Rosetta Protocols  2014.35
Public Member Functions | Protected Attributes | Private Attributes | List of all members
protocols::filters::Filter Class Referenceabstract

#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::filters::MoveBeforeFilter, protocols::enzdes::EnzScoreFilter, protocols::fldsgn::filters::HSSTripletFilter, protocols::fldsgn::filters::HelixPairingFilter, protocols::filters::CombinedFilter, protocols::simple_filters::SaveResfileToDiskFilter, protocols::indexed_structure_store::filters::FragmentLookupFilter, protocols::matdes::OligomericAverageDegreeFilter, protocols::fldsgn::filters::SheetTopologyFilter, protocols::matdes::GetRBDOFValues, protocols::fldsgn::filters::InterlockingAromaFilter, protocols::simple_filters::PackerNeighborGraphFilter, protocols::enzdes::LigInterfaceEnergyFilter, protocols::fldsgn::filters::CoreDunbrackFilter, protocols::simple_filters::TaskAwareSASAFilter, protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter, protocols::fldsgn::filters::FragQualFilter, protocols::fldsgn::filters::NcontactsFilter, protocols::fldsgn::filters::SecondaryStructureFilter, protocols::matdes::ClashCheckFilter, protocols::simple_filters::HolesFilter, protocols::simple_filters::PackStatFilter, protocols::simple_filters::RangeFilter, protocols::simple_filters::ShapeComplementarityFilter, protocols::fldsgn::filters::HelixKinkFilter, protocols::matdes::SymUnsatHbondFilter, protocols::fldsgn::filters::SecondaryStructureCountFilter, protocols::filters::CompoundFilter, protocols::simple_filters::DomainInterfaceFilter, protocols::simple_filters::TaskAwareAlaScan, 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::protein_interface_design::filters::SSamountFilter, protocols::simple_filters::AveragePathLengthFilter, protocols::simple_filters::DisulfideEntropyFilter, protocols::simple_filters::ResidueCountFilter, protocols::protein_interface_design::filters::FilterScanFilter, protocols::protein_interface_design::filters::RmsdSimpleFilter, 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::ResidueSetChainEnergyFilter, protocols::simple_filters::RotamerBoltzmannWeight, protocols::simple_filters::TaskAwareScoreTypeFilter, protocols::protein_interface_design::filters::BindingStrainFilter, protocols::protein_interface_design::filters::DesignableResiduesFilter, protocols::protein_interface_design::filters::LRmsdFilter, protocols::matdes::InterfacePackingFilter, protocols::protein_interface_design::filters::AverageDegreeFilter, protocols::protein_interface_design::filters::SequenceRecoveryFilter, protocols::simple_filters::AtomicContactFilter, protocols::simple_filters::MultipleSigmoids, protocols::simple_filters::MutationsFilter, protocols::simple_filters::Sigmoid, protocols::filters::CalculatorFilter, protocols::protein_interface_design::filters::Torsion, protocols::simple_filters::AtomicDistanceFilter, protocols::simple_filters::NetChargeFilter, protocols::simple_filters::NMerPSSMEnergyFilter, protocols::simple_filters::NMerSVMEnergyFilter, protocols::simple_filters::RelativePoseFilter, protocols::simple_filters::ScoreTypeFilter, protocols::simple_filters::SSMotifFinder, protocols::simple_filters::StemFinder, 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::CircularPermutationFinder, 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::DdgFilter, 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(), protocols::rosetta_scripts::ParsedProtocol::apply_filter(), protocols::simple_filters::RangeFilter::report(), and protocols::pose_selectors::Filter::select_poses().

void protocols::filters::Filter::apply ( core::io::serialization::PipeMap pmap)
virtual
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::filters::MoveBeforeFilter, protocols::enzdes::EnzScoreFilter, protocols::filters::CombinedFilter, protocols::enzdes::LigInterfaceEnergyFilter, protocols::indexed_structure_store::filters::FragmentLookupFilter, 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::SaveResfileToDiskFilter, 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::matdes::GetRBDOFValues, protocols::matdes::OligomericAverageDegreeFilter, protocols::simple_filters::TaskAwareSASAFilter, 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::matdes::ClashCheckFilter, 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::matdes::SymUnsatHbondFilter, 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::simple_filters::TaskAwareAlaScan, 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::ResidueCountFilter, 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::RmsdSimpleFilter, protocols::protein_interface_design::filters::SSamountFilter, protocols::protein_interface_design::filters::StubScoreFilter, protocols::protein_interface_design::filters::StubScoreFilter, protocols::filters::ContingentFilter, protocols::filters::HeavyAtomFilter, protocols::simple_filters::AbinitioBaseFilter, protocols::simple_filters::COFilter, protocols::simple_filters::RGFilter, protocols::simple_filters::RotamerBoltzmannWeight, protocols::simple_filters::TaskAwareScoreTypeFilter, 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::matdes::InterfacePackingFilter, 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::MutationsFilter, protocols::simple_filters::NetChargeFilter, protocols::simple_filters::ResidueSetChainEnergyFilter, protocols::protein_interface_design::filters::LRmsdFilter, protocols::protein_interface_design::filters::Torsion, 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::DdgFilter, 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::SSMotifFinder, protocols::simple_filters::StemFinder, protocols::simple_filters::CircularPermutationFinder, 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(), protocols::protein_interface_design::movers::PlaceStubMover::PlaceStubMover(), protocols::filters::CompoundFilter::reset_filters(), and protocols::filters::CombinedFilter::reset_filters().

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::indexed_structure_store::filters::FragmentLookupFilter, 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::SaveResfileToDiskFilter, 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::matdes::GetRBDOFValues, protocols::matdes::OligomericAverageDegreeFilter, protocols::simple_filters::TaskAwareSASAFilter, 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::matdes::ClashCheckFilter, 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::matdes::SymUnsatHbondFilter, 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::ResidueCountFilter, protocols::simple_filters::ScoreCutoffFilter, protocols::simple_filters::TaskAwareAlaScan, protocols::ligand_docking::CompleteConnectionsFilter, protocols::filters::FalseFilter, protocols::docking::DockingLowResFilter, protocols::filters::HeavyAtomFilter, protocols::protein_interface_design::filters::FilterScanFilter, protocols::protein_interface_design::filters::StubScoreLoopsFilter, protocols::filters::ContingentFilter, protocols::protein_interface_design::filters::RmsdSimpleFilter, protocols::protein_interface_design::filters::SSamountFilter, 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::AtomicDistanceFilter, protocols::simple_filters::NetChargeFilter, protocols::simple_filters::ResidueSetChainEnergyFilter, protocols::simple_filters::RotamerBoltzmannWeight, protocols::simple_filters::TaskAwareScoreTypeFilter, protocols::protein_interface_design::filters::BindingStrainFilter, protocols::protein_interface_design::filters::DesignableResiduesFilter, protocols::protein_interface_design::filters::SequenceRecoveryFilter, 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::simple_filters::GeometryFilter, protocols::simple_filters::MutationsFilter, 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::DdgFilter, 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::simple_filters::SSMotifFinder, protocols::simple_filters::StemFinder, protocols::protein_interface_design::filters::ClashWithTargetFilter, protocols::simple_filters::CircularPermutationFinder, protocols::simple_filters::Operator, and protocols::simple_filters::PoseComment.

virtual std::string protocols::filters::Filter::get_type ( ) const
inlinevirtual
std::string protocols::filters::Filter::get_user_defined_name ( ) const
inline
virtual std::string protocols::filters::Filter::name ( ) const
inlinevirtual

Reimplemented in protocols::fldsgn::filters::HSSTripletFilter, protocols::simple_filters::PackerNeighborGraphFilter, protocols::indexed_structure_store::filters::FragmentLookupFilter, 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::SaveResfileToDiskFilter, protocols::simple_filters::RangeFilter, protocols::fldsgn::filters::HelixKinkFilter, protocols::simple_filters::DomainInterfaceFilter, protocols::matdes::GetRBDOFValues, protocols::matdes::OligomericAverageDegreeFilter, protocols::simple_filters::TaskAwareSASAFilter, protocols::matdes::ClashCheckFilter, protocols::simple_filters::BuriedRegionsFilter, protocols::simple_filters::ShapeComplementarityFilter, protocols::fldsgn::filters::SecondaryStructureCountFilter, protocols::simple_filters::ConservedPosMutationFilter, protocols::simple_filters::SheetFilter, protocols::matdes::SymUnsatHbondFilter, protocols::simple_filters::TaskAwareAlaScan, 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(), protocols::simple_filters::TaskAwareScoreTypeFilter::score_type_name(), set_user_defined_name(), and protocols::simple_filters::TaskAwareScoreTypeFilter::write_to_pdb().

void protocols::filters::Filter::parse_def ( utility::lua::LuaObject const &  def,
utility::lua::LuaObject const &  score_fxns,
utility::lua::LuaObject const &  tasks 
)
virtual
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::indexed_structure_store::filters::FragmentLookupFilter, protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter, protocols::fldsgn::filters::NcontactsFilter, protocols::simple_filters::SaveResfileToDiskFilter, protocols::fldsgn::filters::HelixPairingFilter, protocols::matdes::GetRBDOFValues, protocols::matdes::OligomericAverageDegreeFilter, protocols::fldsgn::filters::SheetTopologyFilter, protocols::fldsgn::filters::InterlockingAromaFilter, protocols::filters::CompoundFilter, protocols::simple_filters::TaskAwareSASAFilter, protocols::fldsgn::filters::CoreDunbrackFilter, protocols::fldsgn::filters::FragQualFilter, protocols::matdes::ClashCheckFilter, 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::simple_filters::TaskAwareAlaScan, protocols::matdes::SymUnsatHbondFilter, protocols::fldsgn::filters::SecondaryStructureCountFilter, protocols::protein_interface_design::filters::DisulfideFilter, protocols::simple_filters::DisulfideEntropyFilter, protocols::simple_filters::ResidueCountFilter, protocols::simple_filters::AveragePathLengthFilter, protocols::simple_filters::DomainInterfaceFilter, protocols::protein_interface_design::filters::FilterScanFilter, protocols::simple_filters::MutationsFilter, 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::DdgFilter, protocols::simple_filters::InterfaceBindingEnergyDensityFilter, protocols::ligand_docking::CompleteConnectionsFilter, protocols::protein_interface_design::filters::RmsdSimpleFilter, protocols::simple_filters::ConservedPosMutationFilter, protocols::protein_interface_design::filters::SSamountFilter, protocols::simple_filters::NetChargeFilter, 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::ResidueIEFilter, protocols::simple_filters::ResiduesInInterfaceFilter, protocols::simple_filters::TerminusDistanceFilter, protocols::protein_interface_design::filters::AverageDegreeFilter, protocols::simple_filters::GeometryFilter, protocols::simple_filters::InterfaceSasaFilter, protocols::simple_filters::TaskAwareScoreTypeFilter, protocols::filters::TimeFilter, protocols::protein_interface_design::filters::BindingStrainFilter, protocols::simple_filters::NeighborTypeFilter, protocols::matdes::InterfacePackingFilter, 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::simple_filters::SSMotifFinder, protocols::simple_filters::StemFinder, protocols::protein_interface_design::filters::ClashWithTargetFilter, protocols::simple_filters::CircularPermutationFinder, 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::indexed_structure_store::filters::FragmentLookupFilter, protocols::filters::CombinedFilter, protocols::matdes::OligomericAverageDegreeFilter, protocols::enzdes::LigInterfaceEnergyFilter, protocols::fldsgn::filters::InterlockingAromaFilter, protocols::matdes::GetRBDOFValues, protocols::fldsgn::filters::CoreDunbrackFilter, protocols::fldsgn::filters::FragQualFilter, protocols::simple_filters::TaskAwareSASAFilter, protocols::matdes::ClashCheckFilter, protocols::simple_filters::HolesFilter, protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter, protocols::fldsgn::filters::NcontactsFilter, protocols::simple_filters::RangeFilter, protocols::matdes::SymUnsatHbondFilter, protocols::fldsgn::filters::SecondaryStructureCountFilter, protocols::simple_filters::TaskAwareAlaScan, 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::AveragePathLengthFilter, protocols::simple_filters::ConstraintScoreCutoffFilter, protocols::simple_filters::DisulfideEntropyFilter, protocols::simple_filters::ResidueCountFilter, protocols::simple_filters::ScoreCutoffFilter, protocols::protein_interface_design::filters::SpecificResiduesNearInterfaceFilter, protocols::enzdes::LigDSasaFilter, protocols::simple_filters::DdgFilter, protocols::simple_filters::InterfaceBindingEnergyDensityFilter, protocols::protein_interface_design::filters::SSamountFilter, protocols::protein_interface_design::filters::RmsdSimpleFilter, 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::simple_filters::TaskAwareScoreTypeFilter, 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::matdes::InterfacePackingFilter, 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::MutationsFilter, protocols::simple_filters::Sigmoid, protocols::filters::CalculatorFilter, protocols::protein_interface_design::filters::Torsion, protocols::simple_filters::NetChargeFilter, protocols::simple_filters::NonSequentialNeighborsFilter, protocols::simple_filters::RelativePoseFilter, protocols::simple_filters::SSMotifFinder, protocols::simple_filters::StemFinder, protocols::protein_interface_design::filters::BoltzmannFilter, protocols::simple_filters::CircularPermutationFinder, 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::rosetta_scripts::ParsedProtocol::apply_filter(), protocols::simple_moves::ddG::fill_energy_vector(), and protocols::rosetta_scripts::ParsedProtocol::report_all().

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::indexed_structure_store::filters::FragmentLookupFilter, protocols::fldsgn::filters::HSSTripletFilter, protocols::filters::CombinedFilter, protocols::matdes::OligomericAverageDegreeFilter, protocols::enzdes::LigInterfaceEnergyFilter, protocols::matdes::GetRBDOFValues, protocols::fldsgn::filters::HelixPairingFilter, protocols::fldsgn::filters::InterlockingAromaFilter, protocols::fldsgn::filters::CoreDunbrackFilter, protocols::simple_filters::TaskAwareSASAFilter, protocols::fldsgn::filters::FragQualFilter, protocols::matdes::ClashCheckFilter, 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::matdes::SymUnsatHbondFilter, 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::AveragePathLengthFilter, protocols::simple_filters::DisulfideEntropyFilter, protocols::simple_filters::ResidueCountFilter, protocols::protein_interface_design::filters::AtomicContactCountFilter, protocols::enzdes::RemoveLigandFilter, protocols::protein_interface_design::filters::SpecificResiduesNearInterfaceFilter, protocols::enzdes::LigDSasaFilter, protocols::simple_filters::DdgFilter, protocols::simple_filters::InterfaceBindingEnergyDensityFilter, protocols::protein_interface_design::filters::SSamountFilter, protocols::protein_interface_design::filters::RmsdSimpleFilter, 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::simple_filters::TaskAwareScoreTypeFilter, 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::matdes::InterfacePackingFilter, 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::MutationsFilter, protocols::simple_filters::Sigmoid, protocols::filters::CalculatorFilter, protocols::protein_interface_design::filters::Torsion, protocols::simple_filters::NetChargeFilter, protocols::simple_filters::NonSequentialNeighborsFilter, protocols::simple_filters::RelativePoseFilter, protocols::simple_filters::SSMotifFinder, protocols::simple_filters::StemFinder, protocols::protein_interface_design::filters::BoltzmannFilter, protocols::simple_filters::CircularPermutationFinder, 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::rosetta_scripts::ParsedProtocol::apply_filter(), 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(), score(), and protocols::pose_selectors::Filter::select_poses().

void protocols::filters::Filter::score ( core::io::serialization::PipeMap pmap)
virtual
core::Real protocols::filters::Filter::score ( core::pose::Pose pose)
virtual
void protocols::filters::Filter::set_user_defined_name ( std::string const &  name)
inline

Member Data Documentation

std::string protocols::filters::Filter::scorename_
protected
std::string const protocols::filters::Filter::type_
private

Referenced by get_type().

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

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