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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  EXCN_CalcFailed
 Super-simple exception to be thrown when the SC calculator fails to compute. More...
 
class  EXCN_InitFailed
 Super-simple exception to be thrown when we can't initialize the SC calculator. More...
 
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  LeastNativeLike9merFilter
 
class  LeastNativeLike9merFilterCreator
 
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  LoopRmsdEvaluator
 
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
 
struct  nmer_svm_res_data
 
class  NMerPSSMEnergyFilter
 
class  NMerPSSMEnergyFilterCreator
 
class  NMerSVMEnergyFilter
 
class  NMerSVMEnergyFilterCreator
 
class  NonSequentialNeighborsFilter
 
class  NonSequentialNeighborsFilterCreator
 
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  ReadPoseExtraScoreFilter
 
class  ReadPoseExtraScoreFilterCreator
 
class  RegionalConnections
 
class  RepeatParameterFilter
 
class  RepeatParameterFilterCreator
 
class  ReportFilter
 
class  ReportFilterCreator
 
class  ResidueBurialFilter
 
class  ResidueBurialFilterCreator
 
class  ResidueChiralityFilter
 
class  ResidueChiralityFilterCreator
 
class  ResidueCountFilter
 
class  ResidueCountFilterCreator
 
class  ResidueDepthCalculator
 
struct  ResidueDepthData
 
class  ResidueDepthFilter
 
class  ResidueDepthFilterCreator
 
class  ResidueDepthFrag
 
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  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  SecretionPredictionFilter
 
class  SecretionPredictionFilterCreator
 
class  SelectGdtEvaluator
 
class  SelectMaxsubEvaluator
 
class  SelectRDC_Evaluator
 
class  SelectRmsdEvaluator
 
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  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...
 
class  SymmetricMotifFilter
 
class  SymmetricMotifFilterCreator
 
class  SymmetricRmsdEvaluator
 
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  TruncatedScoreEvaluator
 

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
< LeastNativeLike9merFilter
LeastNativeLike9merFilterOP
 
typedef
utility::pointer::shared_ptr
< LeastNativeLike9merFilter
const > 
LeastNativeLike9merFilterCOP
 
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
 

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::Sizepositions_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::scoring::methods::ResidualDipolarCouplingEnergy 
energy_evaluator
 

Typedef Documentation

typedef utility::pointer::shared_ptr< AngleToVector const > protocols::simple_filters::AngleToVectorCOP
typedef utility::pointer::shared_ptr< AngleToVector > protocols::simple_filters::AngleToVectorOP
typedef utility::pointer::shared_ptr< ChainCountFilter const > protocols::simple_filters::ChainCountFilterCOP
typedef utility::pointer::shared_ptr< ChainCountFilter > protocols::simple_filters::ChainCountFilterOP
typedef utility::pointer::shared_ptr< DeltaFilter const > protocols::simple_filters::DeltaFilterCOP
typedef utility::pointer::shared_ptr< DeltaFilter > protocols::simple_filters::DeltaFilterOP
typedef utility::pointer::shared_ptr< DomainInterfaceFilter const > protocols::simple_filters::DomainInterfaceFilterCOP
typedef utility::pointer::shared_ptr< HelixHelixAngleFilter const > protocols::simple_filters::HelixHelixAngleFilterCOP
typedef utility::pointer::shared_ptr< HolesFilter const > protocols::simple_filters::HolesFilterCOP
typedef utility::pointer::shared_ptr< HolesFilter > protocols::simple_filters::HolesFilterOP
typedef utility::pointer::shared_ptr< InterfaceHbondsFilter const > protocols::simple_filters::InterfaceHbondsFilterCOP
typedef utility::pointer::shared_ptr< InterfaceSasaFilter const > protocols::simple_filters::InterfaceSasaFilterCOP
typedef utility::pointer::shared_ptr< MotifScoreFilter const > protocols::simple_filters::MotifScoreFilterCOP
typedef utility::pointer::shared_ptr< MotifScoreFilter > protocols::simple_filters::MotifScoreFilterOP
typedef utility::pointer::shared_ptr< MutationsFilter const > protocols::simple_filters::MutationsFilterCOP
typedef utility::pointer::shared_ptr< MutationsFilter > protocols::simple_filters::MutationsFilterOP
typedef utility::pointer::shared_ptr< PackStatFilter const > protocols::simple_filters::PackStatFilterCOP
typedef utility::pointer::shared_ptr< PackStatFilter > protocols::simple_filters::PackStatFilterOP
typedef utility::pointer::shared_ptr< PDDFScoreFilter const > protocols::simple_filters::PDDFScoreFilterCOP
typedef utility::pointer::shared_ptr< PDDFScoreFilter > protocols::simple_filters::PDDFScoreFilterOP
typedef utility::pointer::shared_ptr< PoseComment const > protocols::simple_filters::PoseCommentCOP
typedef utility::pointer::shared_ptr< PoseComment > protocols::simple_filters::PoseCommentOP
typedef utility::pointer::shared_ptr< RangeFilter const > protocols::simple_filters::RangeFilterCOP
typedef utility::pointer::shared_ptr< RangeFilter > protocols::simple_filters::RangeFilterOP
typedef utility::pointer::shared_ptr< RepeatParameterFilter const > protocols::simple_filters::RepeatParameterFilterCOP
typedef utility::pointer::shared_ptr< ResidueDepthData const > protocols::simple_filters::ResidueDepthDataCOP
typedef utility::pointer::shared_ptr< ResidueDepthData > protocols::simple_filters::ResidueDepthDataOP
typedef utility::pointer::shared_ptr< ResidueIEFilter const > protocols::simple_filters::ResidueIEFilterCOP
typedef utility::pointer::shared_ptr< ResidueIEFilter > protocols::simple_filters::ResidueIEFilterOP
typedef utility::pointer::shared_ptr< SAXSScoreFilter const > protocols::simple_filters::SAXSScoreFilterCOP
typedef utility::pointer::shared_ptr< SAXSScoreFilter > protocols::simple_filters::SAXSScoreFilterOP
typedef utility::pointer::shared_ptr< SelectRDC_Evaluator const > protocols::simple_filters::SelectRDC_EvaluatorCOP
typedef utility::pointer::shared_ptr< SimpleMetricFilter const > protocols::simple_filters::SimpleMetricFilterCOP
typedef utility::pointer::shared_ptr< SSElementLengthFilter const > protocols::simple_filters::SSElementLengthFilterCOP
typedef utility::pointer::shared_ptr< SSMotifFinder const > protocols::simple_filters::SSMotifFinderCOP
typedef utility::pointer::shared_ptr< SSMotifFinder > protocols::simple_filters::SSMotifFinderOP
typedef utility::pointer::shared_ptr< StemFinder const > protocols::simple_filters::StemFinderCOP
typedef utility::pointer::shared_ptr< StemFinder > protocols::simple_filters::StemFinderOP
typedef utility::pointer::shared_ptr< TaskAwareSASAFilter const > protocols::simple_filters::TaskAwareSASAFilterCOP
typedef utility::pointer::shared_ptr< TotalSasaFilter const > protocols::simple_filters::TotalSasaFilterCOP
typedef utility::pointer::shared_ptr< TotalSasaFilter > protocols::simple_filters::TotalSasaFilterOP
using protocols::simple_filters::Xform = typedef numeric::xyzTransform<core::Real>

Enumeration Type Documentation

Enumerator
BSAF_all_atoms 
BSAF_hydrophobic_atoms 
BSAF_polar_atoms 
BSAF_end_of_list 

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

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 core::conformation::Residue::xyz().

Referenced by res_rmsd().

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 
)
static basic::Tracer protocols::simple_filters::buried_unsat_hbond_filter_tracer ( "protocols.simple_filters.BuriedUnsatHbondFilter"  )
static
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(), protocols::legacy_sewing::add_linker_segments(), core::conformation::UltraLightResidue::align_to_residue(), protocols::loop_grower::SheetSampler::alignPerfectCA(), protocols::loop_grower::SheetSampler::alignStrand(), protocols::rigid::RollMover::apply(), protocols::matdes::SymDofMover::apply(), protocols::simple_moves::Tumble::apply(), protocols::hybridization::CartesianHybridize::apply_frag(), protocols::hybridization::CartesianHybridize::apply_frame(), protocols::canonical_sampling::mc_convergence_checks::DataBuffer::array_to_farray(), protocols::simple_moves::Ca_coord(), protocols::fold_from_loops::movers::Ca_coord(), protocols::simple_moves::Ca_coords(), protocols::protein_interface_design::filters::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(), protocols::loops::loop_closure::ccd::compute_single_direction_deviation(), core::membrane::concave_shell(), core::pack::scmin::CartSCMinMultifunc::dfunc(), core::chemical::mainchain_potential::MainchainScoreTable::draw_random_mainchain_torsion_values(), protocols::ligand_docking::TransformEnsemble::dump_conformer(), protocols::ligand_docking::Transform::dump_conformer(), core::chemical::mainchain_potential::MainchainScoreTable::energies_from_probs(), 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::FragmentDME::fill_CA_coords(), protocols::frag_picker::scores::FragmentCrmsd::fill_CA_coords(), protocols::frag_picker::scores::FragmentCrmsdResDepth::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(), protocols::membrane::AqueousPoreFinder::find_max_z(), protocols::membrane::AqueousPoreFinder::find_min_z(), protocols::toolbox::fit_centered_coords(), protocols::loops::loop_closure::ccd::get_deviation(), protocols::toolbox::match_enzdes_util::LigandConformer::get_global_coords_as_FArray2D(), protocols::loops::loop_closure::ccd::get_overlap_pos(), protocols::legacy_sewing::LegacyRepeatAssemblyMover::get_segment_coords(), protocols::relax::RangeRelaxMover::get_spherical_repack_residues(), protocols::toolbox::InteratomicVarianceMatrix::init(), core::io::silent::ProteinSilentStruct_Template< T >::init_from_lines(), core::chemical::mainchain_potential::MainchainScoreTable::iteratively_correct_energy_tensor(), protocols::sewing::hashing::LigandBindingResPlacer::LigandBindingResPlacer(), protocols::loops::loop_closure::ccd::load_coords_and_torsions(), core::io::silent::ProteinSilentStruct_Template< T >::operator=(), core::chemical::sdf::MolWriter::output_residue(), protocols::ligand_docking::StartFrom::parse_startfrom_file(), protocols::ligand_docking::ga_ligand_dock::Pharmacophore::Pharmacophore(), 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(), protocols::qsar::scoring_grid::ShapeGrid::score(), protocols::match::downstream::TargetRotamerCoords::set_coords_for_clash_check(), protocols::features::ResidueConformationFeatures::set_coords_for_residue(), protocols::features::ResidueConformationFeatures::set_coords_for_residue_from_compact_schema(), protocols::features::ProteinResidueConformationFeatures::set_coords_for_residue_from_compact_schema(), protocols::features::ProteinResidueConformationFeatures::set_coords_for_residues(), core::chemical::mainchain_potential::MainchainScoreTable::set_up_cumulative_distribution_function(), protocols::topology_broker::CoordConstraintClaimer::superimpose(), protocols::simple_filters::SSMotifFinder::superimpose_pose_on_template(), protocols::toolbox::superposition_transform(), 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().

core::Real protocols::simple_filters::determinant ( bnu::matrix< core::Real > const &  m)
int protocols::simple_filters::determinant_sign ( const bnu::permutation_matrix< std::size_t > &  pm)

Referenced by determinant().

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

potentially useful utility functions

read dssp for a pose and return a string

References core::scoring::dssp::Dssp::dssp_reduced(), and core::scoring::dssp::Dssp::get_dssp_secstruct().

Referenced by protocols::fold_from_loops::utils::Nub::add_binders(), protocols::denovo_design::components::SheetDB::add_sheets_from_pose(), protocols::loop_build::LoopBuildMover::apply(), protocols::splice::AlignEndsMover::apply(), protocols::seeded_abinitio::GrowPeptides::apply(), protocols::simple_filters::StemFinder::apply(), protocols::seeded_abinitio::SegmentHybridizer::apply(), protocols::evolution::AlignmentAAFinder::apply(), protocols::fold_from_loops::movers::DisplayPoseLabelsMover::apply(), protocols::splice::FindEndpointsOperation::apply(), protocols::evolution::AlignmentGapInserter::apply(), protocols::pack_interface::ProteinProteinInterfaceUpweighter::apply(), protocols::moves::DsspMover::apply(), protocols::fold_from_loops::utils::Nub::apply(), protocols::protein_interface_design::movers::LoopMoverFromCommandLine::apply(), protocols::legacy_sewing::LegacyAppendAssemblyMover::apply(), protocols::protein_interface_design::movers::LoopRemodel::apply(), protocols::fldsgn::filters::StrandCurvatureByLevels::apply(), protocols::fldsgn::filters::StrandHelixGeometryFilter::apply(), protocols::flxbb::InterlockAroma::apply(), protocols::splice::Splice::apply(), protocols::antibody::design::AntibodyDesignMover::apply(), protocols::task_operations::DsspDesignOperation::apply(), protocols::fldsgn::BluePrintBDR::apply(), protocols::flxbb::LayerDesignOperation::apply(), protocols::forge::components::BDR::apply(), protocols::forge::remodel::RemodelMover::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::forge::remodel::RemodelData::collectInsertionPose(), protocols::denovo_design::filters::SSPredictionFilter::compute(), protocols::simple_filters::MotifScoreFilter::compute(), protocols::protein_interface_design::filters::AtomicContactCountFilter::compute(), protocols::fldsgn::filters::HelixBendFilter::compute(), protocols::denovo_design::filters::ExposedHydrophobicsFilter::compute(), protocols::simple_filters::LeastNativeLike9merFilter::compute(), protocols::fldsgn::filters::SecondaryStructureHasResidueFilter::compute(), protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter::compute(), protocols::fldsgn::filters::SecondaryStructureCountFilter::compute(), protocols::fldsgn::filters::InterlockingAromaFilter::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::legacy_sewing::create_alpha_beta_models_table(), protocols::hybridization::create_fragment_set(), protocols::legacy_sewing::scoring::LegacyMotifScorer::dump_motif(), core::scoring::methods::CenPairMotifDegreeEnergy::finalize_total_energy(), core::scoring::methods::CenPairMotifEnergy::finalize_total_energy(), protocols::aa_composition::find_helices_over_length(), protocols::splice::SpliceOut::find_non_active_site_cut_site(), protocols::splice::Splice::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::FixAllLoopsMover::get_loops(), protocols::pose_length_moves::AnalyzeLoopModeling::get_loops(), protocols::relax::RepeatProteinRelax::get_midpoint_longest_loop(), core::select::residue_selector::SecondaryStructureSelector::get_secstruct(), protocols::denovo_design::residue_selectors::PairedSheetResidueSelector::get_secstruct(), protocols::fldsgn::SheetConstraintGenerator::get_secstruct(), protocols::fldsgn::filters::SheetTopologyFilter::get_secstruct(), protocols::fldsgn::filters::HSSTripletFilter::get_secstruct(), protocols::fldsgn::potentials::SetSecStructEnergies::get_secstruct(), protocols::struct_fragment::StructFragmentMover::get_secstruct(), protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::get_secstruct(), protocols::membrane::get_secstruct(), protocols::pose_metric_calculators::RotamerRecovery::get_ss(), core::scoring::methods::SSElementMotifContactEnergy::get_ss_elements(), protocols::simple_ddg::SSElementBisectddGFilter::get_ss_elements(), protocols::simple_filters::SSElementLengthFilter::get_ss_elements(), protocols::simple_filters::SSElementMotifContactFilter::get_ss_elements(), protocols::features::SmotifFeatures::get_ss_segments(), core::scoring::methods::SSElementMotifContactEnergy::get_SSelements_in_contact(), protocols::simple_filters::SSElementMotifContactFilter::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::sewing::hashing::LigandBindingResPlacer::parse_ligand_files(), protocols::seeded_abinitio::DefineMovableLoops::parse_my_tag(), protocols::seeded_abinitio::CloseFold::parse_my_tag(), protocols::pose_creation::SliceToMiniProteinMover::parse_ss(), core::select::residue_selector::SSElementSelector::parse_ss(), protocols::splice::SpliceOut::place_cut_site_in_segment(), 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::scoring::methods::P_AA_ss_Energy::setup_for_minimizing(), core::scoring::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::features::ResidueSecondaryStructureFeatures::write_schema_to_db(), protocols::features::SecondaryStructureSegmentFeatures::write_schema_to_db(), and protocols::features::HelixCapFeatures::write_schema_to_db().

static basic::Tracer protocols::simple_filters::energy_per_residue_filter_tracer ( "protocols.simple_filters.EnergyPerResidueFilter"  )
static
boost::dynamic_bitset protocols::simple_filters::get_contact_features ( core::pose::Pose const &  pose,
core::Real const  dist_threshold,
std::string const &  atom_name,
core::Size const  min_seqsep = 12,
core::Size const  skip_res = 0 
)
std::map< std::string, comparison_type > protocols::simple_filters::get_string_comparison_type_map ( )
utility::vector1< std::string > protocols::simple_filters::get_string_comparison_type_strings ( )
utility::vector1< core::pose::PoseOP > protocols::simple_filters::load_poses ( utility::vector1< std::string > const &  filenames)
bool protocols::simple_filters::mycomp ( const std::pair< core::Real, core::Size > &  lhs,
const std::pair< core::Real, core::Size > &  rhs 
)
static basic::Tracer protocols::simple_filters::neighbor_type_filter_tracer ( "protocols.simple_filters.NeighborTypeFilter"  )
static
std::string protocols::simple_filters::NeighborType_subelement_ct_name ( std::string const &  name)
core::Real protocols::simple_filters::pct_features_in_common ( boost::dynamic_bitset<> const &  set1,
boost::dynamic_bitset<> const &  set2 
)
utility::vector1< core::Size > protocols::simple_filters::positions_in_secstruct ( core::pose::Pose const &  pose)

find helix, sheet positions in dssp

References dssp().

void protocols::simple_filters::print_nmer_svm_energy_data ( vector1< nmer_svm_res_data >  nmer_svm_pose_data)
void protocols::simple_filters::quat2R ( Quat &  Q,
numeric::xyzMatrix< core::Real R 
)
void protocols::simple_filters::R2quat ( numeric::xyzMatrix< core::Real R,
Quat &  Q 
)
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::pose::Pose::conformation(), and core::conformation::Conformation::residue().

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

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 
)
static basic::Tracer protocols::simple_filters::residue_burial_filter_tracer ( "protocols.simple_filters.ResidueBurialFilter"  )
static
static basic::Tracer protocols::simple_filters::residue_distance_filter_tracer ( "protocols.simple_filters.ResidueDistanceFilter"  )
static
static basic::Tracer protocols::simple_filters::residues_in_interface_tracer ( "protocols.simple_filters.ResiduesInInterfaceFilter"  )
static
core::Real protocols::simple_filters::RMSwrapper ( utility::vector1< numeric::xyzVector< core::Real > >  chainA,
utility::vector1< numeric::xyzVector< core::Real > >  chainB,
numeric::xyzMatrix< core::Real > &  R,
numeric::xyzVector< core::Real > &  preT,
numeric::xyzVector< core::Real > &  postT 
)
static basic::Tracer protocols::simple_filters::sidechain_rmsd_filter_tracer ( "protocols.simple_filters.SidechainRmsdFilter"  )
static
static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.NonSequentialNeighborsFilter"  )
static
static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.ExpiryFilter"  )
static
static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.PoseComment"  )
static
static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.FileExistFilter"  )
static
static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.ChainBreak"  )
static
static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.SequenceDistance"  )
static
static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.DeltaFilter"  )
static
static basic::Tracer protocols::simple_filters::TR ( "protocols.filters.PoseInfoFilter"  )
static
static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.FileRemoveFilter"  )
static
static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.ReportFilter"  )
static
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::ResidueSelectionDistanceFilter::apply(), protocols::simple_filters::TotalSasaFilter::apply(), protocols::simple_filters::InterfaceSasaFilter::apply(), protocols::simple_filters::FileRemoveFilter::apply(), protocols::simple_filters::ChainBreak::apply(), protocols::simple_filters::SequenceDistance::apply(), protocols::simple_filters::PoseComment::apply(), protocols::simple_filters::ChainCountFilter::apply(), protocols::simple_filters::TerminusDistanceFilter::apply(), protocols::simple_filters::ResidueLipophilicityFilter::apply(), protocols::simple_filters::SSMotifFinder::apply(), protocols::simple_filters::NMerPSSMEnergyFilter::apply(), protocols::simple_filters::NetChargeFilter::apply(), protocols::simple_filters::MPSpanAngleFilter::apply(), protocols::simple_filters::AtomicDistanceFilter::apply(), protocols::simple_filters::MutationsFilter::apply(), protocols::simple_filters::StemFinder::apply(), protocols::simple_filters::NMerSVMEnergyFilter::apply(), protocols::simple_filters::AtomicContactFilter::apply(), protocols::simple_filters::ResidueSetChainEnergyFilter::apply(), protocols::simple_filters::TaskAwareScoreTypeFilter::apply(), protocols::simple_filters::ResidueCountFilter::apply(), protocols::simple_filters::MembAccesResidueLipophilicityFilter::apply(), protocols::simple_filters::AveragePathLengthFilter::apply(), protocols::simple_filters::DisulfideEntropyFilter::apply(), protocols::simple_filters::LongestContinuousPolarSegmentFilter::apply(), protocols::simple_filters::BuriedSurfaceAreaFilter::apply(), protocols::simple_filters::SymmetricMotifFilter::apply(), protocols::simple_filters::LeastNativeLike9merFilter::apply(), protocols::simple_filters::SimpleMetricFilter::apply(), protocols::simple_filters::SSElementMotifContactFilter::apply(), protocols::simple_filters::ResidueDepthFilter::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::PoseInfoFilter::compute(), protocols::simple_filters::TotalSasaFilter::compute(), protocols::simple_filters::InterfaceSasaFilter::compute(), protocols::simple_filters::AngleToVector::compute(), protocols::simple_filters::ChainBreak::compute(), protocols::simple_filters::DeltaFilter::compute(), protocols::simple_filters::SequenceDistance::compute(), protocols::simple_filters::AtomicDistanceFilter::compute(), protocols::simple_filters::ResidueLipophilicityFilter::compute(), protocols::simple_filters::AtomicContactFilter::compute(), protocols::simple_filters::SpanTopologyMatchPoseFilter::compute(), protocols::simple_filters::MPSpanAngleFilter::compute(), protocols::simple_filters::NetChargeFilter::compute(), protocols::simple_filters::NonSequentialNeighborsFilter::compute(), protocols::simple_filters::TMsSpanMembraneFilter::compute(), protocols::simple_filters::HelixHelixAngleFilter::compute(), protocols::simple_filters::MutationsFilter::compute(), protocols::simple_filters::TaskAwareScoreTypeFilter::compute(), protocols::simple_filters::TMsAACompFilter::compute(), protocols::simple_filters::MembAccesResidueLipophilicityFilter::compute(), protocols::simple_filters::SimpleHbondsToAtomFilter::compute(), protocols::simple_filters::LeastNativeLike9merFilter::compute(), protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter::compute(), protocols::simple_filters::SSElementMotifContactFilter::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::PoseComment::parse_my_tag(), protocols::simple_filters::ChainBreak::parse_my_tag(), protocols::simple_filters::AngleToVector::parse_my_tag(), protocols::simple_filters::SSMotifFinder::parse_my_tag(), protocols::simple_filters::DeltaFilter::parse_my_tag(), protocols::simple_filters::StemFinder::parse_my_tag(), protocols::simple_filters::TotalSasaFilter::parse_my_tag(), protocols::simple_filters::NonSequentialNeighborsFilter::parse_my_tag(), protocols::simple_filters::ReportFilter::parse_my_tag(), protocols::simple_filters::TaskAwareScoreTypeFilter::parse_my_tag(), protocols::simple_filters::InterfaceSasaFilter::parse_my_tag(), protocols::simple_filters::TerminusDistanceFilter::parse_my_tag(), protocols::simple_filters::SpanTopologyMatchPoseFilter::parse_my_tag(), protocols::simple_filters::ResidueLipophilicityFilter::parse_my_tag(), protocols::simple_filters::MPSpanAngleFilter::parse_my_tag(), protocols::simple_filters::AtomicDistanceFilter::parse_my_tag(), protocols::simple_filters::AtomicContactFilter::parse_my_tag(), protocols::simple_filters::ResidueSetChainEnergyFilter::parse_my_tag(), protocols::simple_filters::NetChargeFilter::parse_my_tag(), protocols::simple_filters::MutationsFilter::parse_my_tag(), protocols::simple_filters::AveragePathLengthFilter::parse_my_tag(), protocols::simple_filters::SimpleHbondsToAtomFilter::parse_my_tag(), protocols::simple_filters::DisulfideEntropyFilter::parse_my_tag(), protocols::simple_filters::LeastNativeLike9merFilter::parse_my_tag(), protocols::simple_filters::ResidueCountFilter::parse_my_tag(), protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter::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::MPSpanAngleFilter::report_sm(), protocols::simple_filters::MembAccesResidueLipophilicityFilter::report_sm(), protocols::simple_filters::BuriedSurfaceAreaFilter::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::LeastNativeLike9merFilter::write_mean_median().

static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.AveragePathLengthFilter"  )
static
static basic::Tracer protocols::simple_filters::tr ( "protocols.simple_filters.ResidueIEFilter"  )
static
static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.ResidueSelectionDistanceFilter"  )
static
static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.StemFinder"  )
static
static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.MutationsFilter"  )
static
static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.TotalSasaFilter"  )
static
static basic::Tracer protocols::simple_filters::TR ( "protocols.filters.ChainCountFilter"  )
static
static basic::Tracer protocols::simple_filters::TR ( "protocols.filters.AtomicContactFilter"  )
static
static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.InterfaceHydrophobicResidueContactsFilter"  )
static
static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.InterfaceSasaFilter"  )
static
static basic::Tracer protocols::simple_filters::TR ( "protocols.filters.AtomicDistanceFilter"  )
static
static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.RepeatParameterFilter"  )
static
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::SAXSScoreFilter::apply(), protocols::simple_filters::ExternalEvaluator::apply(), protocols::simple_filters::ChiWellRmsdEvaluator::apply(), protocols::simple_filters::RmsdEvaluator::apply(), protocols::simple_filters::TruncatedScoreEvaluator::apply(), protocols::simple_filters::ContactMolecularSurfaceFilter::apply(), protocols::simple_filters::SSElementLengthFilter::apply(), protocols::simple_filters::RangeFilter::apply(), protocols::simple_filters::ShapeComplementarityFilter::apply(), protocols::simple_filters::PackStatFilter::apply(), protocols::simple_filters::InterRepeatContactFilter::apply(), protocols::simple_filters::IntraRepeatContactFilter::apply(), protocols::simple_filters::HolesFilter::apply(), protocols::simple_filters::SecretionPredictionFilter::apply(), protocols::simple_filters::ResidueIEFilter::compute(), protocols::simple_filters::ContactMolecularSurfaceFilter::compute(), protocols::simple_filters::PackStatFilter::compute(), protocols::simple_filters::ShapeComplementarityFilter::compute(), protocols::simple_filters::HolesFilter::compute(), protocols::simple_filters::SecretionPredictionFilter::compute(), protocols::simple_filters::ResidueIEFilter::compute_resnums(), protocols::simple_filters::ExternalEvaluator::ExternalEvaluator(), protocols::simple_filters::ResidueIEFilter::parse_my_tag(), protocols::simple_filters::ContactMolecularSurfaceFilter::parse_my_tag(), protocols::simple_filters::PackStatFilter::parse_my_tag(), protocols::simple_filters::InterRepeatContactFilter::parse_my_tag(), protocols::simple_filters::IntraRepeatContactFilter::parse_my_tag(), protocols::simple_filters::ShapeComplementarityFilter::parse_my_tag(), protocols::simple_filters::HolesFilter::parse_my_tag(), 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().

static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.SSMotifFinder"  )
static
static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_moves.MotifScoreFilter"  )
static
static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.DisulfideEntropyFilter"  )
static
static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.ResidueCountFilter"  )
static
static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.NetChargeFilter"  )
static
static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.ResidueSetChainEnergyFilter"  )
static
static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.NMerPSSMEnergyFilter"  )
static
static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.TaskAwareScoreTypeFilter"  )
static
static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.NMerSVMEnergyFilter"  )
static
static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.InterfaceHbondsFilter"  )
static
static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.TerminusDistanceFilter"  )
static
static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.SymmetricMotifFilter"  )
static
static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.ResidueLipophilicityFilter"  )
static
static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.TMsSpanMembraneFilter"  )
static
static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.MPSpanAngleFilter"  )
static
static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.ResidueChiralityFilter"  )
static
static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.HelixHelixAngleFilter"  )
static
static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.TMsAACompFilter"  )
static
static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.SpanTopologyMatchPoseFilter"  )
static
static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.MembAccesResidueLipophilicityFilter"  )
static
static basic::Tracer protocols::simple_filters::TR ( "protocols.simple_filters.ResidueDepthFilter"  )
static
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 
)

Variable Documentation

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