Rosetta Protocols  2014.16.56682
Classes | Typedefs | Enumerations | Functions | Variables
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  AveragePathLengthFilter
 
class  AveragePathLengthFilterCreator
 
class  BatchEvaluator
 
class  BatchNrEvaluator
 
class  BuriedRegionsFilter
 
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  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  DisulfideEntropyFilter
 
class  DisulfideEntropyFilterCreator
 
class  DomainInterfaceFilter
 
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  GeometryFilter
 
class  GeometryFilterCreator
 
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  LoopRmsdEvaluator
 
class  MinValueEvaluator
 
class  MultipleSigmoids
 simply takes a list of pdbs and creates relative pose then extract sigmoids and call operator (product) More...
 
class  MultipleSigmoidsFilterCreator
 
class  NativeEvaluatorCreator
 creator for the NativeEvaluatorCreator class More...
 
class  NeighborTypeFilter
 
class  NeighborTypeFilterCreator
 
class  NetChargeFilter
 
class  NetChargeFilterCreator
 
struct  nmer_svm_res_data
 
class  NMerPSSMEnergyFilter
 
class  NMerPSSMEnergyFilterCreator
 
class  NMerSVMEnergyFilter
 
class  NMerSVMEnergyFilterCreator
 
class  NonSequentialNeighborsFilter
 
class  NonSequentialNeighborsFilterCreator
 
class  Operator
 simply take a list of filters and combine them using the operation above More...
 
class  OperatorFilterCreator
 
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  PoseComment
 test whether a pose contains a comment that evaluates to a predefined value. This is useful in controlling execution flow in RosettaScripts. More...
 
class  PoseCommentFilterCreator
 
class  PoseInfoFilter
 detects atomic contacts between two atoms of two residues More...
 
class  PoseInfoFilterCreator
 
class  PoseMetricEvaluator
 
class  PredictedBurialEvaluator
 
class  PredictedBurialFnEvaluatorCreator
 creator for the PredictedBurialFnEvaluatorCreator class More...
 
struct  Quat
 
class  RangeFilter
 
class  RangeFilterCreator
 
class  RDC_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  RegionalConnections
 
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  RmsdEvaluatorCreator
 creator for the RmsdEvaluatorCreator class More...
 
class  RmsdTargetEvaluatorCreator
 creator for the RmsdTargetEvaluatorCreator class More...
 
class  RotamerBoltzmannWeight
 
class  RotamerBoltzmannWeightFilterCreator
 
class  RPF_ScoreEvaluator
 
class  SavePoseConstraintToFileFilter
 detects atomic contacts between two atoms of two residues More...
 
class  SavePoseConstraintToFileFilterCreator
 
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  ScoreTypeFilter
 
class  ScoreTypeFilterCreator
 
class  SelectGdtEvaluator
 
class  SelectMaxsubEvaluator
 
class  SelectRDC_Evaluator
 
class  SelectRmsdEvaluator
 
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...
 
class  SymmetricMotifFilter
 
class  SymmetricMotifFilterCreator
 
class  SymmetricRmsdEvaluator
 
class  TerminusDistanceFilter
 
class  TerminusDistanceFilterCreator
 
class  TotalSasaFilter
 
class  TotalSasaFilterCreator
 
class  TruncatedScoreEvaluator
 

Typedefs

typedef
utility::pointer::owning_ptr
< AveragePathLengthFilter > 		AveragePathLengthFilterOP
 
typedef
utility::pointer::owning_ptr
< AveragePathLengthFilter
const > 		AveragePathLengthFilterCOP
 
typedef
utility::pointer::owning_ptr
< BuriedRegionsFilter > 		BuriedRegionsFilterOP
 
typedef
utility::pointer::owning_ptr
< BuriedRegionsFilter const > 		BuriedRegionsFilterCOP
 
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
< DisulfideEntropyFilter > 		DisulfideEntropyFilterOP
 
typedef
utility::pointer::owning_ptr
< DisulfideEntropyFilter const > 		DisulfideEntropyFilterCOP
 
typedef
utility::pointer::owning_ptr
< DomainInterfaceFilter > 		DomainInterfaceFilterOP
 
typedef
utility::pointer::owning_ptr
< DomainInterfaceFilter const > 		DomainInterfaceFilterCOP
 
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
< MultipleSigmoids > 		MultipleSigmoidsOP
 
typedef
utility::pointer::owning_ptr
< MultipleSigmoids const > 		MultipleSigmoidsCOP
 
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
< PoseComment > 		PoseCommentOP
 
typedef
utility::pointer::owning_ptr
< PoseComment const > 		PoseCommentCOP
 
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
 
typedef
utility::pointer::owning_ptr
< TotalSasaFilter > 		TotalSasaFilterOP
 
typedef
utility::pointer::owning_ptr
< TotalSasaFilter const > 		TotalSasaFilterCOP
 

Enumerations

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

Functions

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)
 
int determinant_sign (const bnu::permutation_matrix< std::size_t > &pm)
 
core::Real determinant (bnu::matrix< core::Real > const &m)
 
void print_nmer_svm_energy_data (vector1< nmer_svm_res_data > nmer_svm_pose_data)
 
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)
 

Variables

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 TR ("protocols.simple_filters.AveragePathLengthFilter")
 
static basic::Tracer buried_unsat_hbond_filter_tracer ("protocols.simple_filters.BuriedUnsatHbondFilter")
 
static basic::Tracer TR ("protocols.simple_filters.DdgFilter")
 
static basic::Tracer TR ("protocols.simple_filters.DeltaFilter")
 
static basic::Tracer TR ("protocols.simple_filters.DisulfideEntropyFilter")
 
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.GeometryFilter")
 
static basic::Tracer TR ("protocols.simple_filters.InterfaceBindingEnergyDensityFilter")
 
static basic::Tracer TR ("protocols.simple_filters.InterfaceSasaFilter")
 
static basic::Tracer TR ("protocols.simple_filters.MultipleSigmoids")
 
static basic::Tracer neighbor_type_filter_tracer ("protocols.simple_filters.NeighborTypeFilter")
 
static basic::Tracer TR ("protocols.simple_filters.NetChargeFilter")
 
static basic::Tracer TR ("protocols.simple_filters.NMerPSSMEnergyFilter")
 
static basic::Tracer TR ("protocols.simple_filters.NMerSVMEnergyFilter")
 
static basic::Tracer TR ("protocols.simple_filters.NonSequentialNeighborsFilter")
 
static basic::Tracer TR ("protocols.simple_filters.Operator")
 
static basic::Tracer TR ("protocols.simple_filters.PoseComment")
 
static basic::Tracer TR ("protocols.filters.PoseInfoFilter")
 
static
core::scoring::methods::ResidualDipolarCouplingEnergy 		energy_evaluator
 
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 TR ("protocols.filters.SavePoseConstraintToFileFilter")
 
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")
 
static basic::Tracer TR ("protocols.simple_filters.TerminusDistanceFilter")
 
static basic::Tracer TR ("protocols.simple_filters.TotalSasaFilter")
 

Typedef Documentation

typedef utility::pointer::owning_ptr< AveragePathLengthFilter const > protocols::simple_filters::AveragePathLengthFilterCOP
typedef utility::pointer::owning_ptr< AveragePathLengthFilter > protocols::simple_filters::AveragePathLengthFilterOP
typedef utility::pointer::owning_ptr< BuriedRegionsFilter const > protocols::simple_filters::BuriedRegionsFilterCOP
typedef utility::pointer::owning_ptr< BuriedRegionsFilter > protocols::simple_filters::BuriedRegionsFilterOP
typedef utility::pointer::owning_ptr< ConservedPosMutationFilter const > protocols::simple_filters::ConservedPosMutationFilterCOP
typedef utility::pointer::owning_ptr< ConservedPosMutationFilter > protocols::simple_filters::ConservedPosMutationFilterOP
typedef utility::pointer::owning_ptr< ConstraintScoreCutoffFilter const > protocols::simple_filters::ConstraintScoreCutoffFilterCOP
typedef utility::pointer::owning_ptr< ConstraintScoreCutoffFilter > protocols::simple_filters::ConstraintScoreCutoffFilterOP
typedef utility::pointer::owning_ptr< DdgFilter const > protocols::simple_filters::DdgFilterCOP
typedef utility::pointer::owning_ptr< DdgFilter > protocols::simple_filters::DdgFilterOP
typedef utility::pointer::owning_ptr< DeltaFilter const > protocols::simple_filters::DeltaFilterCOP
typedef utility::pointer::owning_ptr< DeltaFilter > protocols::simple_filters::DeltaFilterOP
typedef utility::pointer::owning_ptr< DisulfideEntropyFilter const > protocols::simple_filters::DisulfideEntropyFilterCOP
typedef utility::pointer::owning_ptr< DisulfideEntropyFilter > protocols::simple_filters::DisulfideEntropyFilterOP
typedef utility::pointer::owning_ptr< DomainInterfaceFilter const > protocols::simple_filters::DomainInterfaceFilterCOP
typedef utility::pointer::owning_ptr< DomainInterfaceFilter > protocols::simple_filters::DomainInterfaceFilterOP
typedef utility::pointer::owning_ptr< EvaluatedTrialMover > protocols::simple_filters::EvaluatedTrialMoverOP
typedef utility::pointer::owning_ptr< HolesFilter const > protocols::simple_filters::HolesFilterCOP
typedef utility::pointer::owning_ptr< HolesFilter > protocols::simple_filters::HolesFilterOP
typedef utility::pointer::owning_ptr< InterfaceBindingEnergyDensityFilter const > protocols::simple_filters::InterfaceBindingEnergyDensityFilterCOP
typedef utility::pointer::owning_ptr< InterfaceBindingEnergyDensityFilter > protocols::simple_filters::InterfaceBindingEnergyDensityFilterOP
typedef utility::pointer::owning_ptr< InterfaceSasaFilter const > protocols::simple_filters::InterfaceSasaFilterCOP
typedef utility::pointer::owning_ptr< InterfaceSasaFilter > protocols::simple_filters::InterfaceSasaFilterOP
typedef utility::pointer::owning_ptr< MultipleSigmoids const > protocols::simple_filters::MultipleSigmoidsCOP
typedef utility::pointer::owning_ptr< MultipleSigmoids > protocols::simple_filters::MultipleSigmoidsOP
typedef utility::pointer::owning_ptr< Operator const > protocols::simple_filters::OperatorCOP
typedef utility::pointer::owning_ptr< Operator > protocols::simple_filters::OperatorOP
typedef utility::pointer::owning_ptr< PackerNeighborGraphFilter const > protocols::simple_filters::PackerNeighborGraphFilterCOP
typedef utility::pointer::owning_ptr< PackerNeighborGraphFilter > protocols::simple_filters::PackerNeighborGraphFilterOP
typedef utility::pointer::owning_ptr< PackStatFilter const > protocols::simple_filters::PackStatFilterCOP
typedef utility::pointer::owning_ptr< PackStatFilter > protocols::simple_filters::PackStatFilterOP
typedef utility::pointer::owning_ptr< PDDFScoreFilter const > protocols::simple_filters::PDDFScoreFilterCOP
typedef utility::pointer::owning_ptr< PDDFScoreFilter > protocols::simple_filters::PDDFScoreFilterOP
typedef utility::pointer::owning_ptr< PoseComment const > protocols::simple_filters::PoseCommentCOP
typedef utility::pointer::owning_ptr< PoseComment > protocols::simple_filters::PoseCommentOP
typedef utility::pointer::owning_ptr< RangeFilter const > protocols::simple_filters::RangeFilterCOP
typedef utility::pointer::owning_ptr< RangeFilter > protocols::simple_filters::RangeFilterOP
typedef utility::pointer::owning_ptr< RelativePoseFilter const > protocols::simple_filters::RelativePoseFilterCOP
typedef utility::pointer::owning_ptr< RelativePoseFilter > protocols::simple_filters::RelativePoseFilterOP
typedef utility::pointer::owning_ptr< ResidueIEFilter const > protocols::simple_filters::ResidueIEFilterCOP
typedef utility::pointer::owning_ptr< ResidueIEFilter > protocols::simple_filters::ResidueIEFilterOP
typedef utility::pointer::owning_ptr< RotamerBoltzmannWeight const > protocols::simple_filters::RotamerBoltzmannWeightFilterCOP
typedef utility::pointer::owning_ptr< RotamerBoltzmannWeight > protocols::simple_filters::RotamerBoltzmannWeightFilterOP
typedef utility::pointer::owning_ptr< SAXSScoreFilter const > protocols::simple_filters::SAXSScoreFilterCOP
typedef utility::pointer::owning_ptr< SAXSScoreFilter > protocols::simple_filters::SAXSScoreFilterOP
typedef utility::pointer::owning_ptr< ScoreCutoffFilter const > protocols::simple_filters::ScoreCutoffFilterCOP
typedef utility::pointer::owning_ptr< ScoreCutoffFilter > protocols::simple_filters::ScoreCutoffFilterOP
typedef utility::pointer::owning_ptr< SelectRDC_Evaluator const > protocols::simple_filters::SelectRDC_EvaluatorCOP
typedef utility::pointer::owning_ptr< SelectRDC_Evaluator > protocols::simple_filters::SelectRDC_EvaluatorOP
typedef utility::pointer::owning_ptr< ShapeComplementarityFilter const > protocols::simple_filters::ShapeComplementarityFilterCOP
typedef utility::pointer::owning_ptr< ShapeComplementarityFilter > protocols::simple_filters::ShapeComplementarityFilterOP
typedef utility::pointer::owning_ptr< Sigmoid const > protocols::simple_filters::SigmoidCOP
typedef utility::pointer::owning_ptr< Sigmoid > protocols::simple_filters::SigmoidOP
typedef utility::pointer::owning_ptr< StructuralSimilarityEvaluator const > protocols::simple_filters::StructuralSimilarityEvaluatorCOP
typedef utility::pointer::owning_ptr< StructuralSimilarityEvaluator > protocols::simple_filters::StructuralSimilarityEvaluatorOP
typedef utility::pointer::owning_ptr< TotalSasaFilter const > protocols::simple_filters::TotalSasaFilterCOP
typedef utility::pointer::owning_ptr< TotalSasaFilter > protocols::simple_filters::TotalSasaFilterOP

Enumeration Type Documentation

enum protocols::simple_filters::Operation
Enumerator
SUM 
PRODUCT 
NORMALIZED_SUM 
MAX 
MIN 
SUBTRACT 
ABS 
BOOLEAN_OR 
XOR 

Function Documentation

core::Real protocols::simple_filters::determinant ( bnu::matrix< core::Real > const &  m)

References determinant_sign().

Referenced by protocols::simple_filters::DisulfideEntropyFilter::compute(), protocols::rotamer_sampler::rigid_body::EulerAngles::convert_to_rotation_matrix(), and protocols::rotamer_sampler::rigid_body::EulerAngles::initialize_from_rotation_matrix().

int protocols::simple_filters::determinant_sign ( const bnu::permutation_matrix< std::size_t > &  pm)

References size().

Referenced by determinant().

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 
)

References numeric::xyzVector< class >::distance_squared(), min_seqsep, protocols::forge::build::SegmentInsertConnectionScheme::N, core::pose::Pose::residue(), core::pose::Pose::total_residue(), and core::conformation::Residue::xyz().

Referenced by protocols::simple_filters::ContactMapEvaluator::apply().

core::Real protocols::simple_filters::pct_features_in_common ( boost::dynamic_bitset<> const &  set1,
boost::dynamic_bitset<> const &  set2 
)

Referenced by protocols::simple_filters::ContactMapEvaluator::apply().

void protocols::simple_filters::print_nmer_svm_energy_data ( vector1< nmer_svm_res_data >  nmer_svm_pose_data)

References utility::io::ozstream::close(), protocols::jd2::current_output_name(), and protocols::jd2::jd2_used().

Referenced by protocols::simple_filters::NMerSVMEnergyFilter::compute().

void protocols::simple_filters::quat2R ( Quat &  Q,
numeric::xyzMatrix< core::Real >  R 
)

References protocols::simple_filters::Quat::w, protocols::simple_filters::Quat::x, numeric::xyzMatrix< class >::xx(), numeric::xyzMatrix< class >::xy(), numeric::xyzMatrix< class >::xz(), protocols::simple_filters::Quat::y, numeric::xyzMatrix< class >::yx(), numeric::xyzMatrix< class >::yy(), numeric::xyzMatrix< class >::yz(), protocols::simple_filters::Quat::z, numeric::xyzMatrix< class >::zx(), numeric::xyzMatrix< class >::zy(), and numeric::xyzMatrix< class >::zz().

Referenced by protocols::simple_filters::SymmetricMotifFilter::process_motifs().

void protocols::simple_filters::R2quat ( numeric::xyzMatrix< core::Real >  R,
Quat &  Q 
)

References protocols::simple_filters::Quat::w, protocols::simple_filters::Quat::x, numeric::xyzMatrix< class >::xx(), numeric::xyzMatrix< class >::xy(), numeric::xyzMatrix< class >::xz(), protocols::simple_filters::Quat::y, numeric::xyzMatrix< class >::yx(), numeric::xyzMatrix< class >::yy(), numeric::xyzMatrix< class >::yz(), protocols::simple_filters::Quat::z, numeric::xyzMatrix< class >::zx(), numeric::xyzMatrix< class >::zy(), and numeric::xyzMatrix< class >::zz().

Referenced by protocols::simple_filters::SymmetricMotifFilter::process_motifs().

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 
)

References numeric::model_quality::calc_rms_fast(), numeric::model_quality::findUU(), j, rms, numeric::xyzMatrix< class >::xx(), numeric::xyzMatrix< class >::xy(), numeric::xyzMatrix< class >::xz(), numeric::xyzMatrix< class >::yx(), numeric::xyzMatrix< class >::yy(), numeric::xyzMatrix< class >::yz(), numeric::xyzMatrix< class >::zx(), numeric::xyzMatrix< class >::zy(), and numeric::xyzMatrix< class >::zz().

Referenced by protocols::simple_filters::SymmetricMotifFilter::compute_d2(), and protocols::simple_filters::SymmetricMotifFilter::process_motifs().

Variable Documentation

basic::Tracer protocols::simple_filters::buried_unsat_hbond_filter_tracer("protocols.simple_filters.BuriedUnsatHbondFilter")
static

Referenced by protocols::simple_filters::BuriedUnsatHbondFilter::apply(), and protocols::simple_filters::BuriedUnsatHbondFilter::compute().

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

Referenced by protocols::simple_filters::RDC_Evaluator::apply(), and protocols::simple_filters::SelectRDC_Evaluator::apply().

basic::Tracer protocols::simple_filters::energy_per_residue_filter_tracer("protocols.simple_filters.EnergyPerResidueFilter")
static
basic::Tracer protocols::simple_filters::neighbor_type_filter_tracer("protocols.simple_filters.NeighborTypeFilter")
static

Referenced by protocols::simple_filters::NeighborTypeFilter::apply().

basic::Tracer protocols::simple_filters::residue_burial_filter_tracer("protocols.simple_filters.ResidueBurialFilter")
static

Referenced by protocols::simple_filters::ResidueBurialFilter::apply(), and protocols::simple_filters::ResidueBurialFilter::compute().

basic::Tracer protocols::simple_filters::residue_distance_filter_tracer("protocols.simple_filters.ResidueDistanceFilter")
static

Referenced by protocols::simple_filters::ResidueDistanceFilter::apply().

basic::Tracer protocols::simple_filters::residues_in_interface_tracer("protocols.simple_filters.ResiduesInInterfaceFilter")
static

Referenced by protocols::simple_filters::ResiduesInInterfaceFilter::apply().

basic::Tracer protocols::simple_filters::score_type_filter_tracer("protocols.simple_filters.ScoreTypeFilter")
static

Referenced by protocols::simple_filters::ScoreTypeFilter::apply(), and protocols::simple_filters::ScoreTypeFilter::parse_def().

basic::Tracer protocols::simple_filters::sidechain_rmsd_filter_tracer("protocols.simple_filters.SidechainRmsdFilter")
static

Referenced by protocols::simple_filters::SidechainRmsdFilter::apply().

basic::Tracer protocols::simple_filters::TR("protocols.simple_filters.ExpiryFilter")
static
basic::Tracer protocols::simple_filters::TR("protocols.simple_filters.NonSequentialNeighborsFilter")
static
basic::Tracer protocols::simple_filters::TR("protocols.simple_filters.PoseComment")
static
basic::Tracer protocols::simple_filters::TR("protocols.simple_filters.FileExistFilter")
static
basic::Tracer protocols::simple_filters::TR("protocols.simple_filters.Sigmoid")
static
basic::Tracer protocols::simple_filters::TR("protocols.simple_filters.DeltaFilter")
static
basic::Tracer protocols::simple_filters::TR("protocols.filters.PoseInfoFilter")
static
basic::Tracer protocols::simple_filters::TR("protocols.simple_filters.ResidueCountFilter")
static
basic::Tracer protocols::simple_filters::TR("protocols.simple_filters.AveragePathLengthFilter")
static
basic::Tracer protocols::simple_filters::TR("protocols.simple_filters.FileRemoveFilter")
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::ShapeComplementarityFilter::apply(), protocols::simple_filters::RangeFilter::apply(), protocols::simple_filters::PackStatFilter::apply(), protocols::simple_filters::HolesFilter::apply(), protocols::simple_filters::ResidueIEFilter::compute(), protocols::simple_filters::ShapeComplementarityFilter::compute(), protocols::simple_filters::PackStatFilter::compute(), protocols::simple_filters::ExternalEvaluator::ExternalEvaluator(), protocols::simple_filters::ShapeComplementarityFilter::parse_def(), protocols::simple_filters::ResidueIEFilter::parse_my_tag(), protocols::simple_filters::ShapeComplementarityFilter::parse_my_tag(), protocols::simple_filters::PackStatFilter::parse_my_tag(), protocols::simple_filters::HolesFilter::parse_my_tag(), protocols::simple_filters::ScoreEvaluator::ScoreEvaluator(), protocols::simple_filters::TruncatedScoreEvaluator::TruncatedScoreEvaluator(), and protocols::simple_filters::ExternalEvaluator::~ExternalEvaluator().

basic::Tracer protocols::simple_filters::TR("protocols.simple_filters.MultipleSigmoids")
static
basic::Tracer protocols::simple_filters::TR("protocols.filters.SavePoseConstraintToFileFilter")
static
basic::Tracer protocols::simple_filters::TR("protocols.simple_filters.ReportFilter")
static
basic::Tracer protocols::simple_filters::TR("protocols.filters.AtomicDistanceFilter")
static
basic::Tracer protocols::simple_filters::TR("protocols.simple_filters.TotalSasaFilter")
static
basic::Tracer protocols::simple_filters::TR("protocols.simple_filters.Operator")
static
basic::Tracer protocols::simple_filters::TR("protocols.filters.AtomicContactFilter")
static
basic::Tracer protocols::simple_filters::TR("protocols.simple_filters.InterfaceSasaFilter")
static
basic::Tracer protocols::simple_filters::TR("protocols.simple_filters.DdgFilter")
static
basic::Tracer protocols::simple_filters::TR("protocols.simple_filters.InterfaceBindingEnergyDensityFilter")
static
basic::Tracer protocols::simple_filters::TR("protocols.simple_filters.DisulfideEntropyFilter")
static
basic::Tracer protocols::simple_filters::TR("protocols.simple_filters.ResidueSetChainEnergyFilter")
static
basic::Tracer protocols::simple_filters::TR("protocols.simple_filters.NetChargeFilter")
static
basic::Tracer protocols::simple_filters::TR("protocols.simple_filters.NMerPSSMEnergyFilter")
static
basic::Tracer protocols::simple_filters::TR("protocols.simple_filters.RelativePoseFilter")
static
basic::Tracer protocols::simple_filters::TR("protocols.simple_filters.NMerSVMEnergyFilter")
static
basic::Tracer protocols::simple_filters::TR("protocols.simple_filters.SymmetricMotifFilter")
static
basic::Tracer protocols::simple_filters::TR("protocols.simple_filters.TerminusDistanceFilter")
static
basic::Tracer protocols::simple_filters::TR("protocols.simple_filters.AlaScan")
static

Referenced by protocols::simple_filters::TotalSasaFilter::apply(), protocols::simple_filters::FileRemoveFilter::apply(), protocols::simple_filters::InterfaceSasaFilter::apply(), protocols::simple_filters::GeometryFilter::apply(), protocols::simple_filters::PoseComment::apply(), protocols::simple_filters::TerminusDistanceFilter::apply(), protocols::simple_filters::Operator::apply(), protocols::simple_filters::NetChargeFilter::apply(), protocols::simple_filters::NMerSVMEnergyFilter::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::AveragePathLengthFilter::apply(), protocols::simple_filters::DisulfideEntropyFilter::apply(), protocols::simple_filters::SymmetricMotifFilter::apply(), protocols::simple_filters::InterfaceBindingEnergyDensityFilter::apply(), protocols::simple_filters::DeltaFilter::baseline(), protocols::simple_filters::ReportFilter::checkpoint_read(), protocols::simple_filters::ReportFilter::checkpoint_write(), protocols::simple_filters::PoseInfoFilter::compute(), protocols::simple_filters::SavePoseConstraintToFileFilter::compute(), protocols::simple_filters::TotalSasaFilter::compute(), protocols::simple_filters::InterfaceSasaFilter::compute(), protocols::simple_filters::GeometryFilter::compute(), protocols::simple_filters::AtomicDistanceFilter::compute(), protocols::simple_filters::AtomicContactFilter::compute(), protocols::simple_filters::DeltaFilter::compute(), protocols::simple_filters::NetChargeFilter::compute(), protocols::simple_filters::NonSequentialNeighborsFilter::compute(), protocols::simple_filters::Operator::compute(), protocols::simple_filters::Sigmoid::compute(), protocols::simple_filters::RelativePoseFilter::compute(), protocols::simple_filters::MultipleSigmoids::compute(), protocols::simple_filters::RotamerBoltzmannWeight::compute(), protocols::simple_filters::DdgFilter::compute(), protocols::simple_filters::RotamerBoltzmannWeight::compute_Boltzmann_weight(), protocols::simple_filters::SymmetricMotifFilter::compute_d2(), protocols::simple_filters::AlaScan::ddG_for_single_residue(), protocols::simple_filters::DdgFilter::DdgFilter(), protocols::simple_filters::RotamerBoltzmannWeight::first_pass_ala_scan(), protocols::simple_filters::Operator::modify_relative_filters_pdb_names(), protocols::simple_filters::InterfaceSasaFilter::parse_def(), protocols::simple_filters::RotamerBoltzmannWeight::parse_def(), protocols::simple_filters::DdgFilter::parse_def(), protocols::simple_filters::PoseComment::parse_my_tag(), protocols::simple_filters::Operator::parse_my_tag(), protocols::simple_filters::Sigmoid::parse_my_tag(), protocols::simple_filters::DeltaFilter::parse_my_tag(), protocols::simple_filters::MultipleSigmoids::parse_my_tag(), protocols::simple_filters::TotalSasaFilter::parse_my_tag(), protocols::simple_filters::NonSequentialNeighborsFilter::parse_my_tag(), protocols::simple_filters::SavePoseConstraintToFileFilter::parse_my_tag(), protocols::simple_filters::RelativePoseFilter::parse_my_tag(), protocols::simple_filters::ReportFilter::parse_my_tag(), protocols::simple_filters::NetChargeFilter::parse_my_tag(), protocols::simple_filters::AtomicDistanceFilter::parse_my_tag(), protocols::simple_filters::RotamerBoltzmannWeight::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::AveragePathLengthFilter::parse_my_tag(), protocols::simple_filters::DisulfideEntropyFilter::parse_my_tag(), protocols::simple_filters::SymmetricMotifFilter::parse_my_tag(), protocols::simple_filters::SymmetricMotifFilter::process_motifs(), protocols::simple_filters::SymmetricMotifFilter::report(), protocols::simple_filters::Operator::report_sm(), protocols::simple_filters::RotamerBoltzmannWeight::report_sm(), protocols::simple_filters::Operator::reset_baseline(), protocols::simple_filters::MultipleSigmoids::reset_baseline(), protocols::simple_filters::Sigmoid::reset_baseline(), and protocols::simple_filters::RelativePoseFilter::thread_seq().

basic::Tracer protocols::simple_filters::TR("protocols.simple_filters.GeometryFilter")
static
basic::Tracer protocols::simple_filters::TR("protocols.simple_filters.RotamerBoltzmannWeight")
static
Generated on Mon Apr 21 2014 16:43:53 for Rosetta Protocols by   doxygen 1.8.7