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protocols::simple_filters Namespace Reference

Classes

class  AbinitioBaseFilter
 
class  AngleToVector
 
class  AngleToVectorFilterCreator
 
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  BuriedSurfaceAreaFilter
 Calculates buried surface area (exposed surface area minus total surface area, on a per-residue basis). Accepts a residue selector to allow buried subsets to be considered. More...
 
class  BuriedSurfaceAreaFilterCreator
 
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  ChainBreak
 test whether a pose contains a comment that evaluates to a predefined value. This is useful in controlling execution flow in RosettaScripts. More...
 
class  ChainBreakFilterCreator
 
class  ChainCountFilter
 detects atomic contacts between two atoms of two residues More...
 
class  ChainCountFilterCreator
 
class  ChiWellRmsdEvaluator
 
class  ChiWellRmsdEvaluatorCreator
 creator for the ChiWellRmsdEvaluatorCreator class More...
 
class  COFilter
 
class  ContactMapEvaluator
 
class  ContactMapEvaluatorCreator
 creator for the ContactMapEvaluatorCreator class More...
 
class  ContactMolecularSurfaceFilter
 
class  ContactMolecularSurfaceFilterCreator
 
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  HelixHelixAngleFilter
 
class  HelixHelixAngleFilterCreator
 
class  HolesFilter
 
class  HolesFilterCreator
 
class  InterfaceHbondsFilter
 
class  InterfaceHbondsFilterCreator
 
class  InterfaceHydrophobicResidueContactsFilter
 
class  InterfaceHydrophobicResidueContactsFilterCreator
 
class  InterfaceSasaFilter
 
class  InterfaceSasaFilterCreator
 
class  InterRepeatContactFilter
 
class  InterRepeatContactFilterCreator
 
class  IntraRepeatContactFilter
 
class  IntraRepeatContactFilterCreator
 
class  JScoreEvaluator
 
class  JScoreEvaluatorCreator
 creator for the JScoreEvaluatorCreator class More...
 
class  JumpEvaluator
 
class  JumpNrEvaluator
 
class  JumpNrEvaluatorCreator
 creator for the JumpNrEvaluatorCreator class More...
 
class  LongestContinuousApolarSegmentFilter
 This filter computes the longest continuous stretch of polar residues within a pose or selection. More...
 
class  LongestContinuousApolarSegmentFilterCreator
 
class  LongestContinuousPolarSegmentFilter
 This filter computes the longest continuous stretch of polar residues within a pose or selection. More...
 
class  LongestContinuousPolarSegmentFilterCreator
 
class  MembAccesResidueLipophilicityFilter
 
class  MembAccesResidueLipophilicityFilterCreator
 
class  MotifScoreFilter
 
class  MotifScoreFilterCreator
 
class  MPSpanAngleFilter
 
class  MPSpanAngleFilterCreator
 
class  MutationsFilter
 
class  MutationsFilterCreator
 
class  NativeEvaluatorCreator
 creator for the NativeEvaluatorCreator class More...
 
class  NeighborTypeFilter
 
class  NeighborTypeFilterCreator
 
class  NetChargeFilter
 
class  NetChargeFilterCreator
 
class  NMerPSSMEnergyFilter
 
class  NMerPSSMEnergyFilterCreator
 
struct  nmer_svm_res_data
 
class  NMerSVMEnergyFilter
 
class  NMerSVMEnergyFilterCreator
 
class  NonSequentialNeighborsFilter
 
class  NonSequentialNeighborsFilterCreator
 
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  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...
 
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  ReadPoseExtraScoreFilter
 
class  ReadPoseExtraScoreFilterCreator
 
class  RepeatParameterFilter
 
class  RepeatParameterFilterCreator
 
class  ReportFilter
 
class  ReportFilterCreator
 
class  ResidueBurialFilter
 
class  ResidueBurialFilterCreator
 
class  ResidueChiralityFilter
 
class  ResidueChiralityFilterCreator
 
class  ResidueCountFilter
 
class  ResidueCountFilterCreator
 
struct  ResidueDepthData
 
class  ResidueDepthFrag
 
class  ResidueDepthCalculator
 
class  ResidueDepthFilter
 
class  ResidueDepthFilterCreator
 
class  ResidueDistanceFilter
 
class  ResidueDistanceFilterCreator
 
class  ResidueIEFilter
 
class  ResidueIEFilterCreator
 
class  ResidueLipophilicityFilter
 
class  ResidueLipophilicityFilterCreator
 
class  ResidueSelectionDistanceFilter
 
class  ResidueSelectionDistanceFilterCreator
 
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  SaveResfileToDiskFilter
 
class  SaveResfileToDiskFilterCreator
 
class  SAXSScoreFilter
 
class  ScoreEvaluator
 that rewrites the whole pss struct all previous entries will be lost... probably not what one wants... More...
 
class  TruncatedScoreEvaluator
 
class  SecretionPredictionFilter
 
class  SecretionPredictionFilterCreator
 
class  SequenceDistance
 test whether a pose contains a comment that evaluates to a predefined value. This is useful in controlling execution flow in RosettaScripts. More...
 
class  SequenceDistanceFilterCreator
 
class  ShapeComplementarityFilter
 
class  EXCN_InitFailed
 Super-simple exception to be thrown when we can't initialize the SC calculator. More...
 
class  EXCN_CalcFailed
 Super-simple exception to be thrown when the SC calculator fails to compute. More...
 
class  ShapeComplementarityFilterCreator
 
class  SheetFilter
 
class  SidechainRmsdFilter
 
class  SidechainRmsdFilterCreator
 
class  SimpleHbondsToAtomFilter
 Simple filter for detercting Hbonds to atom with energy < energy cutoff. More...
 
class  SimpleHbondsToAtomFilterCreator
 
class  SimpleMetricFilter
 A filter takes any SimpleMetric and applies a set cutoff to filter the model. Set the cutoff type to set the behavior of the metric. More...
 
class  SimpleMetricFilterCreator
 
class  SpanTopologyMatchPoseFilter
 
class  SpanTopologyMatchPoseFilterCreator
 
class  SSElementLengthFilter
 
class  SSElementLengthFilterCreator
 
class  SSElementMotifContactFilter
 
class  SSElementMotifContactFilterCreator
 
class  SSMotifFinder
 
class  SSMotifFinderFilterCreator
 
class  StemFinder
 
class  StemFinderFilterCreator
 
class  StructuralSimilarityEvaluator
 
class  StructureSimilarityEvaluatorCreator
 creator for the StructureSimilarityEvaluatorCreator class More...
 
struct  Quat
 
class  SymmetricMotifFilter
 
class  SymmetricMotifFilterCreator
 
class  TaskAwareSASAFilter
 
class  TaskAwareSASAFilterCreator
 
class  TaskAwareScoreTypeFilter
 
class  TaskAwareScoreTypeFilterCreator
 
class  TerminusDistanceFilter
 
class  TerminusDistanceFilterCreator
 
class  TMsAACompFilter
 
class  TMsAACompFilterCreator
 
class  TMsSpanMembraneFilter
 
class  TMsSpanMembraneFilterCreator
 
class  TotalSasaFilter
 
class  TotalSasaFilterCreator
 
class  Worst9merFilter
 
class  Worst9merFilterCreator
 

Typedefs

typedef utility::pointer::shared_ptr< AngleToVector > AngleToVectorOP
 
typedef utility::pointer::shared_ptr< AngleToVector const > AngleToVectorCOP
 
typedef utility::pointer::shared_ptr< AveragePathLengthFilter > AveragePathLengthFilterOP
 
typedef utility::pointer::shared_ptr< AveragePathLengthFilter const > AveragePathLengthFilterCOP
 
typedef utility::pointer::shared_ptr< BuriedSurfaceAreaFilter > BuriedSurfaceAreaFilterOP
 
typedef utility::pointer::shared_ptr< BuriedSurfaceAreaFilter const > BuriedSurfaceAreaFilterCOP
 
typedef utility::pointer::shared_ptr< PoseComment > PoseCommentOP
 
typedef utility::pointer::shared_ptr< PoseComment const > PoseCommentCOP
 
typedef utility::pointer::shared_ptr< ChainCountFilter > ChainCountFilterOP
 
typedef utility::pointer::shared_ptr< ChainCountFilter const > ChainCountFilterCOP
 
typedef utility::pointer::shared_ptr< ContactMolecularSurfaceFilter > ContactMolecularSurfaceFilterOP
 
typedef utility::pointer::shared_ptr< ContactMolecularSurfaceFilter const > ContactMolecularSurfaceFilterCOP
 
typedef utility::pointer::shared_ptr< DeltaFilter > DeltaFilterOP
 
typedef utility::pointer::shared_ptr< DeltaFilter const > DeltaFilterCOP
 
typedef utility::pointer::shared_ptr< DisulfideEntropyFilter > DisulfideEntropyFilterOP
 
typedef utility::pointer::shared_ptr< DisulfideEntropyFilter const > DisulfideEntropyFilterCOP
 
typedef utility::pointer::shared_ptr< DomainInterfaceFilter > DomainInterfaceFilterOP
 
typedef utility::pointer::shared_ptr< DomainInterfaceFilter const > DomainInterfaceFilterCOP
 
typedef utility::pointer::shared_ptr< EvaluatedTrialMover > EvaluatedTrialMoverOP
 
typedef utility::pointer::shared_ptr< HelixHelixAngleFilter > HelixHelixAngleFilterOP
 
typedef utility::pointer::shared_ptr< HelixHelixAngleFilter const > HelixHelixAngleFilterCOP
 
typedef utility::pointer::shared_ptr< HolesFilter > HolesFilterOP
 
typedef utility::pointer::shared_ptr< HolesFilter const > HolesFilterCOP
 
typedef utility::pointer::shared_ptr< InterfaceHbondsFilter > InterfaceHbondsFilterOP
 
typedef utility::pointer::shared_ptr< InterfaceHbondsFilter const > InterfaceHbondsFilterCOP
 
typedef utility::pointer::shared_ptr< InterfaceHydrophobicResidueContactsFilter > InterfaceHydrophobicResidueContactsFilterOP
 
typedef utility::pointer::shared_ptr< InterfaceHydrophobicResidueContactsFilter const > InterfaceHydrophobicResidueContactsFilterCOP
 
typedef utility::pointer::shared_ptr< InterfaceSasaFilter > InterfaceSasaFilterOP
 
typedef utility::pointer::shared_ptr< InterfaceSasaFilter const > InterfaceSasaFilterCOP
 
typedef utility::pointer::shared_ptr< InterRepeatContactFilter > InterRepeatContactFilterOP
 
typedef utility::pointer::shared_ptr< InterRepeatContactFilter const > InterRepeatContactFilterCOP
 
typedef utility::pointer::shared_ptr< IntraRepeatContactFilter > IntraRepeatContactFilterOP
 
typedef utility::pointer::shared_ptr< IntraRepeatContactFilter const > IntraRepeatContactFilterCOP
 
typedef utility::pointer::shared_ptr< LongestContinuousApolarSegmentFilter > LongestContinuousApolarSegmentFilterOP
 
typedef utility::pointer::shared_ptr< LongestContinuousApolarSegmentFilter const > LongestContinuousApolarSegmentFilterCOP
 
typedef utility::pointer::shared_ptr< LongestContinuousPolarSegmentFilter > LongestContinuousPolarSegmentFilterOP
 
typedef utility::pointer::shared_ptr< LongestContinuousPolarSegmentFilter const > LongestContinuousPolarSegmentFilterCOP
 
using Xform = numeric::xyzTransform< core::Real >
 
typedef utility::pointer::shared_ptr< MotifScoreFilter > MotifScoreFilterOP
 
typedef utility::pointer::shared_ptr< MotifScoreFilter const > MotifScoreFilterCOP
 
typedef utility::pointer::shared_ptr< MutationsFilter > MutationsFilterOP
 
typedef utility::pointer::shared_ptr< MutationsFilter const > MutationsFilterCOP
 
typedef utility::pointer::shared_ptr< PackerNeighborGraphFilter > PackerNeighborGraphFilterOP
 
typedef utility::pointer::shared_ptr< PackerNeighborGraphFilter const > PackerNeighborGraphFilterCOP
 
typedef utility::pointer::shared_ptr< PackStatFilter > PackStatFilterOP
 
typedef utility::pointer::shared_ptr< PackStatFilter const > PackStatFilterCOP
 
typedef utility::pointer::shared_ptr< PDDFScoreFilter > PDDFScoreFilterOP
 
typedef utility::pointer::shared_ptr< PDDFScoreFilter const > PDDFScoreFilterCOP
 
typedef utility::pointer::shared_ptr< RangeFilter > RangeFilterOP
 
typedef utility::pointer::shared_ptr< RangeFilter const > RangeFilterCOP
 
typedef utility::pointer::shared_ptr< SelectRDC_Evaluator > SelectRDC_EvaluatorOP
 
typedef utility::pointer::shared_ptr< SelectRDC_Evaluator const > SelectRDC_EvaluatorCOP
 
typedef utility::pointer::shared_ptr< ReadPoseExtraScoreFilter > ReadPoseExtraScoreFilterOP
 
typedef utility::pointer::shared_ptr< ReadPoseExtraScoreFilter const > ReadPoseExtraScoreFilterCOP
 
typedef utility::pointer::shared_ptr< RepeatParameterFilter > RepeatParameterFilterOP
 
typedef utility::pointer::shared_ptr< RepeatParameterFilter const > RepeatParameterFilterCOP
 
typedef utility::pointer::shared_ptr< ResidueDepthData > ResidueDepthDataOP
 
typedef utility::pointer::shared_ptr< ResidueDepthData const > ResidueDepthDataCOP
 
typedef utility::pointer::shared_ptr< ResidueIEFilter > ResidueIEFilterOP
 
typedef utility::pointer::shared_ptr< ResidueIEFilter const > ResidueIEFilterCOP
 
typedef utility::pointer::shared_ptr< SaveResfileToDiskFilter > SaveResfileToDiskFilterOP
 
typedef utility::pointer::shared_ptr< SaveResfileToDiskFilter const > SaveResfileToDiskFilterCOP
 
typedef utility::pointer::shared_ptr< SAXSScoreFilter > SAXSScoreFilterOP
 
typedef utility::pointer::shared_ptr< SAXSScoreFilter const > SAXSScoreFilterCOP
 
typedef utility::pointer::shared_ptr< SecretionPredictionFilter > SecretionPredictionFilterOP
 
typedef utility::pointer::shared_ptr< SecretionPredictionFilter const > SecretionPredictionFilterCOP
 
typedef utility::pointer::shared_ptr< ShapeComplementarityFilter > ShapeComplementarityFilterOP
 
typedef utility::pointer::shared_ptr< ShapeComplementarityFilter const > ShapeComplementarityFilterCOP
 
typedef utility::pointer::shared_ptr< SimpleHbondsToAtomFilter > SimpleHbondsToAtomFilterOP
 
typedef utility::pointer::shared_ptr< SimpleHbondsToAtomFilter const > SimpleHbondsToAtomFilterCOP
 
typedef utility::pointer::shared_ptr< SimpleMetricFilter > SimpleMetricFilterOP
 
typedef utility::pointer::shared_ptr< SimpleMetricFilter const > SimpleMetricFilterCOP
 
typedef utility::pointer::shared_ptr< SSElementLengthFilter > SSElementLengthFilterOP
 
typedef utility::pointer::shared_ptr< SSElementLengthFilter const > SSElementLengthFilterCOP
 
typedef utility::pointer::shared_ptr< SSElementMotifContactFilter > SSElementMotifContactFilterOP
 
typedef utility::pointer::shared_ptr< SSElementMotifContactFilter const > SSElementMotifContactFilterCOP
 
typedef utility::pointer::shared_ptr< SSMotifFinder > SSMotifFinderOP
 
typedef utility::pointer::shared_ptr< SSMotifFinder const > SSMotifFinderCOP
 
typedef utility::pointer::shared_ptr< StemFinder > StemFinderOP
 
typedef utility::pointer::shared_ptr< StemFinder const > StemFinderCOP
 
typedef utility::pointer::shared_ptr< StructuralSimilarityEvaluator > StructuralSimilarityEvaluatorOP
 
typedef utility::pointer::shared_ptr< StructuralSimilarityEvaluator const > StructuralSimilarityEvaluatorCOP
 
typedef utility::pointer::shared_ptr< TaskAwareSASAFilter > TaskAwareSASAFilterOP
 
typedef utility::pointer::shared_ptr< TaskAwareSASAFilter const > TaskAwareSASAFilterCOP
 
typedef utility::pointer::shared_ptr< TaskAwareScoreTypeFilter > TaskAwareScoreTypeFilterOP
 
typedef utility::pointer::shared_ptr< TaskAwareScoreTypeFilter const > TaskAwareScoreTypeFilterCOP
 
typedef utility::pointer::shared_ptr< TotalSasaFilter > TotalSasaFilterOP
 
typedef utility::pointer::shared_ptr< TotalSasaFilter const > TotalSasaFilterCOP
 
typedef utility::pointer::shared_ptr< Worst9merFilter > Worst9merFilterOP
 
typedef utility::pointer::shared_ptr< Worst9merFilter const > Worst9merFilterCOP
 

Enumerations

enum  BSAF_mode { BSAF_all_atoms = 1 , BSAF_hydrophobic_atoms , BSAF_polar_atoms , BSAF_end_of_list = BSAF_polar_atoms }
 
enum  comparison_type {
  eq = 1 , ne , lt , gt ,
  lt_or_eq , gt_or_eq , bogus , comparison_type_total = bogus
}
 Enum that tells us how to interpret the cutoff set. More...
 

Functions

static basic::Tracer TR ("protocols.simple_filters.AngleToVector")
 
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.ChainBreak")
 
static basic::Tracer TR ("protocols.filters.ChainCountFilter")
 
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.DeltaFilter")
 
static basic::Tracer TR ("protocols.simple_filters.DisulfideEntropyFilter")
 
int determinant_sign (const bnu::permutation_matrix< std::size_t > &pm)
 
core::Real determinant (bnu::matrix< core::Real > const &m)
 
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.HelixHelixAngleFilter")
 
static basic::Tracer tr ("protocols.simple_filters.HolesFilter")
 
static basic::Tracer TR ("protocols.simple_filters.InterfaceHbondsFilter")
 
static basic::Tracer TR ("protocols.simple_filters.InterfaceHydrophobicResidueContactsFilter")
 
static basic::Tracer TR ("protocols.simple_filters.InterfaceSasaFilter")
 
static basic::Tracer TR ("protocols.simple_filters.MembAccesResidueLipophilicityFilter")
 
static basic::Tracer TR ("protocols.simple_moves.MotifScoreFilter")
 
static basic::Tracer TR ("protocols.simple_filters.MPSpanAngleFilter")
 
static basic::Tracer TR ("protocols.simple_filters.MutationsFilter")
 
static basic::Tracer neighbor_type_filter_tracer ("protocols.simple_filters.NeighborTypeFilter")
 
std::string NeighborType_subelement_ct_name (std::string const &name)
 
static basic::Tracer TR ("protocols.simple_filters.NetChargeFilter")
 
static basic::Tracer TR ("protocols.simple_filters.NMerPSSMEnergyFilter")
 
static basic::Tracer TR ("protocols.simple_filters.NMerSVMEnergyFilter")
 
void print_nmer_svm_energy_data (vector1< nmer_svm_res_data > nmer_svm_pose_data)
 
static basic::Tracer TR ("protocols.simple_filters.NonSequentialNeighborsFilter")
 
static basic::Tracer TR ("protocols.simple_filters.PoseComment")
 
static basic::Tracer TR ("protocols.filters.PoseInfoFilter")
 
static basic::Tracer TR ("protocols.simple_filters.RepeatParameterFilter")
 
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.ResidueChiralityFilter")
 
static basic::Tracer TR ("protocols.simple_filters.ResidueCountFilter")
 
static basic::Tracer TR ("protocols.simple_filters.ResidueDepthFilter")
 
bool mycomp (const std::pair< core::Real, core::Size > &lhs, const std::pair< core::Real, core::Size > &rhs)
 
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.ResidueLipophilicityFilter")
 
static basic::Tracer TR ("protocols.simple_filters.ResidueSelectionDistanceFilter")
 
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.SequenceDistance")
 
static basic::Tracer sidechain_rmsd_filter_tracer ("protocols.simple_filters.SidechainRmsdFilter")
 
std::map< std::string, comparison_type > get_string_comparison_type_map ()
 
utility::vector1< std::string > get_string_comparison_type_strings ()
 
static basic::Tracer TR ("protocols.simple_filters.SpanTopologyMatchPoseFilter")
 
static basic::Tracer TR ("protocols.simple_filters.SSMotifFinder")
 
core::Real atom_distance (core::conformation::Residue const &r1, std::string const &a1, core::conformation::Residue const &r2, std::string const &a2)
 compute the atomic distance between two atoms on two residues More...
 
core::Real res_rmsd (utility::vector1< core::Size > const pose_res_for_rmsd, utility::vector1< core::Size > const template_res_for_rmsd, core::pose::Pose const &copy_pose, core::pose::Pose const &template_pose)
 
void write_to_file (std::string const &filename, core::Size const stem1, core::Size const stem2, core::Real const rmsd, std::string const &pdbname, core::pose::Pose const &pose)
 
utility::vector1< numeric::xyzVector< core::Real > > coords (core::pose::Pose const &pose, utility::vector1< core::Size > const positions)
 
static basic::Tracer TR ("protocols.simple_filters.StemFinder")
 
std::string dssp (core::pose::Pose const &pose)
 potentially useful utility functions More...
 
utility::vector1< core::Size > positions_in_secstruct (core::pose::Pose const &pose)
 find helix, sheet positions in dssp More...
 
utility::vector1< core::pose::PoseOP > load_poses (utility::vector1< std::string > const &filenames)
 load PDBs into a vector More...
 
core::Real atom_distance (core::pose::Pose const &p1, core::Size const r1, std::string const &a1, core::pose::Pose const &p2, core::Size const r2, std::string const &a2)
 
core::Real res_res_min_distance (core::pose::Pose const &p1, core::Size const r1, core::pose::Pose const &p2, core::Size const r2)
 find the minimal atom-atom distance between two residues More...
 
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.TaskAwareScoreTypeFilter")
 
static basic::Tracer TR ("protocols.simple_filters.TerminusDistanceFilter")
 
static basic::Tracer TR ("protocols.simple_filters.TMsAACompFilter")
 
static basic::Tracer TR ("protocols.simple_filters.TMsSpanMembraneFilter")
 
static basic::Tracer TR ("protocols.simple_filters.TotalSasaFilter")
 

Variables

static core::energy_methods::ResidualDipolarCouplingEnergy energy_evaluator
 

Typedef Documentation

◆ AngleToVectorCOP

typedef utility::pointer::shared_ptr< AngleToVector const > protocols::simple_filters::AngleToVectorCOP

◆ AngleToVectorOP

typedef utility::pointer::shared_ptr< AngleToVector > protocols::simple_filters::AngleToVectorOP

◆ AveragePathLengthFilterCOP

typedef utility::pointer::shared_ptr< AveragePathLengthFilter const > protocols::simple_filters::AveragePathLengthFilterCOP

◆ AveragePathLengthFilterOP

typedef utility::pointer::shared_ptr< AveragePathLengthFilter > protocols::simple_filters::AveragePathLengthFilterOP

◆ BuriedSurfaceAreaFilterCOP

typedef utility::pointer::shared_ptr< BuriedSurfaceAreaFilter const > protocols::simple_filters::BuriedSurfaceAreaFilterCOP

◆ BuriedSurfaceAreaFilterOP

typedef utility::pointer::shared_ptr< BuriedSurfaceAreaFilter > protocols::simple_filters::BuriedSurfaceAreaFilterOP

◆ ChainCountFilterCOP

typedef utility::pointer::shared_ptr< ChainCountFilter const > protocols::simple_filters::ChainCountFilterCOP

◆ ChainCountFilterOP

typedef utility::pointer::shared_ptr< ChainCountFilter > protocols::simple_filters::ChainCountFilterOP

◆ ContactMolecularSurfaceFilterCOP

typedef utility::pointer::shared_ptr< ContactMolecularSurfaceFilter const > protocols::simple_filters::ContactMolecularSurfaceFilterCOP

◆ ContactMolecularSurfaceFilterOP

typedef utility::pointer::shared_ptr< ContactMolecularSurfaceFilter > protocols::simple_filters::ContactMolecularSurfaceFilterOP

◆ DeltaFilterCOP

typedef utility::pointer::shared_ptr< DeltaFilter const > protocols::simple_filters::DeltaFilterCOP

◆ DeltaFilterOP

typedef utility::pointer::shared_ptr< DeltaFilter > protocols::simple_filters::DeltaFilterOP

◆ DisulfideEntropyFilterCOP

typedef utility::pointer::shared_ptr< DisulfideEntropyFilter const > protocols::simple_filters::DisulfideEntropyFilterCOP

◆ DisulfideEntropyFilterOP

typedef utility::pointer::shared_ptr< DisulfideEntropyFilter > protocols::simple_filters::DisulfideEntropyFilterOP

◆ DomainInterfaceFilterCOP

typedef utility::pointer::shared_ptr< DomainInterfaceFilter const > protocols::simple_filters::DomainInterfaceFilterCOP

◆ DomainInterfaceFilterOP

typedef utility::pointer::shared_ptr< DomainInterfaceFilter > protocols::simple_filters::DomainInterfaceFilterOP

◆ EvaluatedTrialMoverOP

typedef utility::pointer::shared_ptr< EvaluatedTrialMover > protocols::simple_filters::EvaluatedTrialMoverOP

◆ HelixHelixAngleFilterCOP

typedef utility::pointer::shared_ptr< HelixHelixAngleFilter const > protocols::simple_filters::HelixHelixAngleFilterCOP

◆ HelixHelixAngleFilterOP

typedef utility::pointer::shared_ptr< HelixHelixAngleFilter > protocols::simple_filters::HelixHelixAngleFilterOP

◆ HolesFilterCOP

typedef utility::pointer::shared_ptr< HolesFilter const > protocols::simple_filters::HolesFilterCOP

◆ HolesFilterOP

typedef utility::pointer::shared_ptr< HolesFilter > protocols::simple_filters::HolesFilterOP

◆ InterfaceHbondsFilterCOP

typedef utility::pointer::shared_ptr< InterfaceHbondsFilter const > protocols::simple_filters::InterfaceHbondsFilterCOP

◆ InterfaceHbondsFilterOP

typedef utility::pointer::shared_ptr< InterfaceHbondsFilter > protocols::simple_filters::InterfaceHbondsFilterOP

◆ InterfaceHydrophobicResidueContactsFilterCOP

typedef utility::pointer::shared_ptr< InterfaceHydrophobicResidueContactsFilter const > protocols::simple_filters::InterfaceHydrophobicResidueContactsFilterCOP

◆ InterfaceHydrophobicResidueContactsFilterOP

typedef utility::pointer::shared_ptr< InterfaceHydrophobicResidueContactsFilter > protocols::simple_filters::InterfaceHydrophobicResidueContactsFilterOP

◆ InterfaceSasaFilterCOP

typedef utility::pointer::shared_ptr< InterfaceSasaFilter const > protocols::simple_filters::InterfaceSasaFilterCOP

◆ InterfaceSasaFilterOP

typedef utility::pointer::shared_ptr< InterfaceSasaFilter > protocols::simple_filters::InterfaceSasaFilterOP

◆ InterRepeatContactFilterCOP

typedef utility::pointer::shared_ptr< InterRepeatContactFilter const > protocols::simple_filters::InterRepeatContactFilterCOP

◆ InterRepeatContactFilterOP

typedef utility::pointer::shared_ptr< InterRepeatContactFilter > protocols::simple_filters::InterRepeatContactFilterOP

◆ IntraRepeatContactFilterCOP

typedef utility::pointer::shared_ptr< IntraRepeatContactFilter const > protocols::simple_filters::IntraRepeatContactFilterCOP

◆ IntraRepeatContactFilterOP

typedef utility::pointer::shared_ptr< IntraRepeatContactFilter > protocols::simple_filters::IntraRepeatContactFilterOP

◆ LongestContinuousApolarSegmentFilterCOP

typedef utility::pointer::shared_ptr< LongestContinuousApolarSegmentFilter const > protocols::simple_filters::LongestContinuousApolarSegmentFilterCOP

◆ LongestContinuousApolarSegmentFilterOP

typedef utility::pointer::shared_ptr< LongestContinuousApolarSegmentFilter > protocols::simple_filters::LongestContinuousApolarSegmentFilterOP

◆ LongestContinuousPolarSegmentFilterCOP

typedef utility::pointer::shared_ptr< LongestContinuousPolarSegmentFilter const > protocols::simple_filters::LongestContinuousPolarSegmentFilterCOP

◆ LongestContinuousPolarSegmentFilterOP

typedef utility::pointer::shared_ptr< LongestContinuousPolarSegmentFilter > protocols::simple_filters::LongestContinuousPolarSegmentFilterOP

◆ MotifScoreFilterCOP

typedef utility::pointer::shared_ptr< MotifScoreFilter const > protocols::simple_filters::MotifScoreFilterCOP

◆ MotifScoreFilterOP

typedef utility::pointer::shared_ptr< MotifScoreFilter > protocols::simple_filters::MotifScoreFilterOP

◆ MutationsFilterCOP

typedef utility::pointer::shared_ptr< MutationsFilter const > protocols::simple_filters::MutationsFilterCOP

◆ MutationsFilterOP

typedef utility::pointer::shared_ptr< MutationsFilter > protocols::simple_filters::MutationsFilterOP

◆ PackerNeighborGraphFilterCOP

typedef utility::pointer::shared_ptr< PackerNeighborGraphFilter const > protocols::simple_filters::PackerNeighborGraphFilterCOP

◆ PackerNeighborGraphFilterOP

typedef utility::pointer::shared_ptr< PackerNeighborGraphFilter > protocols::simple_filters::PackerNeighborGraphFilterOP

◆ PackStatFilterCOP

typedef utility::pointer::shared_ptr< PackStatFilter const > protocols::simple_filters::PackStatFilterCOP

◆ PackStatFilterOP

typedef utility::pointer::shared_ptr< PackStatFilter > protocols::simple_filters::PackStatFilterOP

◆ PDDFScoreFilterCOP

typedef utility::pointer::shared_ptr< PDDFScoreFilter const > protocols::simple_filters::PDDFScoreFilterCOP

◆ PDDFScoreFilterOP

typedef utility::pointer::shared_ptr< PDDFScoreFilter > protocols::simple_filters::PDDFScoreFilterOP

◆ PoseCommentCOP

typedef utility::pointer::shared_ptr< PoseComment const > protocols::simple_filters::PoseCommentCOP

◆ PoseCommentOP

typedef utility::pointer::shared_ptr< PoseComment > protocols::simple_filters::PoseCommentOP

◆ RangeFilterCOP

typedef utility::pointer::shared_ptr< RangeFilter const > protocols::simple_filters::RangeFilterCOP

◆ RangeFilterOP

typedef utility::pointer::shared_ptr< RangeFilter > protocols::simple_filters::RangeFilterOP

◆ ReadPoseExtraScoreFilterCOP

typedef utility::pointer::shared_ptr< ReadPoseExtraScoreFilter const > protocols::simple_filters::ReadPoseExtraScoreFilterCOP

◆ ReadPoseExtraScoreFilterOP

typedef utility::pointer::shared_ptr< ReadPoseExtraScoreFilter > protocols::simple_filters::ReadPoseExtraScoreFilterOP

◆ RepeatParameterFilterCOP

typedef utility::pointer::shared_ptr< RepeatParameterFilter const > protocols::simple_filters::RepeatParameterFilterCOP

◆ RepeatParameterFilterOP

typedef utility::pointer::shared_ptr< RepeatParameterFilter > protocols::simple_filters::RepeatParameterFilterOP

◆ ResidueDepthDataCOP

typedef utility::pointer::shared_ptr< ResidueDepthData const > protocols::simple_filters::ResidueDepthDataCOP

◆ ResidueDepthDataOP

typedef utility::pointer::shared_ptr< ResidueDepthData > protocols::simple_filters::ResidueDepthDataOP

◆ ResidueIEFilterCOP

typedef utility::pointer::shared_ptr< ResidueIEFilter const > protocols::simple_filters::ResidueIEFilterCOP

◆ ResidueIEFilterOP

typedef utility::pointer::shared_ptr< ResidueIEFilter > protocols::simple_filters::ResidueIEFilterOP

◆ SaveResfileToDiskFilterCOP

typedef utility::pointer::shared_ptr< SaveResfileToDiskFilter const > protocols::simple_filters::SaveResfileToDiskFilterCOP

◆ SaveResfileToDiskFilterOP

typedef utility::pointer::shared_ptr< SaveResfileToDiskFilter > protocols::simple_filters::SaveResfileToDiskFilterOP

◆ SAXSScoreFilterCOP

typedef utility::pointer::shared_ptr< SAXSScoreFilter const > protocols::simple_filters::SAXSScoreFilterCOP

◆ SAXSScoreFilterOP

typedef utility::pointer::shared_ptr< SAXSScoreFilter > protocols::simple_filters::SAXSScoreFilterOP

◆ SecretionPredictionFilterCOP

typedef utility::pointer::shared_ptr< SecretionPredictionFilter const > protocols::simple_filters::SecretionPredictionFilterCOP

◆ SecretionPredictionFilterOP

typedef utility::pointer::shared_ptr< SecretionPredictionFilter > protocols::simple_filters::SecretionPredictionFilterOP

◆ SelectRDC_EvaluatorCOP

typedef utility::pointer::shared_ptr< SelectRDC_Evaluator const > protocols::simple_filters::SelectRDC_EvaluatorCOP

◆ SelectRDC_EvaluatorOP

typedef utility::pointer::shared_ptr< SelectRDC_Evaluator > protocols::simple_filters::SelectRDC_EvaluatorOP

◆ ShapeComplementarityFilterCOP

typedef utility::pointer::shared_ptr< ShapeComplementarityFilter const > protocols::simple_filters::ShapeComplementarityFilterCOP

◆ ShapeComplementarityFilterOP

typedef utility::pointer::shared_ptr< ShapeComplementarityFilter > protocols::simple_filters::ShapeComplementarityFilterOP

◆ SimpleHbondsToAtomFilterCOP

typedef utility::pointer::shared_ptr< SimpleHbondsToAtomFilter const > protocols::simple_filters::SimpleHbondsToAtomFilterCOP

◆ SimpleHbondsToAtomFilterOP

typedef utility::pointer::shared_ptr< SimpleHbondsToAtomFilter > protocols::simple_filters::SimpleHbondsToAtomFilterOP

◆ SimpleMetricFilterCOP

typedef utility::pointer::shared_ptr< SimpleMetricFilter const > protocols::simple_filters::SimpleMetricFilterCOP

◆ SimpleMetricFilterOP

typedef utility::pointer::shared_ptr< SimpleMetricFilter > protocols::simple_filters::SimpleMetricFilterOP

◆ SSElementLengthFilterCOP

typedef utility::pointer::shared_ptr< SSElementLengthFilter const > protocols::simple_filters::SSElementLengthFilterCOP

◆ SSElementLengthFilterOP

typedef utility::pointer::shared_ptr< SSElementLengthFilter > protocols::simple_filters::SSElementLengthFilterOP

◆ SSElementMotifContactFilterCOP

typedef utility::pointer::shared_ptr< SSElementMotifContactFilter const > protocols::simple_filters::SSElementMotifContactFilterCOP

◆ SSElementMotifContactFilterOP

typedef utility::pointer::shared_ptr< SSElementMotifContactFilter > protocols::simple_filters::SSElementMotifContactFilterOP

◆ SSMotifFinderCOP

typedef utility::pointer::shared_ptr< SSMotifFinder const > protocols::simple_filters::SSMotifFinderCOP

◆ SSMotifFinderOP

typedef utility::pointer::shared_ptr< SSMotifFinder > protocols::simple_filters::SSMotifFinderOP

◆ StemFinderCOP

typedef utility::pointer::shared_ptr< StemFinder const > protocols::simple_filters::StemFinderCOP

◆ StemFinderOP

typedef utility::pointer::shared_ptr< StemFinder > protocols::simple_filters::StemFinderOP

◆ StructuralSimilarityEvaluatorCOP

typedef utility::pointer::shared_ptr< StructuralSimilarityEvaluator const > protocols::simple_filters::StructuralSimilarityEvaluatorCOP

◆ StructuralSimilarityEvaluatorOP

typedef utility::pointer::shared_ptr< StructuralSimilarityEvaluator > protocols::simple_filters::StructuralSimilarityEvaluatorOP

◆ TaskAwareSASAFilterCOP

typedef utility::pointer::shared_ptr< TaskAwareSASAFilter const > protocols::simple_filters::TaskAwareSASAFilterCOP

◆ TaskAwareSASAFilterOP

typedef utility::pointer::shared_ptr< TaskAwareSASAFilter > protocols::simple_filters::TaskAwareSASAFilterOP

◆ TaskAwareScoreTypeFilterCOP

typedef utility::pointer::shared_ptr< TaskAwareScoreTypeFilter const > protocols::simple_filters::TaskAwareScoreTypeFilterCOP

◆ TaskAwareScoreTypeFilterOP

typedef utility::pointer::shared_ptr< TaskAwareScoreTypeFilter > protocols::simple_filters::TaskAwareScoreTypeFilterOP

◆ TotalSasaFilterCOP

typedef utility::pointer::shared_ptr< TotalSasaFilter const > protocols::simple_filters::TotalSasaFilterCOP

◆ TotalSasaFilterOP

typedef utility::pointer::shared_ptr< TotalSasaFilter > protocols::simple_filters::TotalSasaFilterOP

◆ Worst9merFilterCOP

typedef utility::pointer::shared_ptr< Worst9merFilter const > protocols::simple_filters::Worst9merFilterCOP

◆ Worst9merFilterOP

typedef utility::pointer::shared_ptr< Worst9merFilter > protocols::simple_filters::Worst9merFilterOP

◆ Xform

using protocols::simple_filters::Xform = typedef numeric::xyzTransform<core::Real>

Enumeration Type Documentation

◆ BSAF_mode

enum protocols::simple_filters::BSAF_mode
Enumerator
BSAF_all_atoms 
BSAF_hydrophobic_atoms 
BSAF_polar_atoms 
BSAF_end_of_list 

◆ comparison_type

enum protocols::simple_filters::comparison_type

Enum that tells us how to interpret the cutoff set.

Enumerator
eq 
ne 
lt 
gt 
lt_or_eq 
gt_or_eq 
bogus 
comparison_type_total 

Function Documentation

◆ atom_distance() [1/2]

core::Real protocols::simple_filters::atom_distance ( core::conformation::Residue const &  r1,
std::string const &  a1,
core::conformation::Residue const &  r2,
std::string const &  a2 
)

compute the atomic distance between two atoms on two residues

References protocols::hybridization::r1, and protocols::hybridization::r2.

Referenced by res_rmsd().

◆ atom_distance() [2/2]

core::Real protocols::simple_filters::atom_distance ( core::pose::Pose const &  p1,
core::Size const  r1,
std::string const &  a1,
core::pose::Pose const &  p2,
core::Size const  r2,
std::string const &  a2 
)

References core::pose::Pose::conformation(), protocols::hybridization::r1, protocols::hybridization::r2, core::conformation::Conformation::residue(), and core::conformation::Residue::xyz().

◆ buried_unsat_hbond_filter_tracer()

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

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

◆ coords()

utility::vector1< numeric::xyzVector< core::Real > > protocols::simple_filters::coords ( core::pose::Pose const &  pose,
utility::vector1< core::Size > const  positions 
)

References core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::add(), core::conformation::symmetry::VirtualCoordinate::add_coordinate_from_string(), protocols::ligand_docking::StartFrom::add_coords(), protocols::ligand_docking::StartFrom::add_coords_hash(), protocols::legacy_sewing::add_linker_segments(), core::membrane::add_shell(), core::conformation::UltraLightResidue::align_to_residue(), protocols::loop_grower::SheetSampler::alignPerfectCA(), protocols::loop_grower::SheetSampler::alignStrand(), protocols::rigid::RollMover::apply(), protocols::simple_moves::Tumble::apply(), protocols::matdes::SymDofMover::apply(), protocols::hybridization::CartesianHybridize::apply_frag(), protocols::hybridization::CartesianHybridize::apply_frame(), protocols::canonical_sampling::mc_convergence_checks::DataBuffer::array_to_farray(), protocols::qsar::scoring_grid::LipidMemGrid::atom_score(), protocols::fold_from_loops::movers::Ca_coord(), protocols::simple_moves::Ca_coord(), protocols::protein_interface_design::filters::Ca_coords(), protocols::simple_moves::Ca_coords(), protocols::toolbox::CA_superimpose(), protocols::design_opt::calc_pareto_front(), protocols::matdes::calc_pareto_front(), protocols::design_opt::calc_pareto_front_nbrs(), protocols::matdes::calc_pareto_front_nbrs(), core::optimization::cartesian_collect_torsional_deriv(), protocols::environment::com_calc(), core::chemical::sdf::MolWriter::compose_atoms(), core::chemical::sdf::MolWriter::compose_ctab(), protocols::loops::loop_closure::ccd::compute_single_direction_deviation(), core::membrane::concave_hull(), core::membrane::concave_shell(), core::membrane::convex_hull(), core::pack::scmin::CartSCMinMultifunc::dfunc(), protocols::qsar::scoring_grid::SingleGrid::diffuse_ring(), core::chemical::mainchain_potential::MainchainScoreTable::draw_random_mainchain_torsion_values(), protocols::ligand_docking::Transform::dump_conformer(), protocols::ligand_docking::TransformEnsemble::dump_conformer(), core::chemical::mainchain_potential::MainchainScoreTable::energies_from_probs(), core::chemical::mainchain_potential::MainchainScoreTable::energy(), core::chemical::mainchain_potential::MainchainScoreTable::energy_tensor(), protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::evaluate(), protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::evaluate_and_add(), protocols::canonical_sampling::mc_convergence_checks::DataBuffer::farray_to_array(), protocols::frag_picker::scores::FragmentCrmsd::fill_CA_coords(), protocols::frag_picker::scores::FragmentCrmsdResDepth::fill_CA_coords(), protocols::frag_picker::scores::FragmentDME::fill_CA_coords(), protocols::toolbox::fill_CA_coords(), protocols::frag_picker::scores::FragmentAllAtomCrmsd::fill_coords(), core::io::silent::ProteinSilentStruct_Template< T >::fill_struct(), core::chemical::mainchain_potential::MainchainScoreTable::finalize_de_novo_scoretable_from_energies(), core::membrane::find_closest(), core::membrane::find_farthest(), protocols::membrane::AqueousPoreFinder::find_max_z(), protocols::membrane::AqueousPoreFinder::find_min_z(), protocols::toolbox::fit_centered_coords(), protocols::sewing::hashing::LigandBindingResPlacer::generate_ligand_key(), core::membrane::get_angles(), protocols::loops::loop_closure::ccd::get_deviation(), core::membrane::get_distances(), protocols::toolbox::match_enzdes_util::LigandConformer::get_global_coords_as_FArray2D(), protocols::loops::loop_closure::ccd::get_overlap_pos(), protocols::qsar::scoring_grid::SingleGrid::get_point(), protocols::legacy_sewing::LegacyRepeatAssemblyMover::get_segment_coords(), protocols::relax::RangeRelaxMover::get_spherical_repack_residues(), core::chemical::mainchain_potential::MainchainScoreTable::increment_coords(), core::chemical::mainchain_potential::MainchainScoreTable::increment_energy_coords(), protocols::toolbox::InteratomicVarianceMatrix::init(), core::io::silent::ProteinSilentStruct_Template< T >::init_from_lines(), protocols::simple_moves::DEEROptimizeCoordsMover::init_model(), core::membrane::inside_polygon(), core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyVoxelGrid::is_buried(), core::chemical::mainchain_potential::MainchainScoreTable::iteratively_correct_energy_tensor(), protocols::sewing::hashing::LigandBindingResPlacer::LigandBindingResPlacer(), protocols::loops::loop_closure::ccd::load_coords_and_torsions(), core::chemical::rdkit::RestypeToRDMol::Mol(), protocols::drug_design::ConformationSelectionToRDMol::Mol(), core::scoring::nmr::NMRDummySpinlabelConformer::NMRDummySpinlabelConformer(), core::io::silent::ProteinSilentStruct_Template< T >::operator=(), core::chemical::sdf::MolWriter::output_residue(), core::chemical::sdf::MolWriter::output_residue_impl(), protocols::ligand_docking::StartFrom::parse_startfrom_file(), protocols::match::output::UpstreamDownstreamCollisionFilter::passes_hardsphere_filter(), protocols::cyclic_peptide::CycpepRigidBodyPermutationMover::perturb_cycpep_pose_orientation(), protocols::ligand_docking::ga_ligand_dock::Pharmacophore::Pharmacophore(), core::membrane::points_in_triangle(), protocols::match::downstream::SecondaryMatcherToDownstreamResidue::prepare_for_hit_generation_at_target_build_point(), core::io::silent::ProteinSilentStruct_Template< T >::print_conformation(), protocols::qsar::scoring_grid::ShapeGrid::refresh(), protocols::relax::RangeRelaxMover::repack_spherical_range(), protocols::features::ProteinResidueConformationFeatures::report_features(), protocols::features::ResidueConformationFeatures::report_features(), protocols::legacy_sewing::result_to_five_ss_models(), protocols::legacy_sewing::result_to_models(), core::scoring::retrieve_coordinates(), protocols::cluster::calibur::rotate(), protocols::simple_moves::DEEROptimizeCoordsMover::score(), protocols::qsar::scoring_grid::LipidMemGrid::score(), protocols::qsar::scoring_grid::ShapeGrid::score(), protocols::match::downstream::TargetRotamerCoords::set_coords_for_clash_check(), protocols::features::ResidueConformationFeatures::set_coords_for_residue(), protocols::features::ProteinResidueConformationFeatures::set_coords_for_residue_from_compact_schema(), protocols::features::ResidueConformationFeatures::set_coords_for_residue_from_compact_schema(), protocols::features::ProteinResidueConformationFeatures::set_coords_for_residues(), protocols::qsar::scoring_grid::SingleGrid::set_distance_sphere_for_atom(), core::chemical::mainchain_potential::MainchainScoreTable::set_energy(), protocols::qsar::scoring_grid::SingleGrid::set_point(), core::pack::scmin::ResidueAtomTreeCollection::set_rescoords(), protocols::qsar::scoring_grid::SingleGrid::set_ring(), protocols::qsar::scoring_grid::SingleGrid::set_score_sphere_for_atom(), protocols::qsar::scoring_grid::SingleGrid::set_sphere(), core::chemical::mainchain_potential::MainchainScoreTable::set_up_cumulative_distribution_function(), protocols::topology_broker::CoordConstraintClaimer::superimpose(), protocols::toolbox::superimpose(), protocols::simple_filters::SSMotifFinder::superimpose_pose_on_template(), protocols::toolbox::superposition_transform(), protocols::motif_grafting::movers::MotifGraftMover::superposition_transform(), protocols::protein_interface_design::filters::RmsdSimpleFilter::superposition_transform(), core::optimization::tors_deriv_to_cartesian(), protocols::ligand_docking::ga_ligand_dock::Pharmacophore::update_com(), protocols::match::output::SingleDownstreamResidueWriter::write_downstream_coordinates(), core::chemical::mainchain_potential::MainchainScoreTable::write_mainchain_scoretable_to_stream(), and protocols::qsar::RenderGridsToKinemage::write_points().

◆ determinant()

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

References determinant_sign().

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

◆ determinant_sign()

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

Referenced by determinant().

◆ dssp()

std::string protocols::simple_filters::dssp ( core::pose::Pose const &  pose)

potentially useful utility functions

read dssp for a pose and return a string

Referenced by protocols::fold_from_loops::utils::Nub::add_binders(), protocols::denovo_design::components::SheetDB::add_sheets_from_pose(), protocols::antibody::design::AntibodyDesignMover::apply(), protocols::fold_from_loops::movers::DisplayPoseLabelsMover::apply(), protocols::legacy_sewing::LegacyAppendAssemblyMover::apply(), protocols::loop_build::LoopBuildMover::apply(), protocols::moves::DsspMover::apply(), protocols::pose_sewing::movers::BlockwiseAnalysisMover::apply(), protocols::pose_sewing::movers::OmnibusDisulfideAnalysisLabelerMover::apply(), protocols::pose_sewing::movers::SewAnythingAddMover::apply(), protocols::protein_interface_design::movers::LoopMoverFromCommandLine::apply(), protocols::protein_interface_design::movers::LoopRemodel::apply(), protocols::seeded_abinitio::GrowPeptides::apply(), protocols::seeded_abinitio::SegmentHybridizer::apply(), protocols::splice::FindEndpointsOperation::apply(), protocols::evolution::AlignmentAAFinder::apply(), protocols::evolution::AlignmentGapInserter::apply(), protocols::fldsgn::filters::StrandCurvatureByLevels::apply(), protocols::fldsgn::filters::StrandHelixGeometryFilter::apply(), protocols::simple_filters::StemFinder::apply(), protocols::fold_from_loops::utils::Nub::apply(), protocols::fldsgn::BluePrintBDR::apply(), protocols::flxbb::InterlockAroma::apply(), protocols::forge::components::BDR::apply(), protocols::forge::remodel::RemodelMover::apply(), protocols::splice::Splice::apply(), protocols::task_operations::DsspDesignOperation::apply(), protocols::flxbb::LayerDesignOperation::apply(), protocols::pack_interface::ProteinProteinInterfaceUpweighter::apply(), protocols::antibody::design::AntibodyDesignMover::apply_to_cdr(), protocols::jumping::assign_ss_dssp(), protocols::protein_interface_design::best_cutpoint(), protocols::analysis::InterfaceAnalyzerMover::calc_per_residue_and_regional_data(), protocols::surface_docking::FullatomRelaxMover::calc_secondary_struct(), protocols::surface_docking::SurfaceDockingProtocol::calc_secondary_structure(), protocols::surface_docking::SurfaceDockingProtocol::calc_secondary_structure_with_surface(), protocols::fldsgn::topology::calc_strand_pairing_set(), core::simple_metrics::metrics::SecondaryStructureMetric::calculate(), protocols::splice::calculate_rmsd(), protocols::seeded_abinitio::SegmentHybridizer::check_and_create_fragments(), protocols::rbsegment_relax::ConfChangeMover::check_or_create_fragments(), protocols::forge::remodel::RemodelData::collectInsertionPose(), protocols::simple_filters::Worst9merFilter::compute(), protocols::protein_interface_design::filters::AtomicContactCountFilter::compute(), protocols::denovo_design::filters::ExposedHydrophobicsFilter::compute(), protocols::denovo_design::filters::SSPredictionFilter::compute(), protocols::fldsgn::filters::HelixBendFilter::compute(), protocols::simple_filters::MotifScoreFilter::compute(), protocols::fldsgn::filters::InterlockingAromaFilter::compute(), protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter::compute(), protocols::fldsgn::filters::SecondaryStructureCountFilter::compute(), protocols::fldsgn::filters::SecondaryStructureHasResidueFilter::compute(), protocols::fldsgn::filters::SecondaryStructureFilter::compute(), core::select::util::SelectResiduesByLayer::compute(), protocols::denovo_design::filters::SSShapeComplementarityFilter::compute_from_ss_info(), protocols::flxbb::constraints_sheet(), protocols::pose_sewing::data_storage::TerminalDSSPSortedPoseVector::convert_pose_into_segment_vector(), protocols::legacy_sewing::create_alpha_beta_models_table(), protocols::hybridization::create_fragment_set(), protocols::legacy_sewing::scoring::LegacyMotifScorer::dump_motif(), core::energy_methods::CenPairMotifDegreeEnergy::finalize_total_energy(), core::energy_methods::CenPairMotifEnergy::finalize_total_energy(), protocols::aa_composition::find_helices_over_length(), protocols::splice::Splice::find_non_active_site_cut_site(), protocols::splice::SpliceOut::find_non_active_site_cut_site(), protocols::features::ModelFeatures::find_segments(), protocols::simple_filters::HelixHelixAngleFilter::get_helix_start_stop(), protocols::indexed_structure_store::SSHashedFragmentStore::get_hits_below_rms(), protocols::pose_length_moves::AnalyzeLoopModeling::get_loops(), protocols::pose_length_moves::FixAllLoopsMover::get_loops(), protocols::relax::RepeatProteinRelax::get_midpoint_longest_loop(), protocols::membrane::get_secstruct(), core::select::residue_selector::SecondaryStructureSelector::get_secstruct(), protocols::denovo_design::residue_selectors::PairedSheetResidueSelector::get_secstruct(), protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::get_secstruct(), protocols::fldsgn::filters::SheetTopologyFilter::get_secstruct(), protocols::fldsgn::SheetConstraintGenerator::get_secstruct(), protocols::struct_fragment::StructFragmentMover::get_secstruct(), protocols::fldsgn::filters::HSSTripletFilter::get_secstruct(), protocols::fldsgn::potentials::SetSecStructEnergies::get_secstruct(), protocols::pose_metric_calculators::RotamerRecovery::get_ss(), protocols::simple_ddg::SSElementBisectddGFilter::get_ss_elements(), protocols::simple_filters::SSElementLengthFilter::get_ss_elements(), protocols::simple_filters::SSElementMotifContactFilter::get_ss_elements(), core::energy_methods::SSElementMotifContactEnergy::get_ss_elements(), protocols::features::SmotifFeatures::get_ss_segments(), protocols::simple_filters::SSElementMotifContactFilter::get_SSelements_in_contact(), core::energy_methods::SSElementMotifContactEnergy::get_SSelements_in_contact(), protocols::pose_creation::MergePDBatOverlapMover::increase_range_to_ignore_ss_element(), protocols::pose_creation::MergePDBMover::increase_range_to_ignore_ss_element(), protocols::denovo_design::components::StructureDataFactory::infer_from_pose(), protocols::comparative_modeling::initialize_ss(), protocols::legacy_sewing::scoring::LegacyPartnerMotifScorer::interface_motif_score(), protocols::sewing::scoring::PartnerMotifScorer::interface_motif_score(), protocols::sewing::scoring::SubsetPartnerMotifScorer::interface_motif_score(), protocols::loops::loopfinder(), protocols::fold_from_loops::NubInitioMover::make_unfolded_pose(), protocols::splice::neighbors_in_vector(), protocols::sewing::hashing::LigandBindingResPlacer::parse_ligand_files(), protocols::seeded_abinitio::CloseFold::parse_my_tag(), protocols::seeded_abinitio::DefineMovableLoops::parse_my_tag(), core::select::residue_selector::SSElementSelector::parse_ss(), protocols::pose_creation::SliceToMiniProteinMover::parse_ss(), protocols::splice::SpliceOut::place_cut_site_in_segment(), protocols::pose_sewing::data_storage::DsspShiftArray::populate(), protocols::pose_sewing::data_storage::TerminalDSSPSortedPoseVector::populate_from_pdb_list(), protocols::pose_sewing::data_storage::PoseSegment::PoseSegment(), positions_in_secstruct(), protocols::fold_from_loops::NubInitioMover::post_process(), protocols::denovo_design::components::prune_unpaired_residues(), protocols::splice::AlignEndsMover::reference_positions(), protocols::denovo_design::components::reorder_chains(), protocols::features::strand_assembly::SandwichFeatures::report_features(), protocols::legacy_sewing::result_to_five_ss_models(), protocols::legacy_sewing::result_to_models(), protocols::mpi_refinement::WorkUnit_RamaPerturber::run(), protocols::sic_dock::XfoxmScore::score(), protocols::fldsgn::filters::HelixPairingFilter::secstruct(), protocols::moves::PyMOLMover::send_ss(), protocols::normalmode::NormalMode::set_harmonic_constant_map(), protocols::forge::remodel::RemodelLoopMover::set_ideal_helices(), protocols::fldsgn::BluePrintBDR::set_instruction_blueprint(), core::energy_methods::P_AA_ss_Energy::setup_for_minimizing(), core::energy_methods::P_AA_ss_Energy::setup_for_scoring(), core::scoring::hbonds::HBondEnergy::setup_for_scoring(), protocols::frag_picker::FragmentScoreFilter::setup_fragment_picker(), protocols::forge::remodel::RemodelMover::setup_remodel_data_for_loop_btw_parametric_components(), protocols::pose_sewing::data_storage::TerminalDSSPSortedPoseVector::simultaneously_populate_and_write_segment_file_pdb_using_stored_motifs(), protocols::pose_sewing::data_storage::TerminalDSSPSortedPoseVector::store_pose(), protocols::features::HelixCapFeatures::write_schema_to_db(), protocols::features::ResidueSecondaryStructureFeatures::write_schema_to_db(), and protocols::features::SecondaryStructureSegmentFeatures::write_schema_to_db().

◆ energy_per_residue_filter_tracer()

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

Referenced by protocols::simple_filters::EnergyPerResidueFilter::apply(), protocols::simple_filters::EnergyPerResidueFilter::apply_helper(), protocols::simple_filters::EnergyPerResidueFilter::compute(), and protocols::simple_filters::EnergyPerResidueFilter::parse_my_tag().

◆ get_contact_features()

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 core::chemical::element::N, core::pose::Pose::residue(), core::pose::Pose::size(), and core::conformation::Residue::xyz().

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

◆ get_string_comparison_type_map()

std::map< std::string, comparison_type > protocols::simple_filters::get_string_comparison_type_map ( )

References eq, gt, gt_or_eq, lt, lt_or_eq, and ne.

Referenced by get_string_comparison_type_strings(), and protocols::simple_filters::SimpleMetricFilter::parse_my_tag().

◆ get_string_comparison_type_strings()

utility::vector1< std::string > protocols::simple_filters::get_string_comparison_type_strings ( )

References get_string_comparison_type_map().

Referenced by protocols::simple_filters::SimpleMetricFilter::provide_xml_schema().

◆ load_poses()

utility::vector1< core::pose::PoseOP > protocols::simple_filters::load_poses ( utility::vector1< std::string > const &  filenames)

load PDBs into a vector

References core::import_pose::PDB_file, core::import_pose::pose_from_file(), and TR().

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

◆ mycomp()

bool protocols::simple_filters::mycomp ( const std::pair< core::Real, core::Size > &  lhs,
const std::pair< core::Real, core::Size > &  rhs 
)

Referenced by protocols::simple_filters::ResidueDepthFilter::get_residue_similarity().

◆ neighbor_type_filter_tracer()

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

Referenced by protocols::simple_filters::NeighborTypeFilter::apply(), and protocols::simple_filters::NeighborTypeFilter::parse_my_tag().

◆ NeighborType_subelement_ct_name()

std::string protocols::simple_filters::NeighborType_subelement_ct_name ( std::string const &  name)

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

◆ pct_features_in_common()

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().

◆ positions_in_secstruct()

utility::vector1< core::Size > protocols::simple_filters::positions_in_secstruct ( core::pose::Pose const &  pose)

find helix, sheet positions in dssp

References dssp().

◆ print_nmer_svm_energy_data()

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

References protocols::jd2::current_output_name(), protocols::jd2::jd2_used(), and core::conformation::membrane::out.

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

◆ quat2R()

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

References protocols::simple_filters::Quat::w, protocols::simple_filters::Quat::x, protocols::simple_filters::Quat::y, and protocols::simple_filters::Quat::z.

Referenced by protocols::simple_filters::SymmetricMotifFilter::process_motifs(), and protocols::ligand_docking::ga_ligand_dock::LigandConformer::to_pose().

◆ R2quat()

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

References core::chemical::element::S, protocols::simple_filters::Quat::w, protocols::simple_filters::Quat::x, protocols::simple_filters::Quat::y, and protocols::simple_filters::Quat::z.

Referenced by protocols::simple_filters::SymmetricMotifFilter::process_motifs(), and protocols::ligand_docking::ga_ligand_dock::LigandConformer::update_conf().

◆ res_res_min_distance()

core::Real protocols::simple_filters::res_res_min_distance ( core::pose::Pose const &  p1,
core::Size const  r1,
core::pose::Pose const &  p2,
core::Size const  r2 
)

find the minimal atom-atom distance between two residues

References core::conformation::Residue::atom(), core::pose::Pose::conformation(), core::conformation::Residue::natoms(), protocols::hybridization::r1, protocols::hybridization::r2, and core::conformation::Conformation::residue().

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

◆ res_rmsd()

core::Real protocols::simple_filters::res_rmsd ( utility::vector1< core::Size > const  pose_res_for_rmsd,
utility::vector1< core::Size > const  template_res_for_rmsd,
core::pose::Pose const &  copy_pose,
core::pose::Pose const &  template_pose 
)

References atom_distance(), core::pose::Pose::conformation(), protocols::hybridization::r1, protocols::hybridization::r2, and core::conformation::Conformation::residue().

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

◆ residue_burial_filter_tracer()

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

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

◆ residue_distance_filter_tracer()

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

Referenced by protocols::simple_filters::ResidueDistanceFilter::apply(), and protocols::simple_filters::ResidueDistanceFilter::parse_my_tag().

◆ residues_in_interface_tracer()

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

Referenced by protocols::simple_filters::ResiduesInInterfaceFilter::apply(), and protocols::simple_filters::ResiduesInInterfaceFilter::parse_my_tag().

◆ RMSwrapper()

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 protocols::mean_field::min(), and core::scoring::rms.

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

◆ sidechain_rmsd_filter_tracer()

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

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

◆ TR() [1/43]

static basic::Tracer protocols::simple_filters::TR ( "protocols.filters.AtomicContactFilter"  )
static

◆ TR() [2/43]

static basic::Tracer protocols::simple_filters::TR ( "protocols.filters.AtomicDistanceFilter"  )
static

◆ TR() [3/43]

static basic::Tracer protocols::simple_filters::TR ( "protocols.filters.ChainCountFilter"  )
static

◆ TR() [4/43]

static basic::Tracer protocols::simple_filters::TR ( "protocols.filters.PoseInfoFilter"  )
static

◆ TR() [5/43]

static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.AngleToVector"  )
static

Referenced by protocols::simple_filters::SpanTopologyMatchPoseFilter::actual_topology(), protocols::simple_filters::ResidueCountFilter::add_residue_property_by_name(), protocols::simple_filters::SSElementMotifContactFilter::apply(), protocols::simple_filters::Worst9merFilter::apply(), protocols::simple_filters::ResidueDepthFilter::apply(), protocols::simple_filters::AtomicContactFilter::apply(), protocols::simple_filters::AtomicDistanceFilter::apply(), protocols::simple_filters::AveragePathLengthFilter::apply(), protocols::simple_filters::BuriedSurfaceAreaFilter::apply(), protocols::simple_filters::ChainBreak::apply(), protocols::simple_filters::ChainCountFilter::apply(), protocols::simple_filters::DisulfideEntropyFilter::apply(), protocols::simple_filters::FileRemoveFilter::apply(), protocols::simple_filters::InterfaceSasaFilter::apply(), protocols::simple_filters::LongestContinuousPolarSegmentFilter::apply(), protocols::simple_filters::MembAccesResidueLipophilicityFilter::apply(), protocols::simple_filters::MPSpanAngleFilter::apply(), protocols::simple_filters::MutationsFilter::apply(), protocols::simple_filters::NetChargeFilter::apply(), protocols::simple_filters::NMerPSSMEnergyFilter::apply(), protocols::simple_filters::NMerSVMEnergyFilter::apply(), protocols::simple_filters::PoseComment::apply(), protocols::simple_filters::ResidueCountFilter::apply(), protocols::simple_filters::ResidueLipophilicityFilter::apply(), protocols::simple_filters::ResidueSelectionDistanceFilter::apply(), protocols::simple_filters::ResidueSetChainEnergyFilter::apply(), protocols::simple_filters::SequenceDistance::apply(), protocols::simple_filters::SimpleMetricFilter::apply(), protocols::simple_filters::SSMotifFinder::apply(), protocols::simple_filters::StemFinder::apply(), protocols::simple_filters::SymmetricMotifFilter::apply(), protocols::simple_filters::TaskAwareScoreTypeFilter::apply(), protocols::simple_filters::TerminusDistanceFilter::apply(), protocols::simple_filters::TotalSasaFilter::apply(), protocols::simple_filters::DeltaFilter::baseline(), protocols::simple_filters::HelixHelixAngleFilter::calc_shortest_dist_by_atoms(), protocols::simple_filters::RepeatParameterFilter::calculate_helical_parameters_helper(), protocols::simple_filters::ReportFilter::checkpoint_read(), protocols::simple_filters::ReportFilter::checkpoint_write(), protocols::simple_filters::ResidueDepthFilter::compare_by_superposition(), protocols::simple_filters::SimpleMetricFilter::compare_composites(), protocols::simple_filters::SimpleMetricFilter::compare_metric(), protocols::simple_filters::SSElementMotifContactFilter::compute(), protocols::simple_filters::Worst9merFilter::compute(), protocols::simple_filters::AngleToVector::compute(), protocols::simple_filters::AtomicContactFilter::compute(), protocols::simple_filters::AtomicDistanceFilter::compute(), protocols::simple_filters::ChainBreak::compute(), protocols::simple_filters::DeltaFilter::compute(), protocols::simple_filters::HelixHelixAngleFilter::compute(), protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter::compute(), protocols::simple_filters::InterfaceSasaFilter::compute(), protocols::simple_filters::MembAccesResidueLipophilicityFilter::compute(), protocols::simple_filters::MPSpanAngleFilter::compute(), protocols::simple_filters::NetChargeFilter::compute(), protocols::simple_filters::NonSequentialNeighborsFilter::compute(), protocols::simple_filters::PoseInfoFilter::compute(), protocols::simple_filters::ResidueLipophilicityFilter::compute(), protocols::simple_filters::SequenceDistance::compute(), protocols::simple_filters::SimpleHbondsToAtomFilter::compute(), protocols::simple_filters::SpanTopologyMatchPoseFilter::compute(), protocols::simple_filters::TMsAACompFilter::compute(), protocols::simple_filters::TMsSpanMembraneFilter::compute(), protocols::simple_filters::TotalSasaFilter::compute(), protocols::simple_filters::MutationsFilter::compute(), protocols::simple_filters::TaskAwareScoreTypeFilter::compute(), protocols::simple_filters::TaskAwareSASAFilter::compute(), protocols::simple_filters::LongestContinuousPolarSegmentFilter::compute(), protocols::simple_filters::BuriedSurfaceAreaFilter::compute(), protocols::simple_filters::SymmetricMotifFilter::compute_d2(), protocols::simple_filters::InterfaceHbondsFilter::compute_hbonds(), protocols::simple_filters::SSMotifFinder::compute_jump(), protocols::simple_filters::InterfaceHbondsFilter::compute_salt_bridges(), protocols::simple_filters::ResidueDepthCalculator::duplicate_waterbox(), protocols::simple_filters::ResidueDepthCalculator::estimate_sidechain_depth(), protocols::simple_filters::TMsAACompFilter::find_aa_composition(), protocols::simple_filters::HelixHelixAngleFilter::find_closest_pnts(), protocols::simple_filters::HelixHelixAngleFilter::find_closest_res(), protocols::simple_filters::ResidueDepthCalculator::get_exclusion_index(), protocols::simple_filters::HelixHelixAngleFilter::get_helix_start_stop(), protocols::simple_filters::ResidueDepthFilter::get_residue_similarity(), protocols::simple_filters::ResidueDepthFilter::get_SDE_score(), load_poses(), protocols::simple_filters::Worst9merFilter::parse_my_tag(), protocols::simple_filters::AngleToVector::parse_my_tag(), protocols::simple_filters::AtomicContactFilter::parse_my_tag(), protocols::simple_filters::AtomicDistanceFilter::parse_my_tag(), protocols::simple_filters::AveragePathLengthFilter::parse_my_tag(), protocols::simple_filters::ChainBreak::parse_my_tag(), protocols::simple_filters::DeltaFilter::parse_my_tag(), protocols::simple_filters::DisulfideEntropyFilter::parse_my_tag(), protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter::parse_my_tag(), protocols::simple_filters::InterfaceSasaFilter::parse_my_tag(), protocols::simple_filters::MPSpanAngleFilter::parse_my_tag(), protocols::simple_filters::MutationsFilter::parse_my_tag(), protocols::simple_filters::NetChargeFilter::parse_my_tag(), protocols::simple_filters::NonSequentialNeighborsFilter::parse_my_tag(), protocols::simple_filters::PoseComment::parse_my_tag(), protocols::simple_filters::ReportFilter::parse_my_tag(), protocols::simple_filters::ResidueCountFilter::parse_my_tag(), protocols::simple_filters::ResidueLipophilicityFilter::parse_my_tag(), protocols::simple_filters::ResidueSetChainEnergyFilter::parse_my_tag(), protocols::simple_filters::SpanTopologyMatchPoseFilter::parse_my_tag(), protocols::simple_filters::SSMotifFinder::parse_my_tag(), protocols::simple_filters::StemFinder::parse_my_tag(), protocols::simple_filters::TaskAwareScoreTypeFilter::parse_my_tag(), protocols::simple_filters::TerminusDistanceFilter::parse_my_tag(), protocols::simple_filters::TotalSasaFilter::parse_my_tag(), protocols::simple_filters::SimpleHbondsToAtomFilter::parse_my_tag(), protocols::simple_filters::SymmetricMotifFilter::parse_my_tag(), protocols::simple_filters::ResidueDepthCalculator::pert_protein(), protocols::simple_filters::SymmetricMotifFilter::process_motifs(), protocols::simple_filters::ResidueDepthFilter::read_db(), protocols::simple_filters::ResidueDepthCalculator::read_unit_waterbox(), protocols::simple_filters::MPSpanAngleFilter::report(), protocols::simple_filters::SymmetricMotifFilter::report(), protocols::simple_filters::BuriedSurfaceAreaFilter::report_sm(), protocols::simple_filters::MembAccesResidueLipophilicityFilter::report_sm(), protocols::simple_filters::MPSpanAngleFilter::report_sm(), protocols::simple_filters::SimpleMetricFilter::report_sm(), protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter::sanity_check(), protocols::simple_filters::ResidueDepthFilter::search_close_frags(), protocols::simple_filters::SaveResfileToDiskFilter::select_residues(), protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter::set_scorefxn(), protocols::simple_filters::SimpleMetricFilter::set_use_cached_data(), protocols::simple_filters::ResidueDepthCalculator::stack_and_getaverage(), and protocols::simple_filters::Worst9merFilter::write_mean_median().

◆ TR() [6/43]

static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.AveragePathLengthFilter"  )
static

◆ TR() [7/43]

static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.ChainBreak"  )
static

◆ TR() [8/43]

static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.DeltaFilter"  )
static

◆ TR() [9/43]

static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.DisulfideEntropyFilter"  )
static

◆ TR() [10/43]

static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.ExpiryFilter"  )
static

◆ TR() [11/43]

static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.FileExistFilter"  )
static

◆ TR() [12/43]

static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.FileRemoveFilter"  )
static

◆ TR() [13/43]

static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.HelixHelixAngleFilter"  )
static

◆ tr() [1/2]

static basic::Tracer protocols::simple_filters::tr ( "protocols.simple_filters.HolesFilter"  )
static

Referenced by protocols::simple_filters::ChiWellRmsdEvaluatorCreator::add_evaluators(), protocols::simple_filters::ContactMapEvaluatorCreator::add_evaluators(), protocols::simple_filters::RmsdEvaluatorCreator::add_evaluators(), protocols::simple_filters::SecretionPredictionFilter::apply(), protocols::simple_filters::SSElementLengthFilter::apply(), protocols::simple_filters::ChiWellRmsdEvaluator::apply(), protocols::simple_filters::TruncatedScoreEvaluator::apply(), protocols::simple_filters::ExternalEvaluator::apply(), protocols::simple_filters::RmsdEvaluator::apply(), protocols::simple_filters::SAXSScoreFilter::apply(), protocols::simple_filters::ContactMolecularSurfaceFilter::apply(), protocols::simple_filters::HolesFilter::apply(), protocols::simple_filters::InterRepeatContactFilter::apply(), protocols::simple_filters::IntraRepeatContactFilter::apply(), protocols::simple_filters::PackStatFilter::apply(), protocols::simple_filters::RangeFilter::apply(), protocols::simple_filters::ShapeComplementarityFilter::apply(), protocols::simple_filters::SecretionPredictionFilter::compute(), protocols::simple_filters::ResidueIEFilter::compute(), protocols::simple_filters::ContactMolecularSurfaceFilter::compute(), protocols::simple_filters::HolesFilter::compute(), protocols::simple_filters::PackStatFilter::compute(), protocols::simple_filters::ShapeComplementarityFilter::compute(), protocols::simple_filters::ResidueIEFilter::compute_resnums(), protocols::simple_filters::ExternalEvaluator::ExternalEvaluator(), protocols::simple_filters::InterRepeatContactFilter::parse_my_tag(), protocols::simple_filters::IntraRepeatContactFilter::parse_my_tag(), protocols::simple_filters::PackStatFilter::parse_my_tag(), protocols::simple_filters::ContactMolecularSurfaceFilter::parse_my_tag(), protocols::simple_filters::HolesFilter::parse_my_tag(), protocols::simple_filters::ShapeComplementarityFilter::parse_my_tag(), protocols::simple_filters::ResidueIEFilter::parse_my_tag(), protocols::simple_filters::ShapeComplementarityFilter::print_sc_results(), protocols::simple_filters::ContactMolecularSurfaceFilter::report_sm(), protocols::simple_filters::ShapeComplementarityFilter::report_sm(), protocols::simple_filters::ScoreEvaluator::ScoreEvaluator(), protocols::simple_filters::ContactMolecularSurfaceFilter::setup_from_selectors(), protocols::simple_filters::ShapeComplementarityFilter::setup_from_selectors(), protocols::simple_filters::ShapeComplementarityFilter::setup_multi_component_symm(), protocols::simple_filters::TruncatedScoreEvaluator::TruncatedScoreEvaluator(), and protocols::simple_filters::ExternalEvaluator::~ExternalEvaluator().

◆ TR() [14/43]

static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.InterfaceHbondsFilter"  )
static

◆ TR() [15/43]

static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.InterfaceHydrophobicResidueContactsFilter"  )
static

◆ TR() [16/43]

static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.InterfaceSasaFilter"  )
static

◆ TR() [17/43]

static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.MembAccesResidueLipophilicityFilter"  )
static

◆ TR() [18/43]

static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.MPSpanAngleFilter"  )
static

◆ TR() [19/43]

static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.MutationsFilter"  )
static

◆ TR() [20/43]

static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.NetChargeFilter"  )
static

◆ TR() [21/43]

static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.NMerPSSMEnergyFilter"  )
static

◆ TR() [22/43]

static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.NMerSVMEnergyFilter"  )
static

◆ TR() [23/43]

static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.NonSequentialNeighborsFilter"  )
static

◆ TR() [24/43]

static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.PoseComment"  )
static

◆ TR() [25/43]

static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.RepeatParameterFilter"  )
static

◆ TR() [26/43]

static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.ReportFilter"  )
static

◆ TR() [27/43]

static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.ResidueChiralityFilter"  )
static

◆ TR() [28/43]

static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.ResidueCountFilter"  )
static

◆ TR() [29/43]

static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.ResidueDepthFilter"  )
static

◆ tr() [2/2]

static basic::Tracer protocols::simple_filters::tr ( "protocols.simple_filters.ResidueIEFilter"  )
static

◆ TR() [30/43]

static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.ResidueLipophilicityFilter"  )
static

◆ TR() [31/43]

static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.ResidueSelectionDistanceFilter"  )
static

◆ TR() [32/43]

static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.ResidueSetChainEnergyFilter"  )
static

◆ TR() [33/43]

static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.SequenceDistance"  )
static

◆ TR() [34/43]

static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.SpanTopologyMatchPoseFilter"  )
static

◆ TR() [35/43]

static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.SSMotifFinder"  )
static

◆ TR() [36/43]

static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.StemFinder"  )
static

◆ TR() [37/43]

static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.SymmetricMotifFilter"  )
static

◆ TR() [38/43]

static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.TaskAwareScoreTypeFilter"  )
static

◆ TR() [39/43]

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

◆ TR() [40/43]

static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.TMsAACompFilter"  )
static

◆ TR() [41/43]

static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.TMsSpanMembraneFilter"  )
static

◆ TR() [42/43]

static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.TotalSasaFilter"  )
static

◆ TR() [43/43]

static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_moves.MotifScoreFilter"  )
static

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

◆ write_to_file()

void protocols::simple_filters::write_to_file ( std::string const &  filename,
core::Size const  stem1,
core::Size const  stem2,
core::Real const  rmsd,
std::string const &  pdbname,
core::pose::Pose const &  pose 
)

References protocols::abinitio::filename(), and core::pose::Pose::pdb_info().

Referenced by protocols::simple_filters::SSMotifFinder::apply(), protocols::electron_density::DockPDBIntoDensityMover::apply_refinement(), protocols::canonical_sampling::SimulatedTempering::finalize_simulation(), protocols::canonical_sampling::SimulatedTempering::temperature_move(), and protocols::optimize_weights::PSSMOptEPositionData::write_to_file().

Variable Documentation

◆ energy_evaluator

core::energy_methods::ResidualDipolarCouplingEnergy protocols::simple_filters::energy_evaluator
static

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

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