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protocols::filters::Filter Class Referenceabstract

#include <Filter.hh>

Inherits utility::pointer::ReferenceCount.

Inherited by 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::RepackWithoutLigandFilter, protocols::filters::CalculatorFilter, protocols::filters::CombinedFilter, protocols::filters::CompoundFilter, protocols::filters::ContingentFilter, protocols::filters::FalseFilter, protocols::filters::HeavyAtomFilter, protocols::filters::IfThenFilter, protocols::filters::MoveBeforeFilter, protocols::filters::ReplicateFilter, protocols::filters::StochasticFilter, protocols::filters::TimeFilter, protocols::filters::TrueFilter, protocols::fldsgn::filters::CoreDunbrackFilter, protocols::fldsgn::filters::FragQualFilter, 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::SecondaryStructureFilter, protocols::fldsgn::filters::SheetTopologyFilter, 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::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::DesignableResiduesFilter, protocols::protein_interface_design::filters::DisulfideFilter, protocols::protein_interface_design::filters::FilterScanFilter, protocols::protein_interface_design::filters::HbondsToResidueFilter, protocols::protein_interface_design::filters::InterfaceHolesFilter, protocols::protein_interface_design::filters::RelativeSegmentFilter, protocols::protein_interface_design::filters::RmsdFilter, protocols::protein_interface_design::filters::SequenceRecoveryFilter, protocols::protein_interface_design::filters::SpecificResiduesNearInterfaceFilter, protocols::protein_interface_design::filters::StubScoreFilter, protocols::protein_interface_design::filters::StubScoreFilter, protocols::protein_interface_design::filters::Torsion, protocols::simple_filters::AbinitioBaseFilter, protocols::simple_filters::AlaScan, protocols::simple_filters::AtomicContactFilter, protocols::simple_filters::AtomicDistanceFilter, protocols::simple_filters::BuriedUnsatHbondFilter, protocols::simple_filters::ConservedPosMutationFilter, protocols::simple_filters::ConstraintScoreCutoffFilter, protocols::simple_filters::DdgFilter, protocols::simple_filters::DeltaFilter, protocols::simple_filters::EnergyPerResidueFilter, protocols::simple_filters::ExpiryFilter, protocols::simple_filters::FileExistFilter, protocols::simple_filters::FileRemoveFilter, protocols::simple_filters::HolesFilter, protocols::simple_filters::InterfaceBindingEnergyDensityFilter, protocols::simple_filters::InterfaceSasaFilter, protocols::simple_filters::NeighborTypeFilter, protocols::simple_filters::NMerPSSMEnergyFilter, protocols::simple_filters::NonSequentialNeighborsFilter, protocols::simple_filters::Operator, protocols::simple_filters::PackerNeighborGraphFilter, protocols::simple_filters::PackStatFilter, protocols::simple_filters::PDDFScoreFilter, protocols::simple_filters::PoseInfoFilter, protocols::simple_filters::RangeFilter, protocols::simple_filters::RelativePoseFilter, protocols::simple_filters::ReportFilter, protocols::simple_filters::ResidueBurialFilter, protocols::simple_filters::ResidueCountFilter, protocols::simple_filters::ResidueDistanceFilter, protocols::simple_filters::ResidueIEFilter, protocols::simple_filters::ResidueSetChainEnergyFilter, protocols::simple_filters::ResiduesInInterfaceFilter, protocols::simple_filters::RotamerBoltzmannWeight, protocols::simple_filters::SAXSScoreFilter, protocols::simple_filters::ScoreCutoffFilter, protocols::simple_filters::ScoreTypeFilter, protocols::simple_filters::ShapeComplementarityFilter, protocols::simple_filters::SidechainRmsdFilter, protocols::simple_filters::Sigmoid, protocols::simple_filters::SymmetricMotifFilter, and protocols::simple_filters::TerminusDistanceFilter.

Collaboration diagram for protocols::filters::Filter:
Collaboration graph
[legend]

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::TagPtr const, moves::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::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::simple_filters::ShapeComplementarityFilter, protocols::fldsgn::filters::CoreDunbrackFilter, protocols::enzdes::LigInterfaceEnergyFilter, 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::fldsgn::filters::HelixKinkFilter, protocols::filters::CompoundFilter, protocols::enzdes::LigBurialFilter, protocols::docking::DockingHighResFilter, protocols::simple_filters::ConstraintScoreCutoffFilter, protocols::protein_interface_design::filters::DisulfideFilter, protocols::simple_filters::ScoreCutoffFilter, protocols::simple_filters::SheetFilter, protocols::simple_filters::ConservedPosMutationFilter, protocols::filters::StochasticFilter, 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::ligand_docking::AtomCountFilter, protocols::ligand_docking::HBondAcceptorFilter, protocols::ligand_docking::HeavyAtomFilter, protocols::ligand_docking::MolarMassFilter, protocols::ligand_docking::MolecularMassFilter, protocols::enzdes::LigDSasaFilter, 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::DdgFilter, protocols::protein_interface_design::filters::FilterScanFilter, 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::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::AverageDegreeFilter, protocols::protein_interface_design::filters::SequenceRecoveryFilter, protocols::simple_filters::AtomicContactFilter, protocols::simple_filters::Sigmoid, protocols::filters::CalculatorFilter, protocols::protein_interface_design::filters::Torsion, protocols::simple_filters::AtomicDistanceFilter, protocols::simple_filters::NMerPSSMEnergyFilter, protocols::simple_filters::Operator, 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::ResidueIEFilter, protocols::simple_filters::TerminusDistanceFilter, protocols::simple_filters::EnergyPerResidueFilter, protocols::filters::TimeFilter, protocols::simple_filters::DeltaFilter, protocols::simple_filters::NeighborTypeFilter, protocols::protein_interface_design::filters::InterfaceHolesFilter, protocols::simple_filters::BuriedUnsatHbondFilter, 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::simple_filters::NonSequentialNeighborsFilter, protocols::simple_filters::PoseInfoFilter, protocols::simple_filters::ResidueDistanceFilter, protocols::simple_filters::SidechainRmsdFilter, and protocols::simple_filters::ResidueBurialFilter.

Referenced by protocols::protein_interface_design::filters::SequenceRecoveryFilter::apply(), and apply().

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

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

References apply(), clear(), and core::sequence::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::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::fldsgn::filters::SheetTopologyFilter, protocols::enzdes::LigBurialFilter, protocols::fldsgn::filters::NcontactsFilter, 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::ShapeComplementarityFilter, 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::SymmetricMotifFilter, protocols::filters::StochasticFilter, 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::ConstraintScoreCutoffFilter, 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::DdgFilter, protocols::simple_filters::ResidueCountFilter, 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::simple_filters::AtomicDistanceFilter, protocols::simple_filters::ResidueSetChainEnergyFilter, protocols::protein_interface_design::filters::Torsion, protocols::simple_filters::RelativePoseFilter, protocols::simple_filters::TerminusDistanceFilter, protocols::protein_interface_design::filters::BoltzmannFilter, protocols::filters::TimeFilter, protocols::protein_interface_design::filters::AtomicContactCountFilter, protocols::simple_filters::NeighborTypeFilter, protocols::simple_filters::NMerPSSMEnergyFilter, 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::BuriedUnsatHbondFilter, protocols::simple_filters::EnergyPerResidueFilter, protocols::filters::ReplicateFilter, protocols::simple_filters::InterfaceSasaFilter, protocols::protein_interface_design::filters::InterfaceHolesFilter, protocols::simple_filters::PoseInfoFilter, protocols::simple_filters::ResidueDistanceFilter, 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::simple_filters::NonSequentialNeighborsFilter, protocols::simple_filters::Sigmoid, and protocols::simple_filters::Operator.

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

Implemented in 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::fldsgn::filters::SheetTopologyFilter, protocols::enzdes::LigBurialFilter, protocols::fldsgn::filters::NcontactsFilter, protocols::fldsgn::filters::CoreDunbrackFilter, protocols::fldsgn::filters::InterlockingAromaFilter, protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter, protocols::fldsgn::filters::HelixKinkFilter, protocols::fldsgn::filters::FragQualFilter, protocols::simple_filters::ShapeComplementarityFilter, 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::SymmetricMotifFilter, protocols::filters::StochasticFilter, protocols::protein_interface_design::filters::HbondsToResidueFilter, protocols::simple_filters::SheetFilter, protocols::protein_interface_design::filters::SpecificResiduesNearInterfaceFilter, protocols::enzdes::LigDSasaFilter, 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::ConservedPosMutationFilter, protocols::simple_filters::ConstraintScoreCutoffFilter, 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::DdgFilter, protocols::simple_filters::RGFilter, protocols::filters::CalculatorFilter, protocols::simple_filters::AbinitioBaseFilter, protocols::simple_filters::AtomicContactFilter, 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::TerminusDistanceFilter, protocols::filters::TrueFilter, protocols::protein_interface_design::filters::AverageDegreeFilter, protocols::filters::TimeFilter, protocols::protein_interface_design::filters::Torsion, protocols::simple_filters::NeighborTypeFilter, protocols::simple_filters::NMerPSSMEnergyFilter, 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::simple_filters::EnergyPerResidueFilter, protocols::filters::ReplicateFilter, protocols::protein_interface_design::filters::RmsdFilter, protocols::simple_filters::DeltaFilter, protocols::protein_interface_design::filters::InterfaceHolesFilter, protocols::simple_filters::BuriedUnsatHbondFilter, protocols::simple_filters::PoseInfoFilter, protocols::simple_filters::ResidueDistanceFilter, 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::Operator, and protocols::simple_filters::ResidueBurialFilter.

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

References type_.

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::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::ShapeComplementarityFilter, 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.

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

Reimplemented in protocols::enzdes::EnzdesScorefileFilter, protocols::enzdes::RepackWithoutLigandFilter, protocols::enzdes::DiffAtomSasaFilter, protocols::filters::IfThenFilter, protocols::enzdes::EnzScoreFilter, protocols::filters::MoveBeforeFilter, protocols::filters::CombinedFilter, protocols::fldsgn::filters::HSSTripletFilter, protocols::enzdes::LigInterfaceEnergyFilter, 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::simple_filters::ShapeComplementarityFilter, 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::fldsgn::filters::HelixKinkFilter, protocols::enzdes::LigBurialFilter, protocols::protein_interface_design::filters::DisulfideFilter, protocols::simple_filters::ResidueCountFilter, protocols::protein_interface_design::filters::FilterScanFilter, protocols::filters::StochasticFilter, protocols::protein_interface_design::filters::SequenceRecoveryFilter, protocols::simple_filters::DdgFilter, protocols::simple_filters::AlaScan, protocols::enzdes::LigDSasaFilter, 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::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::StubScoreFilter, protocols::protein_interface_design::filters::StubScoreFilter, protocols::simple_filters::AtomicContactFilter, protocols::simple_filters::NMerPSSMEnergyFilter, protocols::filters::CalculatorFilter, 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::EnergyPerResidueFilter, protocols::simple_filters::InterfaceSasaFilter, protocols::filters::TimeFilter, protocols::protein_interface_design::filters::BindingStrainFilter, protocols::simple_filters::NeighborTypeFilter, protocols::protein_interface_design::filters::RmsdFilter, 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::DeltaFilter, protocols::simple_filters::Sigmoid, protocols::simple_filters::BuriedUnsatHbondFilter, protocols::simple_filters::Operator, protocols::simple_filters::ResidueBurialFilter, and protocols::simple_filters::SidechainRmsdFilter.

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

Reimplemented in protocols::enzdes::RepackWithoutLigandFilter, protocols::enzdes::DiffAtomSasaFilter, protocols::filters::IfThenFilter, protocols::enzdes::EnzScoreFilter, protocols::filters::MoveBeforeFilter, protocols::filters::CombinedFilter, protocols::fldsgn::filters::InterlockingAromaFilter, protocols::enzdes::LigInterfaceEnergyFilter, 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::filters::CompoundFilter, protocols::enzdes::LigBurialFilter, protocols::simple_filters::SymmetricMotifFilter, protocols::protein_interface_design::filters::DisulfideFilter, protocols::protein_interface_design::filters::HbondsToResidueFilter, protocols::filters::StochasticFilter, protocols::simple_filters::DdgFilter, protocols::simple_filters::ConstraintScoreCutoffFilter, protocols::simple_filters::ScoreCutoffFilter, protocols::protein_interface_design::filters::SpecificResiduesNearInterfaceFilter, protocols::simple_filters::ResidueCountFilter, protocols::enzdes::LigDSasaFilter, protocols::simple_filters::InterfaceBindingEnergyDensityFilter, protocols::simple_filters::ResidueSetChainEnergyFilter, protocols::docking::DockingLowResFilter, protocols::protein_interface_design::filters::InterfaceHolesFilter, protocols::simple_filters::NMerPSSMEnergyFilter, protocols::simple_filters::ScoreTypeFilter, protocols::protein_interface_design::filters::FilterScanFilter, 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::simple_filters::EnergyPerResidueFilter, 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::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::Sigmoid, protocols::filters::CalculatorFilter, protocols::protein_interface_design::filters::Torsion, protocols::simple_filters::NonSequentialNeighborsFilter, protocols::simple_filters::Operator, protocols::simple_filters::RelativePoseFilter, protocols::protein_interface_design::filters::BoltzmannFilter, protocols::simple_filters::TerminusDistanceFilter, protocols::filters::TimeFilter, protocols::simple_filters::DeltaFilter, protocols::simple_filters::NeighborTypeFilter, protocols::simple_filters::BuriedUnsatHbondFilter, protocols::simple_filters::InterfaceSasaFilter, protocols::simple_filters::PoseInfoFilter, protocols::filters::ReplicateFilter, protocols::simple_filters::ResidueDistanceFilter, protocols::simple_filters::SidechainRmsdFilter, and protocols::simple_filters::ResidueBurialFilter.

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::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::simple_filters::ShapeComplementarityFilter, protocols::fldsgn::filters::CoreDunbrackFilter, protocols::fldsgn::filters::FragQualFilter, protocols::simple_filters::HolesFilter, protocols::simple_filters::PackStatFilter, protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter, protocols::fldsgn::filters::NcontactsFilter, protocols::filters::CompoundFilter, protocols::simple_filters::SymmetricMotifFilter, protocols::enzdes::LigBurialFilter, protocols::protein_interface_design::filters::DisulfideFilter, protocols::protein_interface_design::filters::HbondsToResidueFilter, protocols::simple_filters::DdgFilter, protocols::protein_interface_design::filters::AtomicContactCountFilter, protocols::simple_filters::ResidueCountFilter, protocols::protein_interface_design::filters::SpecificResiduesNearInterfaceFilter, protocols::enzdes::LigDSasaFilter, protocols::simple_filters::InterfaceBindingEnergyDensityFilter, protocols::simple_filters::ResidueSetChainEnergyFilter, protocols::protein_interface_design::filters::InterfaceHolesFilter, protocols::simple_filters::AlaScan, protocols::simple_filters::NMerPSSMEnergyFilter, protocols::simple_filters::ScoreTypeFilter, protocols::protein_interface_design::filters::FilterScanFilter, 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::simple_filters::EnergyPerResidueFilter, 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::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::Sigmoid, protocols::filters::CalculatorFilter, protocols::protein_interface_design::filters::Torsion, protocols::simple_filters::NonSequentialNeighborsFilter, protocols::simple_filters::Operator, protocols::simple_filters::RelativePoseFilter, protocols::protein_interface_design::filters::BoltzmannFilter, protocols::simple_filters::TerminusDistanceFilter, protocols::filters::TimeFilter, protocols::simple_filters::DeltaFilter, protocols::simple_filters::NeighborTypeFilter, protocols::simple_filters::BuriedUnsatHbondFilter, protocols::simple_filters::InterfaceSasaFilter, protocols::simple_filters::PoseInfoFilter, protocols::filters::ReplicateFilter, protocols::simple_filters::ResidueDistanceFilter, protocols::simple_filters::SidechainRmsdFilter, and protocols::simple_filters::ResidueBurialFilter.

Referenced by score().

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

References clear().

Referenced by protocols::simple_filters::NMerPSSMEnergyFilter::apply(), protocols::simple_filters::ScoreTypeFilter::apply(), protocols::simple_filters::ResidueSetChainEnergyFilter::apply(), protocols::simple_filters::PackStatFilter::apply(), protocols::fldsgn::filters::NcontactsFilter::apply(), protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter::apply(), protocols::simple_filters::EnergyPerResidueFilter::compute(), protocols::simple_filters::ScoreTypeFilter::compute(), protocols::simple_filters::NMerPSSMEnergyFilter::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::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().

The documentation for this class was generated from the following files:
Generated on Sat Jun 1 2013 12:35:27 for Rosetta 3.5 by   doxygen 1.8.4