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protocols::simple_filters Namespace Reference

Classes

class  AbinitioBaseFilter
 
class  AlaScan
 
class  AlaScanFilterCreator
 
class  AtomicContactFilter
 detects atomic (<4Ang) contacts between any two atoms of two residues More...
 
class  AtomicContactFilterCreator
 
class  AtomicDistanceFilter
 detects atomic contacts between two atoms of two residues More...
 
class  AtomicDistanceFilterCreator
 
class  BatchEvaluator
 
class  BatchNrEvaluator
 
class  BuriedUnsatHbondFilter
 filters based on an upper bound # of buried unsatisfied polar residues More...
 
class  BuriedUnsatHbondFilterCreator
 
class  CamShiftEvaluator
 
class  CamShiftEvaluatorCreator
 creator for the CamShiftEvaluatorCreator class More...
 
class  ChiWellRmsdEvaluator
 
class  ChiWellRmsdEvaluatorCreator
 creator for the ChiWellRmsdEvaluatorCreator class More...
 
class  PoseMetricEvaluator
 
class  COFilter
 
class  ConservedPosMutationFilter
 
class  ConservedPosMutationFilterCreator
 
class  ConstraintScoreCutoffFilter
 
class  ConstraintScoreCutoffFilterCreator
 
class  ContactMapEvaluator
 
class  ContactMapEvaluatorCreator
 creator for the ContactMapEvaluatorCreator class More...
 
class  DdgFilter
 
class  DdgFilterCreator
 
class  DeltaFilter
 
class  DeltaFilterCreator
 
class  EnergyPerResidueFilter
 
class  EnergyPerResidueFilterCreator
 
class  EvaluatedTrialMover
 
class  ExpiryFilter
 
class  ExpiryFilterCreator
 
class  ExternalEvaluator
 
class  ExtraScoreEvaluatorCreator
 creator for the ExtraScoreEvaluatorCreator class More...
 
class  FileExistFilter
 
class  FileExistFilterCreator
 
class  FileRemoveFilter
 
class  FileRemoveFilterCreator
 
class  HolesFilter
 
class  HolesFilterCreator
 
class  InterfaceBindingEnergyDensityFilter
 
class  InterfaceBindingEnergyDensityFilterCreator
 
class  InterfaceSasaFilter
 
class  InterfaceSasaFilterCreator
 
class  JScoreEvaluator
 
class  JScoreEvaluatorCreator
 creator for the JScoreEvaluatorCreator class More...
 
class  JumpEvaluator
 
class  JumpNrEvaluator
 
class  JumpNrEvaluatorCreator
 creator for the JumpNrEvaluatorCreator class More...
 
class  MinValueEvaluator
 
class  NativeEvaluatorCreator
 creator for the NativeEvaluatorCreator class More...
 
class  NeighborTypeFilter
 
class  NeighborTypeFilterCreator
 
class  NMerPSSMEnergyFilter
 
class  NMerPSSMEnergyFilterCreator
 
class  NonSequentialNeighborsFilter
 
class  NonSequentialNeighborsFilterCreator
 
class  Operator
 simply take a list of filters and combine them using the operation above More...
 
class  OperatorFilterCreator
 
class  RegionalConnections
 
class  PackerNeighborGraphFilter
 
class  PackStatFilter
 
class  PackStatFilterCreator
 
class  PalesEvaluator
 
class  PalesEvaluatorCreator
 creator for the PalesEvaluatorCreator class More...
 
class  PDDFScoreFilter
 
class  PoolEvaluatorCreator
 creator for the PoolEvaluatorCreator class More...
 
class  PoseInfoFilter
 detects atomic contacts between two atoms of two residues More...
 
class  PoseInfoFilterCreator
 
class  PredictedBurialEvaluator
 
class  PredictedBurialFnEvaluatorCreator
 creator for the PredictedBurialFnEvaluatorCreator class More...
 
class  RangeFilter
 
class  RangeFilterCreator
 
class  RDC_Evaluator
 
class  SelectRDC_Evaluator
 
class  RdcEvaluatorCreator
 creator for the RdcEvaluatorCreator class More...
 
class  RdcSelectEvaluatorCreator
 creator for the RdcSelectEvaluatorCreator class More...
 
class  RdcTargetEvaluatorCreator
 creator for the RdcTargetEvaluatorCreator class More...
 
class  RelativePoseFilter
 
class  RelativePoseFilterCreator
 
class  ReportFilter
 
class  ReportFilterCreator
 
class  ResidueBurialFilter
 
class  ResidueBurialFilterCreator
 
class  ResidueCountFilter
 
class  ResidueCountFilterCreator
 
class  ResidueDistanceFilter
 
class  ResidueDistanceFilterCreator
 
class  ResidueIEFilter
 
class  ResidueIEFilterCreator
 
class  ResidueSetChainEnergyFilter
 
class  ResidueSetChainEnergyFilterCreator
 
class  ResiduesInInterfaceFilter
 
class  ResiduesInInterfaceFilterCreator
 
class  RGFilter
 
class  RmsdEvaluator
 
class  SelectRmsdEvaluator
 
class  SelectGdtEvaluator
 
class  SelectMaxsubEvaluator
 
class  SymmetricRmsdEvaluator
 
class  LoopRmsdEvaluator
 
class  RmsdEvaluatorCreator
 creator for the RmsdEvaluatorCreator class More...
 
class  RmsdTargetEvaluatorCreator
 creator for the RmsdTargetEvaluatorCreator class More...
 
class  RotamerBoltzmannWeight
 
class  RotamerBoltzmannWeightFilterCreator
 
class  RPF_ScoreEvaluator
 
class  SAXSScoreFilter
 
class  ScoreCutoffFilter
 
class  ScoreCutoffFilterCreator
 
class  ScoreEvaluator
 that rewrites the whole pss struct all previous entries will be lost... probably not what one wants... More...
 
class  TruncatedScoreEvaluator
 
class  ScoreTypeFilter
 
class  ScoreTypeFilterCreator
 
class  ShapeComplementarityFilter
 
class  ShapeComplementarityFilterCreator
 
class  SheetFilter
 
class  SidechainRmsdFilter
 
class  SidechainRmsdFilterCreator
 
class  Sigmoid
 transform the output from a regular filter into a sigmoid ranging from 0-1 according to: fx = 1/[1 + exp[ ( x - offset ) * steepness ] The function asymptotically reaches 1 at negative values and 0 at positive values. It's 0.5 at the offset and steepness determines its slope at the offset More...
 
class  SigmoidFilterCreator
 
class  StructuralSimilarityEvaluator
 
class  StructureSimilarityEvaluatorCreator
 creator for the StructureSimilarityEvaluatorCreator class More...
 
struct  Quat
 
class  SymmetricMotifFilter
 
class  SymmetricMotifFilterCreator
 
class  TerminusDistanceFilter
 
class  TerminusDistanceFilterCreator
 

Typedefs

typedef
utility::pointer::owning_ptr
< ConservedPosMutationFilter
ConservedPosMutationFilterOP
 
typedef
utility::pointer::owning_ptr
< ConservedPosMutationFilter
const > 
ConservedPosMutationFilterCOP
 
typedef
utility::pointer::owning_ptr
< ConstraintScoreCutoffFilter
ConstraintScoreCutoffFilterOP
 
typedef
utility::pointer::owning_ptr
< ConstraintScoreCutoffFilter
const > 
ConstraintScoreCutoffFilterCOP
 
typedef
utility::pointer::owning_ptr
< DdgFilter
DdgFilterOP
 
typedef
utility::pointer::owning_ptr
< DdgFilter const > 
DdgFilterCOP
 
typedef
utility::pointer::owning_ptr
< DeltaFilter
DeltaFilterOP
 
typedef
utility::pointer::owning_ptr
< DeltaFilter const > 
DeltaFilterCOP
 
typedef
utility::pointer::owning_ptr
< EvaluatedTrialMover
EvaluatedTrialMoverOP
 
typedef
utility::pointer::owning_ptr
< HolesFilter
HolesFilterOP
 
typedef
utility::pointer::owning_ptr
< HolesFilter const > 
HolesFilterCOP
 
typedef
utility::pointer::owning_ptr
< InterfaceBindingEnergyDensityFilter
InterfaceBindingEnergyDensityFilterOP
 
typedef
utility::pointer::owning_ptr
< InterfaceBindingEnergyDensityFilter
const > 
InterfaceBindingEnergyDensityFilterCOP
 
typedef
utility::pointer::owning_ptr
< InterfaceSasaFilter
InterfaceSasaFilterOP
 
typedef
utility::pointer::owning_ptr
< InterfaceSasaFilter const > 
InterfaceSasaFilterCOP
 
typedef
utility::pointer::owning_ptr
< Operator
OperatorOP
 
typedef
utility::pointer::owning_ptr
< Operator const > 
OperatorCOP
 
typedef
utility::pointer::owning_ptr
< PackerNeighborGraphFilter
PackerNeighborGraphFilterOP
 
typedef
utility::pointer::owning_ptr
< PackerNeighborGraphFilter
const > 
PackerNeighborGraphFilterCOP
 
typedef
utility::pointer::owning_ptr
< PackStatFilter
PackStatFilterOP
 
typedef
utility::pointer::owning_ptr
< PackStatFilter const > 
PackStatFilterCOP
 
typedef
utility::pointer::owning_ptr
< PDDFScoreFilter
PDDFScoreFilterOP
 
typedef
utility::pointer::owning_ptr
< PDDFScoreFilter const > 
PDDFScoreFilterCOP
 
typedef
utility::pointer::owning_ptr
< RangeFilter
RangeFilterOP
 
typedef
utility::pointer::owning_ptr
< RangeFilter const > 
RangeFilterCOP
 
typedef
utility::pointer::owning_ptr
< SelectRDC_Evaluator
SelectRDC_EvaluatorOP
 
typedef
utility::pointer::owning_ptr
< SelectRDC_Evaluator const > 
SelectRDC_EvaluatorCOP
 
typedef
utility::pointer::owning_ptr
< RelativePoseFilter
RelativePoseFilterOP
 
typedef
utility::pointer::owning_ptr
< RelativePoseFilter const > 
RelativePoseFilterCOP
 
typedef
utility::pointer::owning_ptr
< ResidueIEFilter
ResidueIEFilterOP
 
typedef
utility::pointer::owning_ptr
< ResidueIEFilter const > 
ResidueIEFilterCOP
 
typedef
utility::pointer::owning_ptr
< RotamerBoltzmannWeight
RotamerBoltzmannWeightFilterOP
 
typedef
utility::pointer::owning_ptr
< RotamerBoltzmannWeight const > 
RotamerBoltzmannWeightFilterCOP
 
typedef
utility::pointer::owning_ptr
< SAXSScoreFilter
SAXSScoreFilterOP
 
typedef
utility::pointer::owning_ptr
< SAXSScoreFilter const > 
SAXSScoreFilterCOP
 
typedef
utility::pointer::owning_ptr
< ScoreCutoffFilter
ScoreCutoffFilterOP
 
typedef
utility::pointer::owning_ptr
< ScoreCutoffFilter const > 
ScoreCutoffFilterCOP
 
typedef
utility::pointer::owning_ptr
< ShapeComplementarityFilter
ShapeComplementarityFilterOP
 
typedef
utility::pointer::owning_ptr
< ShapeComplementarityFilter
const > 
ShapeComplementarityFilterCOP
 
typedef
utility::pointer::owning_ptr
< Sigmoid
SigmoidOP
 
typedef
utility::pointer::owning_ptr
< Sigmoid const > 
SigmoidCOP
 
typedef
utility::pointer::owning_ptr
< StructuralSimilarityEvaluator
StructuralSimilarityEvaluatorOP
 
typedef
utility::pointer::owning_ptr
< StructuralSimilarityEvaluator
const > 
StructuralSimilarityEvaluatorCOP
 

Enumerations

enum  Operation {
  SUM, PRODUCT, NORMALIZED_SUM, MAX,
  MIN, SUBTRACT, ABS, BOOLEAN_OR
}
 

Functions

static basic::Tracer TR ("protocols.simple_filters.AlaScan")
 
static basic::Tracer TR ("protocols.filters.AtomicContactFilter")
 
static basic::Tracer TR ("protocols.filters.AtomicDistanceFilter")
 
static basic::Tracer buried_unsat_hbond_filter_tracer ("protocols.simple_filters.BuriedUnsatHbondFilter")
 
boost::dynamic_bitset get_contact_features (core::pose::Pose const &pose, core::Real const dist_threshold, std::string const &atom_name, core::Size const min_seqsep=12, core::Size const skip_res=0)
 
core::Real pct_features_in_common (boost::dynamic_bitset<> const &set1, boost::dynamic_bitset<> const &set2)
 
static basic::Tracer TR ("protocols.simple_filters.DdgFilter")
 
static basic::Tracer TR ("protocols.simple_filters.DeltaFilter")
 
static basic::Tracer energy_per_residue_filter_tracer ("protocols.simple_filters.EnergyPerResidueFilter")
 
static basic::Tracer TR ("protocols.simple_filters.ExpiryFilter")
 
static basic::Tracer TR ("protocols.simple_filters.FileExistFilter")
 
static basic::Tracer TR ("protocols.simple_filters.FileRemoveFilter")
 
static basic::Tracer TR ("protocols.simple_filters.InterfaceBindingEnergyDensityFilter")
 
static basic::Tracer TR ("protocols.simple_filters.InterfaceSasaFilter")
 
static basic::Tracer neighbor_type_filter_tracer ("protocols.simple_filters.NeighborTypeFilter")
 
static basic::Tracer TR ("protocols.simple_filters.NMerPSSMEnergyFilter")
 
static basic::Tracer TR ("protocols.simple_filters.NonSequentialNeighborsFilter")
 
static basic::Tracer TR ("protocols.simple_filters.Operator")
 
static basic::Tracer TR ("protocols.filters.PoseInfoFilter")
 
static basic::Tracer TR ("protocols.simple_filters.RelativePoseFilter")
 
static basic::Tracer TR ("protocols.simple_filters.ReportFilter")
 
static basic::Tracer residue_burial_filter_tracer ("protocols.simple_filters.ResidueBurialFilter")
 
static basic::Tracer TR ("protocols.simple_filters.ResidueCountFilter")
 
static basic::Tracer residue_distance_filter_tracer ("protocols.simple_filters.ResidueDistanceFilter")
 
static basic::Tracer tr ("protocols.simple_filters.ResidueIEFilter")
 
static basic::Tracer TR ("protocols.simple_filters.ResidueSetChainEnergyFilter")
 
static basic::Tracer residues_in_interface_tracer ("protocols.simple_filters.ResiduesInInterfaceFilter")
 
static basic::Tracer TR ("protocols.simple_filters.RotamerBoltzmannWeight")
 
static basic::Tracer score_type_filter_tracer ("protocols.simple_filters.ScoreTypeFilter")
 
static basic::Tracer sidechain_rmsd_filter_tracer ("protocols.simple_filters.SidechainRmsdFilter")
 
static basic::Tracer TR ("protocols.simple_filters.Sigmoid")
 
static basic::Tracer TR ("protocols.simple_filters.SymmetricMotifFilter")
 
void R2quat (numeric::xyzMatrix< core::Real > R, Quat &Q)
 
void quat2R (Quat &Q, numeric::xyzMatrix< core::Real > R)
 
core::Real RMSwrapper (utility::vector1< numeric::xyzVector< core::Real > > chainA, utility::vector1< numeric::xyzVector< core::Real > > chainB, numeric::xyzMatrix< core::Real > &R, numeric::xyzVector< core::Real > &preT, numeric::xyzVector< core::Real > &postT)
 
static basic::Tracer TR ("protocols.simple_filters.TerminusDistanceFilter")
 

Variables

static
core::scoring::methods::ResidualDipolarCouplingEnergy 
energy_evaluator
 

Typedef Documentation

Enumeration Type Documentation

Enumerator
SUM 
PRODUCT 
NORMALIZED_SUM 
MAX 
MIN 
SUBTRACT 
ABS 
BOOLEAN_OR 

Function Documentation

static basic::Tracer protocols::simple_filters::buried_unsat_hbond_filter_tracer ( "protocols.simple_filters.BuriedUnsatHbondFilter"  )
static
static basic::Tracer protocols::simple_filters::energy_per_residue_filter_tracer ( "protocols.simple_filters.EnergyPerResidueFilter"  )
static
boost::dynamic_bitset protocols::simple_filters::get_contact_features ( core::pose::Pose const &  pose,
core::Real const  dist_threshold,
std::string const &  atom_name,
core::Size const  min_seqsep = 12,
core::Size const  skip_res = 0 
)
static basic::Tracer protocols::simple_filters::neighbor_type_filter_tracer ( "protocols.simple_filters.NeighborTypeFilter"  )
static
core::Real protocols::simple_filters::pct_features_in_common ( boost::dynamic_bitset<> const &  set1,
boost::dynamic_bitset<> const &  set2 
)
void protocols::simple_filters::quat2R ( Quat &  Q,
numeric::xyzMatrix< core::Real R 
)
void protocols::simple_filters::R2quat ( numeric::xyzMatrix< core::Real R,
Quat &  Q 
)
static basic::Tracer protocols::simple_filters::residue_burial_filter_tracer ( "protocols.simple_filters.ResidueBurialFilter"  )
static
static basic::Tracer protocols::simple_filters::residue_distance_filter_tracer ( "protocols.simple_filters.ResidueDistanceFilter"  )
static
static basic::Tracer protocols::simple_filters::residues_in_interface_tracer ( "protocols.simple_filters.ResiduesInInterfaceFilter"  )
static
core::Real protocols::simple_filters::RMSwrapper ( utility::vector1< numeric::xyzVector< core::Real > >  chainA,
utility::vector1< numeric::xyzVector< core::Real > >  chainB,
numeric::xyzMatrix< core::Real > &  R,
numeric::xyzVector< core::Real > &  preT,
numeric::xyzVector< core::Real > &  postT 
)
static basic::Tracer protocols::simple_filters::score_type_filter_tracer ( "protocols.simple_filters.ScoreTypeFilter"  )
static
static basic::Tracer protocols::simple_filters::sidechain_rmsd_filter_tracer ( "protocols.simple_filters.SidechainRmsdFilter"  )
static
static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.NonSequentialNeighborsFilter"  )
static
static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.ExpiryFilter"  )
static
static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.FileExistFilter"  )
static
static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.DeltaFilter"  )
static
static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.Sigmoid"  )
static
static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.Operator"  )
static
static basic::Tracer protocols::simple_filters::TR ( "protocols.filters.PoseInfoFilter"  )
static
static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.ReportFilter"  )
static
static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.ResidueCountFilter"  )
static
static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.FileRemoveFilter"  )
static
static basic::Tracer protocols::simple_filters::tr ( "protocols.simple_filters.ResidueIEFilter"  )
static

Referenced by protocols::simple_filters::ChiWellRmsdEvaluatorCreator::add_evaluators(), protocols::simple_filters::ContactMapEvaluatorCreator::add_evaluators(), protocols::simple_filters::RmsdEvaluatorCreator::add_evaluators(), protocols::simple_filters::ScoreCutoffFilter::add_score_type(), protocols::simple_filters::SAXSScoreFilter::apply(), protocols::simple_filters::ExternalEvaluator::apply(), protocols::simple_filters::ChiWellRmsdEvaluator::apply(), protocols::simple_filters::RmsdEvaluator::apply(), protocols::simple_filters::ConservedPosMutationFilter::apply(), protocols::simple_filters::TruncatedScoreEvaluator::apply(), protocols::simple_filters::RangeFilter::apply(), protocols::simple_filters::PackStatFilter::apply(), protocols::simple_filters::HolesFilter::apply(), protocols::simple_filters::ShapeComplementarityFilter::apply(), protocols::simple_filters::PackStatFilter::compute(), protocols::simple_filters::ShapeComplementarityFilter::compute(), protocols::simple_filters::ExternalEvaluator::ExternalEvaluator(), protocols::simple_filters::ShapeComplementarityFilter::parse_def(), protocols::simple_filters::PackStatFilter::parse_my_tag(), protocols::simple_filters::HolesFilter::parse_my_tag(), protocols::simple_filters::ShapeComplementarityFilter::parse_my_tag(), protocols::simple_filters::ScoreEvaluator::ScoreEvaluator(), protocols::simple_filters::TruncatedScoreEvaluator::TruncatedScoreEvaluator(), and protocols::simple_filters::ExternalEvaluator::~ExternalEvaluator().

static basic::Tracer protocols::simple_filters::TR ( "protocols.filters.AtomicDistanceFilter"  )
static
static basic::Tracer protocols::simple_filters::TR ( "protocols.filters.AtomicContactFilter"  )
static
static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.DdgFilter"  )
static
static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.InterfaceSasaFilter"  )
static
static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.InterfaceBindingEnergyDensityFilter"  )
static
static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.ResidueSetChainEnergyFilter"  )
static
static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.NMerPSSMEnergyFilter"  )
static
static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.RelativePoseFilter"  )
static
static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.SymmetricMotifFilter"  )
static
static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.AlaScan"  )
static

Referenced by protocols::simple_filters::TerminusDistanceFilter::apply(), protocols::simple_filters::NMerPSSMEnergyFilter::apply(), protocols::simple_filters::AtomicDistanceFilter::apply(), protocols::simple_filters::AtomicContactFilter::apply(), protocols::simple_filters::ResidueSetChainEnergyFilter::apply(), protocols::simple_filters::DdgFilter::apply(), protocols::simple_filters::SymmetricMotifFilter::apply(), protocols::simple_filters::InterfaceBindingEnergyDensityFilter::apply(), protocols::simple_filters::DeltaFilter::baseline(), protocols::simple_filters::PoseInfoFilter::compute(), protocols::simple_filters::AtomicDistanceFilter::compute(), protocols::simple_filters::AtomicContactFilter::compute(), protocols::simple_filters::DeltaFilter::compute(), protocols::simple_filters::NonSequentialNeighborsFilter::compute(), protocols::simple_filters::Sigmoid::compute(), protocols::simple_filters::DdgFilter::compute(), protocols::simple_filters::SymmetricMotifFilter::compute_d2(), protocols::simple_filters::AlaScan::ddG_for_single_residue(), protocols::simple_filters::DdgFilter::DdgFilter(), protocols::simple_filters::DdgFilter::parse_def(), protocols::simple_filters::DeltaFilter::parse_my_tag(), protocols::simple_filters::Sigmoid::parse_my_tag(), protocols::simple_filters::NonSequentialNeighborsFilter::parse_my_tag(), protocols::simple_filters::AtomicDistanceFilter::parse_my_tag(), protocols::simple_filters::AtomicContactFilter::parse_my_tag(), protocols::simple_filters::ResidueSetChainEnergyFilter::parse_my_tag(), protocols::simple_filters::ResidueCountFilter::parse_my_tag(), protocols::simple_filters::SymmetricMotifFilter::parse_my_tag(), protocols::simple_filters::SymmetricMotifFilter::process_motifs(), protocols::simple_filters::SymmetricMotifFilter::report(), and protocols::simple_filters::Sigmoid::reset_baseline().

static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.TerminusDistanceFilter"  )
static
static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.RotamerBoltzmannWeight"  )
static

Variable Documentation

core::scoring::methods::ResidualDipolarCouplingEnergy protocols::simple_filters::energy_evaluator
static