter, protocols::fldsgn::filters::SheetTopologyFilter, protocols::fldsgn::filters::InterlockingAromaFilter, protocols::fldsgn::filters::CoreDunbrackFilter, protocols::filters::CompoundFilter, protocols::fldsgn::filters::FragQualFilter, protocols::fldsgn::filters::SecondaryStructureFilter, protocols::simple_filters::HolesFilter, protocols::simple_filters::PackStatFilter, protocols::simple_filters::SymmetricMotifFilter, protocols::simple_filters::RangeFilter, protocols::simple_filters::ShapeComplementarityFilter, protocols::enzdes::LigBurialFilter, protocols::fldsgn::filters::HelixKinkFilter, protocols::fldsgn::filters::SecondaryStructureCountFilter, protocols::protein_interface_design::filters::DisulfideFilter, protocols::simple_filters::DisulfideEntropyFilter, protocols::simple_filters::AveragePathLengthFilter, protocols::simple_filters::DomainInterfaceFilter, protocols::simple_filters::ResidueCountFilter, protocols::protein_interface_design::filters::FilterScanFilter, protocols::simple_filters::DdgFilter, protocols::filters::StochasticFilter, protocols::protein_interface_design::filters::SequenceRecoveryFilter, protocols::enzdes::LigDSasaFilter, protocols::simple_filters::AlaScan, protocols::simple_filters::BuriedRegionsFilter, protocols::ligand_docking::AtomCountFilter, protocols::ligand_docking::HBondAcceptorFilter, protocols::ligand_docking::HeavyAtomFilter, protocols::ligand_docking::MolarMassFilter, protocols::ligand_docking::MolecularMassFilter, protocols::enzdes::RemoveLigandFilter, protocols::ligand_docking::HBondDonorFilter, protocols::ligand_docking::ChainExistsFilter, protocols::simple_filters::ScoreCutoffFilter, protocols::simple_filters::ConstraintScoreCutoffFilter, protocols::simple_filters::InterfaceBindingEnergyDensityFilter, protocols::ligand_docking::CompleteConnectionsFilter, protocols::simple_filters::ConservedPosMutationFilter, protocols::simple_filters::ResidueSetChainEnergyFilter, protocols::filters::ContingentFilter, protocols::filters::HeavyAtomFilter, protocols::protein_interface_design::filters::AtomicContactCountFilter, protocols::protein_interface_design::filters::InterfaceHolesFilter, protocols::protein_interface_design::filters::FNatFilter, protocols::protein_interface_design::filters::IRmsdFilter, protocols::protein_interface_design::filters::StubScoreFilter, protocols::protein_interface_design::filters::StubScoreFilter, protocols::simple_filters::AtomicContactFilter, protocols::simple_filters::NMerPSSMEnergyFilter, protocols::simple_filters::NMerSVMEnergyFilter, protocols::denovo_design::filters::ExposedHydrophobicsFilter, protocols::filters::CalculatorFilter, protocols::protein_interface_design::filters::LRmsdFilter, protocols::protein_interface_design::filters::RmsdFilter, protocols::protein_interface_design::filters::StubScoreLoopsFilter, protocols::simple_filters::AtomicDistanceFilter, protocols::simple_filters::RotamerBoltzmannWeight, protocols::simple_filters::ScoreTypeFilter, protocols::protein_interface_design::filters::DesignableResiduesFilter, protocols::simple_filters::NetChargeFilter, protocols::simple_filters::ResidueIEFilter, protocols::simple_filters::ResiduesInInterfaceFilter, protocols::simple_filters::TerminusDistanceFilter, protocols::protein_interface_design::filters::AverageDegreeFilter, protocols::simple_filters::GeometryFilter, protocols::simple_filters::InterfaceSasaFilter, protocols::filters::TimeFilter, protocols::protein_interface_design::filters::BindingStrainFilter, protocols::simple_filters::NeighborTypeFilter, protocols::simple_filters::EnergyPerResidueFilter, protocols::protein_interface_design::filters::Torsion, protocols::simple_filters::RelativePoseFilter, protocols::simple_filters::ReportFilter, protocols::filters::ReplicateFilter, protocols::protein_interface_design::filters::BoltzmannFilter, protocols::protein_interface_design::filters::SpecificResiduesNearInterfaceFilter, protocols::simple_filters::ExpiryFilter, protocols::simple_filters::FileExistFilter, protocols::simple_filters::FileRemoveFilter, protocols::simple_filters::NonSequentialNeighborsFilter, protocols::simple_filters::PoseInfoFilter, protocols::simple_filters::ResidueDistanceFilter, protocols::simple_filters::SavePoseConstraintToFileFilter, protocols::simple_filters::TotalSasaFilter, protocols::simple_filters::DeltaFilter, protocols::simple_filters::MultipleSigmoids, protocols::simple_filters::Sigmoid, protocols::simple_filters::BuriedUnsatHbondFilter, protocols::protein_interface_design::filters::ClashWithTargetFilter, protocols::simple_filters::Operator, protocols::simple_filters::PoseComment, protocols::simple_filters::ResidueBurialFilter, and protocols::simple_filters::SidechainRmsdFilter.

Referenced by protocols::filters::FilterFactory::newFilter().

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

inlinevirtual

Reimplemented in protocols::enzdes::ResidueConformerFilter, protocols::enzdes::RepackWithoutLigandFilter, protocols::enzdes::DiffAtomSasaFilter, protocols::filters::IfThenFilter, protocols::enzdes::EnzScoreFilter, protocols::filters::MoveBeforeFilter, protocols::filters::CombinedFilter, protocols::enzdes::LigInterfaceEnergyFilter, protocols::fldsgn::filters::InterlockingAromaFilter, protocols::fldsgn::filters::CoreDunbrackFilter, protocols::fldsgn::filters::FragQualFilter, protocols::simple_filters::HolesFilter, protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter, protocols::fldsgn::filters::NcontactsFilter, protocols::simple_filters::RangeFilter, protocols::fldsgn::filters::SecondaryStructureCountFilter, protocols::filters::CompoundFilter, protocols::enzdes::LigBurialFilter, protocols::simple_filters::SymmetricMotifFilter, protocols::protein_interface_design::filters::DisulfideFilter, protocols::denovo_design::filters::ExposedHydrophobicsFilter, protocols::protein_interface_design::filters::HbondsToAtomFilter, protocols::protein_interface_design::filters::HbondsToResidueFilter, protocols::filters::StochasticFilter, protocols::simple_filters::DdgFilter, protocols::simple_filters::AveragePathLengthFilter, protocols::simple_filters::ConstraintScoreCutoffFilter, protocols::simple_filters::DisulfideEntropyFilter, protocols::simple_filters::ScoreCutoffFilter, protocols::protein_interface_design::filters::SpecificResiduesNearInterfaceFilter, protocols::enzdes::LigDSasaFilter, protocols::simple_filters::ResidueCountFilter, protocols::simple_filters::InterfaceBindingEnergyDensityFilter, protocols::simple_filters::ResidueSetChainEnergyFilter, protocols::docking::DockingLowResFilter, protocols::protein_interface_design::filters::InterfaceHolesFilter, protocols::protein_interface_design::filters::FNatFilter, protocols::protein_interface_design::filters::IRmsdFilter, protocols::simple_filters::NMerPSSMEnergyFilter, protocols::simple_filters::NMerSVMEnergyFilter, protocols::simple_filters::ScoreTypeFilter, protocols::protein_interface_design::filters::FilterScanFilter, protocols::protein_interface_design::filters::LRmsdFilter, protocols::protein_interface_design::filters::RelativeSegmentFilter, protocols::simple_filters::AlaScan, protocols::simple_filters::ResidueIEFilter, protocols::simple_filters::ResiduesInInterfaceFilter, protocols::protein_interface_design::filters::StubScoreFilter, protocols::protein_interface_design::filters::StubScoreFilter, protocols::filters::ContingentFilter, protocols::protein_interface_design::filters::RmsdFilter, protocols::simple_filters::RotamerBoltzmannWeight, protocols::protein_interface_design::filters::BindingStrainFilter, protocols::protein_interface_design::filters::DesignableResiduesFilter, protocols::protein_interface_design::filters::SequenceRecoveryFilter, protocols::simple_filters::AtomicContactFilter, protocols::simple_filters::EnergyPerResidueFilter, protocols::simple_filters::ReportFilter, protocols::protein_interface_design::filters::AverageDegreeFilter, protocols::simple_filters::AtomicDistanceFilter, protocols::simple_filters::ExpiryFilter, protocols::simple_filters::FileExistFilter, protocols::simple_filters::FileRemoveFilter, protocols::simple_filters::MultipleSigmoids, protocols::simple_filters::Sigmoid, protocols::filters::CalculatorFilter, protocols::protein_interface_design::filters::Torsion, protocols::simple_filters::NonSequentialNeighborsFilter, protocols::simple_filters::RelativePoseFilter, protocols::protein_interface_design::filters::BoltzmannFilter, protocols::simple_filters::NetChargeFilter, protocols::simple_filters::Operator, protocols::simple_filters::TerminusDistanceFilter, protocols::filters::TimeFilter, protocols::simple_filters::GeometryFilter, protocols::simple_filters::PoseComment, protocols::protein_interface_design::filters::ClashWithTargetFilter, protocols::simple_filters::DeltaFilter, protocols::simple_filters::NeighborTypeFilter, protocols::simple_filters::BuriedUnsatHbondFilter, protocols::simple_filters::InterfaceSasaFilter, protocols::simple_filters::PoseInfoFilter, protocols::simple_filters::SavePoseConstraintToFileFilter, protocols::filters::ReplicateFilter, protocols::simple_filters::ResidueDistanceFilter, protocols::simple_filters::TotalSasaFilter, protocols::simple_filters::SidechainRmsdFilter, and protocols::simple_filters::ResidueBurialFilter.

Referenced by protocols::simple_moves::ddG::fill_energy_vector().

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::enzdes::DiffAtomSasaFilter, protocols::filters::IfThenFilter, protocols::enzdes::EnzScoreFilter, protocols::filters::MoveBeforeFilter, protocols::fldsgn::filters::HSSTripletFilter, protocols::filters::CombinedFilter, protocols::enzdes::LigInterfaceEnergyFilter, protocols::fldsgn::filters::HelixPairingFilter, protocols::fldsgn::filters::InterlockingAromaFilter, protocols::fldsgn::filters::CoreDunbrackFilter, protocols::fldsgn::filters::FragQualFilter, protocols::fldsgn::filters::SecondaryStructureFilter, protocols::simple_filters::HolesFilter, protocols::simple_filters::PackStatFilter, protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter, protocols::simple_filters::ShapeComplementarityFilter, protocols::fldsgn::filters::NcontactsFilter, protocols::filters::CompoundFilter, protocols::fldsgn::filters::SecondaryStructureCountFilter, protocols::simple_filters::SymmetricMotifFilter, protocols::enzdes::LigBurialFilter, protocols::protein_interface_design::filters::DisulfideFilter, protocols::denovo_design::filters::ExposedHydrophobicsFilter, protocols::protein_interface_design::filters::HbondsToAtomFilter, protocols::protein_interface_design::filters::HbondsToResidueFilter, protocols::simple_filters::DdgFilter, protocols::simple_filters::AveragePathLengthFilter, protocols::simple_filters::DisulfideEntropyFilter, protocols::protein_interface_design::filters::AtomicContactCountFilter, protocols::simple_filters::ResidueCountFilter, protocols::enzdes::RemoveLigandFilter, protocols::protein_interface_design::filters::SpecificResiduesNearInterfaceFilter, protocols::enzdes::LigDSasaFilter, protocols::simple_filters::InterfaceBindingEnergyDensityFilter, protocols::simple_filters::ResidueSetChainEnergyFilter, protocols::protein_interface_design::filters::InterfaceHolesFilter, protocols::protein_interface_design::filters::FNatFilter, protocols::protein_interface_design::filters::IRmsdFilter, protocols::protein_interface_design::filters::RmsdFilter, protocols::simple_filters::AlaScan, protocols::simple_filters::NMerPSSMEnergyFilter, protocols::simple_filters::NMerSVMEnergyFilter, protocols::simple_filters::ScoreTypeFilter, protocols::protein_interface_design::filters::FilterScanFilter, protocols::protein_interface_design::filters::LRmsdFilter, protocols::protein_interface_design::filters::RelativeSegmentFilter, protocols::simple_filters::ResidueIEFilter, protocols::simple_filters::ResiduesInInterfaceFilter, protocols::protein_interface_design::filters::StubScoreFilter, protocols::protein_interface_design::filters::StubScoreFilter, protocols::filters::ContingentFilter, protocols::simple_filters::RotamerBoltzmannWeight, protocols::protein_interface_design::filters::BindingStrainFilter, protocols::protein_interface_design::filters::DesignableResiduesFilter, protocols::protein_interface_design::filters::SequenceRecoveryFilter, protocols::simple_filters::AtomicContactFilter, protocols::simple_filters::EnergyPerResidueFilter, protocols::simple_filters::ReportFilter, protocols::protein_interface_design::filters::AverageDegreeFilter, protocols::simple_filters::AtomicDistanceFilter, protocols::simple_filters::ExpiryFilter, protocols::simple_filters::FileExistFilter, protocols::simple_filters::FileRemoveFilter, protocols::simple_filters::MultipleSigmoids, protocols::simple_filters::Sigmoid, protocols::filters::CalculatorFilter, protocols::protein_interface_design::filters::Torsion, protocols::simple_filters::NonSequentialNeighborsFilter, protocols::simple_filters::RelativePoseFilter, protocols::protein_interface_design::filters::BoltzmannFilter, protocols::simple_filters::NetChargeFilter, protocols::simple_filters::Operator, protocols::simple_filters::TerminusDistanceFilter, protocols::filters::TimeFilter, protocols::simple_filters::GeometryFilter, protocols::simple_filters::PoseComment, protocols::protein_interface_design::filters::ClashWithTargetFilter, protocols::simple_filters::DeltaFilter, protocols::simple_filters::NeighborTypeFilter, protocols::simple_filters::BuriedUnsatHbondFilter, protocols::simple_filters::InterfaceSasaFilter, protocols::simple_filters::PoseInfoFilter, protocols::simple_filters::SavePoseConstraintToFileFilter, protocols::filters::ReplicateFilter, protocols::simple_filters::ResidueDistanceFilter, protocols::simple_filters::TotalSasaFilter, protocols::simple_filters::SidechainRmsdFilter, and protocols::simple_filters::ResidueBurialFilter.

Referenced by protocols::simple_moves::ContingentAcceptMover::apply(), protocols::protein_interface_design::movers::SetTemperatureFactor::apply(), protocols::loophash::LoopHashMoverWrapper::apply(), protocols::protein_interface_design::filters::FilterScanFilter::apply(), protocols::loophash::LoopHashDiversifier::apply(), protocols::simple_filters::RangeFilter::apply(), protocols::simple_filters::DeltaFilter::baseline(), protocols::filters::ReplicateFilter::compute(), protocols::simple_moves::ddG::fill_energy_vector(), protocols::pose_reporters::FilterReporter::report_property(), protocols::simple_filters::Operator::report_sm(), protocols::enzdes::RemoveLigandFilter::report_sm(), protocols::simple_filters::Sigmoid::reset_baseline(), and score().

void protocols::filters::Filter::score ( core::io::serialization::PipeMap &  pmap )

virtual

References begin, and clear().

Referenced by protocols::simple_filters::NMerPSSMEnergyFilter::apply(), protocols::simple_filters::ScoreTypeFilter::apply(), protocols::simple_filters::NMerSVMEnergyFilter::apply(), protocols::simple_filters::ResidueSetChainEnergyFilter::apply(), protocols::simple_filters::PackStatFilter::apply(), protocols::fldsgn::filters::NcontactsFilter::apply(), protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter::apply(), protocols::protein_interface_design::filters::ClashWithTargetFilter::compute(), protocols::simple_filters::GeometryFilter::compute(), protocols::simple_filters::EnergyPerResidueFilter::compute(), protocols::simple_filters::ScoreTypeFilter::compute(), protocols::simple_filters::NMerPSSMEnergyFilter::compute(), protocols::simple_filters::NMerSVMEnergyFilter::compute(), protocols::simple_filters::ResidueSetChainEnergyFilter::compute(), protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter::compute(), protocols::fldsgn::filters::FragQualFilter::compute(), protocols::enzdes::EnzScoreFilter::compute(), protocols::simple_filters::RotamerBoltzmannWeight::compute_Boltzmann_weight(), protocols::simple_filters::PackStatFilter::filtered_score(), protocols::simple_filters::ScoreCutoffFilter::output_residue_pair_energies(), and score().

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

virtual

References report_sm(), score(), scorename_, and core::pose::setPoseExtraScores().

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

inline

References name(), and user_defined_name_.

Referenced by protocols::filters::FilterFactory::newFilter(), and protocols::simple_filters::ConstraintScoreCutoffFilter::parse_my_tag().

Member Data Documentation

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

protected

Referenced by protocols::simple_filters::DdgFilter::DdgFilter(), protocols::simple_filters::DdgFilter::parse_def(), 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:

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