protocols::simple_filters Namespace Reference

Classes
class	AbinitioBaseFilter
class	AlaScan
class	AlaScanFilterCreator
class	AtomicContactFilter
	detects atomic (<4Ang) contacts between any two atoms of two residues More...
class	AtomicContactFilterCreator
class	AtomicDistanceFilter
	detects atomic contacts between two atoms of two residues More...
class	AtomicDistanceFilterCreator
class	AveragePathLengthFilter
class	AveragePathLengthFilterCreator
class	BatchEvaluator
class	BatchNrEvaluator
class	BuriedRegionsFilter
class	BuriedUnsatHbondFilter
	filters based on an upper bound # of buried unsatisfied polar residues More...
class	BuriedUnsatHbondFilterCreator
class	CamShiftEvaluator
class	CamShiftEvaluatorCreator
	creator for the CamShiftEvaluatorCreator class More...
class	ChiWellRmsdEvaluator
class	ChiWellRmsdEvaluatorCreator
	creator for the ChiWellRmsdEvaluatorCreator class More...
class	CircularPermutationFinder
class	CircularPermutationFinderFilterCreator
class	COFilter
class	ConservedPosMutationFilter
class	ConservedPosMutationFilterCreator
class	ConstraintScoreCutoffFilter
class	ConstraintScoreCutoffFilterCreator
class	ContactMapEvaluator
class	ContactMapEvaluatorCreator
	creator for the ContactMapEvaluatorCreator class More...
class	DdgFilter
class	DdgFilterCreator
class	DeltaFilter
class	DeltaFilterCreator
class	DisulfideEntropyFilter
class	DisulfideEntropyFilterCreator
class	DomainInterfaceFilter
class	EnergyPerResidueFilter
class	EnergyPerResidueFilterCreator
class	EvaluatedTrialMover
class	ExpiryFilter
class	ExpiryFilterCreator
class	ExternalEvaluator
class	ExtraScoreEvaluatorCreator
	creator for the ExtraScoreEvaluatorCreator class More...
class	FileExistFilter
class	FileExistFilterCreator
class	FileRemoveFilter
class	FileRemoveFilterCreator
class	GeometryFilter
class	GeometryFilterCreator
class	HolesFilter
class	HolesFilterCreator
class	InterfaceBindingEnergyDensityFilter
class	InterfaceBindingEnergyDensityFilterCreator
class	InterfaceSasaFilter
class	InterfaceSasaFilterCreator
class	JScoreEvaluator
class	JScoreEvaluatorCreator
	creator for the JScoreEvaluatorCreator class More...
class	JumpEvaluator
class	JumpNrEvaluator
class	JumpNrEvaluatorCreator
	creator for the JumpNrEvaluatorCreator class More...
class	LoopRmsdEvaluator
class	MinValueEvaluator
class	MultipleSigmoids
	simply takes a list of pdbs and creates relative pose then extract sigmoids and call operator (product) More...
class	MultipleSigmoidsFilterCreator
class	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	Operator
	simply take a list of filters and combine them using the operation above More...
class	OperatorFilterCreator
class	PackerNeighborGraphFilter
class	PackStatFilter
class	PackStatFilterCreator
class	PalesEvaluator
class	PalesEvaluatorCreator
	creator for the PalesEvaluatorCreator class More...
class	PDDFScoreFilter
class	PoolEvaluatorCreator
	creator for the PoolEvaluatorCreator class More...
class	PoseComment
	test whether a pose contains a comment that evaluates to a predefined value. This is useful in controlling execution flow in RosettaScripts. More...
class	PoseCommentFilterCreator
class	PoseInfoFilter
	detects atomic contacts between two atoms of two residues More...
class	PoseInfoFilterCreator
class	PoseMetricEvaluator
class	PredictedBurialEvaluator
class	PredictedBurialFnEvaluatorCreator
	creator for the PredictedBurialFnEvaluatorCreator class More...
struct	Quat
class	RangeFilter
class	RangeFilterCreator
class	RDC_Evaluator
class	RdcEvaluatorCreator
	creator for the RdcEvaluatorCreator class More...
class	RdcSelectEvaluatorCreator
	creator for the RdcSelectEvaluatorCreator class More...
class	RdcTargetEvaluatorCreator
	creator for the RdcTargetEvaluatorCreator class More...
class	RegionalConnections
class	RelativePoseFilter
class	RelativePoseFilterCreator
class	ReportFilter
class	ReportFilterCreator
class	ResidueBurialFilter
class	ResidueBurialFilterCreator
class	ResidueCountFilter
class	ResidueCountFilterCreator
class	ResidueDistanceFilter
class	ResidueDistanceFilterCreator
class	ResidueIEFilter
class	ResidueIEFilterCreator
class	ResidueSetChainEnergyFilter
class	ResidueSetChainEnergyFilterCreator
class	ResiduesInInterfaceFilter
class	ResiduesInInterfaceFilterCreator
class	RGFilter
class	RmsdEvaluator
class	RmsdEvaluatorCreator
	creator for the RmsdEvaluatorCreator class More...
class	RmsdTargetEvaluatorCreator
	creator for the RmsdTargetEvaluatorCreator class More...
class	RotamerBoltzmannWeight
class	RotamerBoltzmannWeightFilterCreator
class	RPF_ScoreEvaluator
class	SavePoseConstraintToFileFilter
	detects atomic contacts between two atoms of two residues More...
class	SavePoseConstraintToFileFilterCreator
class	SaveResfileToDiskFilter
class	SaveResfileToDiskFilterCreator
class	SAXSScoreFilter
class	ScoreCutoffFilter
class	ScoreCutoffFilterCreator
class	ScoreEvaluator
	that rewrites the whole pss struct all previous entries will be lost... probably not what one wants... More...
class	ScoreTypeFilter
class	ScoreTypeFilterCreator
class	SelectGdtEvaluator
class	SelectMaxsubEvaluator
class	SelectRDC_Evaluator
class	SelectRmsdEvaluator
class	ShapeComplementarityFilter
class	ShapeComplementarityFilterCreator
class	SheetFilter
class	SidechainRmsdFilter
class	SidechainRmsdFilterCreator
class	Sigmoid
	transform the output from a regular filter into a sigmoid ranging from 0-1 according to: fx = 1/[1 + exp[ ( x - offset ) * steepness ] The function asymptotically reaches 1 at negative values and 0 at positive values. It's 0.5 at the offset and steepness determines its slope at the offset More...
class	SigmoidFilterCreator
class	SSMotifFinder
class	SSMotifFinderFilterCreator
class	StemFinder
class	StemFinderFilterCreator
class	StructuralSimilarityEvaluator
class	StructureSimilarityEvaluatorCreator
	creator for the StructureSimilarityEvaluatorCreator class More...
class	SymmetricMotifFilter
class	SymmetricMotifFilterCreator
class	SymmetricRmsdEvaluator
class	TaskAwareAlaScan
class	TaskAwareAlaScanCreator
class	TaskAwareSASAFilter
class	TaskAwareSASAFilterCreator
class	TaskAwareScoreTypeFilter
class	TaskAwareScoreTypeFilterCreator
class	TerminusDistanceFilter
class	TerminusDistanceFilterCreator
class	TotalSasaFilter
class	TotalSasaFilterCreator
class	TruncatedScoreEvaluator

Typedefs
typedef utility::pointer::owning_ptr < AveragePathLengthFilter >	AveragePathLengthFilterOP
typedef utility::pointer::owning_ptr < AveragePathLengthFilter const >	AveragePathLengthFilterCOP
typedef utility::pointer::owning_ptr < BuriedRegionsFilter >	BuriedRegionsFilterOP
typedef utility::pointer::owning_ptr < BuriedRegionsFilter const >	BuriedRegionsFilterCOP
typedef utility::pointer::owning_ptr < CircularPermutationFinder >	CircularPermutationFinderOP
typedef utility::pointer::owning_ptr < CircularPermutationFinder const >	CircularPermutationFinderCOP
typedef utility::pointer::owning_ptr < ConservedPosMutationFilter >	ConservedPosMutationFilterOP
typedef utility::pointer::owning_ptr < ConservedPosMutationFilter const >	ConservedPosMutationFilterCOP
typedef utility::pointer::owning_ptr < ConstraintScoreCutoffFilter >	ConstraintScoreCutoffFilterOP
typedef utility::pointer::owning_ptr < ConstraintScoreCutoffFilter const >	ConstraintScoreCutoffFilterCOP
typedef utility::pointer::owning_ptr < DdgFilter >	DdgFilterOP
typedef utility::pointer::owning_ptr < DdgFilter const >	DdgFilterCOP
typedef utility::pointer::owning_ptr < DeltaFilter >	DeltaFilterOP
typedef utility::pointer::owning_ptr < DeltaFilter const >	DeltaFilterCOP
typedef utility::pointer::owning_ptr < DisulfideEntropyFilter >	DisulfideEntropyFilterOP
typedef utility::pointer::owning_ptr < DisulfideEntropyFilter const >	DisulfideEntropyFilterCOP
typedef utility::pointer::owning_ptr < DomainInterfaceFilter >	DomainInterfaceFilterOP
typedef utility::pointer::owning_ptr < DomainInterfaceFilter const >	DomainInterfaceFilterCOP
typedef utility::pointer::owning_ptr < EvaluatedTrialMover >	EvaluatedTrialMoverOP
typedef utility::pointer::owning_ptr < HolesFilter >	HolesFilterOP
typedef utility::pointer::owning_ptr < HolesFilter const >	HolesFilterCOP
typedef utility::pointer::owning_ptr < InterfaceBindingEnergyDensityFilter >	InterfaceBindingEnergyDensityFilterOP
typedef utility::pointer::owning_ptr < InterfaceBindingEnergyDensityFilter const >	InterfaceBindingEnergyDensityFilterCOP
typedef utility::pointer::owning_ptr < InterfaceSasaFilter >	InterfaceSasaFilterOP
typedef utility::pointer::owning_ptr < InterfaceSasaFilter const >	InterfaceSasaFilterCOP
typedef utility::pointer::owning_ptr < MultipleSigmoids >	MultipleSigmoidsOP
typedef utility::pointer::owning_ptr < MultipleSigmoids const >	MultipleSigmoidsCOP
typedef utility::pointer::owning_ptr < MutationsFilter >	MutationsFilterOP
typedef utility::pointer::owning_ptr < MutationsFilter const >	MutationsFilterCOP
typedef utility::pointer::owning_ptr < Operator >	OperatorOP
typedef utility::pointer::owning_ptr < Operator const >	OperatorCOP
typedef utility::pointer::owning_ptr < PackerNeighborGraphFilter >	PackerNeighborGraphFilterOP
typedef utility::pointer::owning_ptr < PackerNeighborGraphFilter const >	PackerNeighborGraphFilterCOP
typedef utility::pointer::owning_ptr < PackStatFilter >	PackStatFilterOP
typedef utility::pointer::owning_ptr < PackStatFilter const >	PackStatFilterCOP
typedef utility::pointer::owning_ptr < PDDFScoreFilter >	PDDFScoreFilterOP
typedef utility::pointer::owning_ptr < PDDFScoreFilter const >	PDDFScoreFilterCOP
typedef utility::pointer::owning_ptr < PoseComment >	PoseCommentOP
typedef utility::pointer::owning_ptr < PoseComment const >	PoseCommentCOP
typedef utility::pointer::owning_ptr < RangeFilter >	RangeFilterOP
typedef utility::pointer::owning_ptr < RangeFilter const >	RangeFilterCOP
typedef utility::pointer::owning_ptr < SelectRDC_Evaluator >	SelectRDC_EvaluatorOP
typedef utility::pointer::owning_ptr < SelectRDC_Evaluator const >	SelectRDC_EvaluatorCOP
typedef utility::pointer::owning_ptr < RelativePoseFilter >	RelativePoseFilterOP
typedef utility::pointer::owning_ptr < RelativePoseFilter const >	RelativePoseFilterCOP
typedef utility::pointer::owning_ptr < ResidueIEFilter >	ResidueIEFilterOP
typedef utility::pointer::owning_ptr < ResidueIEFilter const >	ResidueIEFilterCOP
typedef utility::pointer::owning_ptr < RotamerBoltzmannWeight >	RotamerBoltzmannWeightFilterOP
typedef utility::pointer::owning_ptr < RotamerBoltzmannWeight const >	RotamerBoltzmannWeightFilterCOP
typedef utility::pointer::owning_ptr < SaveResfileToDiskFilter >	SaveResfileToDiskFilterOP
typedef utility::pointer::owning_ptr < SaveResfileToDiskFilter const >	SaveResfileToDiskFilterCOP
typedef utility::pointer::owning_ptr < SAXSScoreFilter >	SAXSScoreFilterOP
typedef utility::pointer::owning_ptr < SAXSScoreFilter const >	SAXSScoreFilterCOP
typedef utility::pointer::owning_ptr < ScoreCutoffFilter >	ScoreCutoffFilterOP
typedef utility::pointer::owning_ptr < ScoreCutoffFilter const >	ScoreCutoffFilterCOP
typedef utility::pointer::owning_ptr < ShapeComplementarityFilter >	ShapeComplementarityFilterOP
typedef utility::pointer::owning_ptr < ShapeComplementarityFilter const >	ShapeComplementarityFilterCOP
typedef utility::pointer::owning_ptr < Sigmoid >	SigmoidOP
typedef utility::pointer::owning_ptr < Sigmoid const >	SigmoidCOP
typedef utility::pointer::owning_ptr < SSMotifFinder >	SSMotifFinderOP
typedef utility::pointer::owning_ptr < SSMotifFinder const >	SSMotifFinderCOP
typedef utility::pointer::owning_ptr < StemFinder >	StemFinderOP
typedef utility::pointer::owning_ptr < StemFinder const >	StemFinderCOP
typedef utility::pointer::owning_ptr < StructuralSimilarityEvaluator >	StructuralSimilarityEvaluatorOP
typedef utility::pointer::owning_ptr < StructuralSimilarityEvaluator const >	StructuralSimilarityEvaluatorCOP
typedef utility::pointer::owning_ptr < TaskAwareAlaScan >	TaskAwareAlaScanOP
typedef utility::pointer::owning_ptr < TaskAwareAlaScan const >	TaskAwareAlaScanCOP
typedef utility::pointer::owning_ptr < TaskAwareSASAFilter >	TaskAwareSASAFilterOP
typedef utility::pointer::owning_ptr < TaskAwareSASAFilter const >	TaskAwareSASAFilterCOP
typedef utility::pointer::owning_ptr < TaskAwareScoreTypeFilter >	TaskAwareScoreTypeFilterOP
typedef utility::pointer::owning_ptr < TaskAwareScoreTypeFilter const >	TaskAwareScoreTypeFilterCOP
typedef utility::pointer::owning_ptr < TotalSasaFilter >	TotalSasaFilterOP
typedef utility::pointer::owning_ptr < TotalSasaFilter const >	TotalSasaFilterCOP

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

Functions
void	write_to_file (std::string const filename, core::pose::Pose const &pose, core::Size const interface_begin, core::Size const cut, core::Size const interface_end, core::Real const rmsd)
vector< numeric::xyzVector < core::Real > >	bb_coords (core::pose::Pose const &pose, utility::vector1< core::Size > const &positions)
core::Real	coord_rmsd (vector< numeric::xyzVector< core::Real > > const &c1, vector< numeric::xyzVector< core::Real > > const &c2)
core::Real	superimpose_parts (vector< numeric::xyzVector< core::Real > > &ref_coords, core::Size const cut)
core::Real	superimpose_parts (core::pose::Pose const &pose, utility::vector1< core::Size > const &vec, core::Size const cut)
core::pose::Pose	rotate_pose (core::pose::Pose const &pose, core::Size const cut)
core::Real	superimpose_parts (core::pose::Pose const &pose, core::Size const cut)
boost::dynamic_bitset	get_contact_features (core::pose::Pose const &pose, core::Real const dist_threshold, std::string const &atom_name, core::Size const min_seqsep=12, core::Size const skip_res=0)
core::Real	pct_features_in_common (boost::dynamic_bitset<> const &set1, boost::dynamic_bitset<> const &set2)
int	determinant_sign (const bnu::permutation_matrix< std::size_t > &pm)
core::Real	determinant (bnu::matrix< core::Real > const &m)
void	print_nmer_svm_energy_data (vector1< nmer_svm_res_data > nmer_svm_pose_data)
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)
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...
void	R2quat (numeric::xyzMatrix< core::Real > R, Quat &Q)
void	quat2R (Quat &Q, numeric::xyzMatrix< core::Real > R)
core::Real	RMSwrapper (utility::vector1< numeric::xyzVector< core::Real > > chainA, utility::vector1< numeric::xyzVector< core::Real > > chainB, numeric::xyzMatrix< core::Real > &R, numeric::xyzVector< core::Real > &preT, numeric::xyzVector< core::Real > &postT)

Variables
static basic::Tracer	TR ("protocols.simple_filters.AlaScan")
static basic::Tracer	TR ("protocols.filters.AtomicContactFilter")
static basic::Tracer	TR ("protocols.filters.AtomicDistanceFilter")
static basic::Tracer	TR ("protocols.simple_filters.AveragePathLengthFilter")
static basic::Tracer	buried_unsat_hbond_filter_tracer ("protocols.simple_filters.BuriedUnsatHbondFilter")
static basic::Tracer	TR ("protocols.simple_filters.CircularPermutationFinder")
static basic::Tracer	TR ("protocols.simple_filters.DdgFilter")
static basic::Tracer	TR ("protocols.simple_filters.DeltaFilter")
static basic::Tracer	TR ("protocols.simple_filters.DisulfideEntropyFilter")
static basic::Tracer	energy_per_residue_filter_tracer ("protocols.simple_filters.EnergyPerResidueFilter")
static basic::Tracer	TR ("protocols.simple_filters.ExpiryFilter")
static basic::Tracer	TR ("protocols.simple_filters.FileExistFilter")
static basic::Tracer	TR ("protocols.simple_filters.FileRemoveFilter")
static basic::Tracer	TR ("protocols.simple_filters.GeometryFilter")
static basic::Tracer	TR ("protocols.simple_filters.InterfaceBindingEnergyDensityFilter")
static basic::Tracer	TR ("protocols.simple_filters.InterfaceSasaFilter")
static basic::Tracer	TR ("protocols.simple_filters.MultipleSigmoids")
static basic::Tracer	TR ("protocols.simple_filters.MutationsFilter")
static basic::Tracer	neighbor_type_filter_tracer ("protocols.simple_filters.NeighborTypeFilter")
static basic::Tracer	TR ("protocols.simple_filters.NetChargeFilter")
static basic::Tracer	TR ("protocols.simple_filters.NMerPSSMEnergyFilter")
static basic::Tracer	TR ("protocols.simple_filters.NMerSVMEnergyFilter")
static basic::Tracer	TR ("protocols.simple_filters.NonSequentialNeighborsFilter")
static basic::Tracer	TR ("protocols.simple_filters.Operator")
static basic::Tracer	TR ("protocols.simple_filters.PoseComment")
static basic::Tracer	TR ("protocols.filters.PoseInfoFilter")
static core::scoring::methods::ResidualDipolarCouplingEnergy	energy_evaluator
static basic::Tracer	TR ("protocols.simple_filters.RelativePoseFilter")
static basic::Tracer	TR ("protocols.simple_filters.ReportFilter")
static basic::Tracer	residue_burial_filter_tracer ("protocols.simple_filters.ResidueBurialFilter")
static basic::Tracer	TR ("protocols.simple_filters.ResidueCountFilter")
static basic::Tracer	residue_distance_filter_tracer ("protocols.simple_filters.ResidueDistanceFilter")
static basic::Tracer	tr ("protocols.simple_filters.ResidueIEFilter")
static basic::Tracer	TR ("protocols.simple_filters.ResidueSetChainEnergyFilter")
static basic::Tracer	residues_in_interface_tracer ("protocols.simple_filters.ResiduesInInterfaceFilter")
static basic::Tracer	TR ("protocols.simple_filters.RotamerBoltzmannWeight")
static basic::Tracer	TR ("protocols.filters.SavePoseConstraintToFileFilter")
static basic::Tracer	score_type_filter_tracer ("protocols.simple_filters.ScoreTypeFilter")
static basic::Tracer	sidechain_rmsd_filter_tracer ("protocols.simple_filters.SidechainRmsdFilter")
static basic::Tracer	TR ("protocols.simple_filters.Sigmoid")
static basic::Tracer	TR ("protocols.simple_filters.SSMotifFinder")
static basic::Tracer	TR ("protocols.simple_filters.StemFinder")
static basic::Tracer	TR ("protocols.simple_filters.SymmetricMotifFilter")
static basic::Tracer	TR ("protocols.simple_filters.TaskAwareScoreTypeFilter")
static basic::Tracer	TR ("protocols.simple_filters.TerminusDistanceFilter")
static basic::Tracer	TR ("protocols.simple_filters.TotalSasaFilter")

Typedef Documentation

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

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

typedef utility::pointer::owning_ptr< BuriedRegionsFilter const > protocols::simple_filters::BuriedRegionsFilterCOP

typedef utility::pointer::owning_ptr< BuriedRegionsFilter > protocols::simple_filters::BuriedRegionsFilterOP

typedef utility::pointer::owning_ptr< CircularPermutationFinder const > protocols::simple_filters::CircularPermutationFinderCOP

typedef utility::pointer::owning_ptr< CircularPermutationFinder > protocols::simple_filters::CircularPermutationFinderOP

typedef utility::pointer::owning_ptr< ConservedPosMutationFilter const > protocols::simple_filters::ConservedPosMutationFilterCOP

typedef utility::pointer::owning_ptr< ConservedPosMutationFilter > protocols::simple_filters::ConservedPosMutationFilterOP

typedef utility::pointer::owning_ptr< ConstraintScoreCutoffFilter const > protocols::simple_filters::ConstraintScoreCutoffFilterCOP

typedef utility::pointer::owning_ptr< ConstraintScoreCutoffFilter > protocols::simple_filters::ConstraintScoreCutoffFilterOP

typedef utility::pointer::owning_ptr< DdgFilter const > protocols::simple_filters::DdgFilterCOP

typedef utility::pointer::owning_ptr< DdgFilter > protocols::simple_filters::DdgFilterOP

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

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

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

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

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

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

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

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

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

typedef utility::pointer::owning_ptr< InterfaceBindingEnergyDensityFilter const > protocols::simple_filters::InterfaceBindingEnergyDensityFilterCOP

typedef utility::pointer::owning_ptr< InterfaceBindingEnergyDensityFilter > protocols::simple_filters::InterfaceBindingEnergyDensityFilterOP

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

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

typedef utility::pointer::owning_ptr< MultipleSigmoids const > protocols::simple_filters::MultipleSigmoidsCOP

typedef utility::pointer::owning_ptr< MultipleSigmoids > protocols::simple_filters::MultipleSigmoidsOP

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

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

typedef utility::pointer::owning_ptr< Operator const > protocols::simple_filters::OperatorCOP

typedef utility::pointer::owning_ptr< Operator > protocols::simple_filters::OperatorOP

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

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

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

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

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

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

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

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

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

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

typedef utility::pointer::owning_ptr< RelativePoseFilter const > protocols::simple_filters::RelativePoseFilterCOP

typedef utility::pointer::owning_ptr< RelativePoseFilter > protocols::simple_filters::RelativePoseFilterOP

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

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

typedef utility::pointer::owning_ptr< RotamerBoltzmannWeight const > protocols::simple_filters::RotamerBoltzmannWeightFilterCOP

typedef utility::pointer::owning_ptr< RotamerBoltzmannWeight > protocols::simple_filters::RotamerBoltzmannWeightFilterOP

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

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

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

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

typedef utility::pointer::owning_ptr< ScoreCutoffFilter const > protocols::simple_filters::ScoreCutoffFilterCOP

typedef utility::pointer::owning_ptr< ScoreCutoffFilter > protocols::simple_filters::ScoreCutoffFilterOP

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

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

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

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

typedef utility::pointer::owning_ptr< Sigmoid const > protocols::simple_filters::SigmoidCOP

typedef utility::pointer::owning_ptr< Sigmoid > protocols::simple_filters::SigmoidOP

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

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

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

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

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

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

typedef utility::pointer::owning_ptr< TaskAwareAlaScan const > protocols::simple_filters::TaskAwareAlaScanCOP

typedef utility::pointer::owning_ptr< TaskAwareAlaScan > protocols::simple_filters::TaskAwareAlaScanOP

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

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

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

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

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

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

Enumeration Type Documentation

enum protocols::simple_filters::Operation

Enumerator
SUM
PRODUCT
NORMALIZED_SUM
MAX
MIN
SUBTRACT
ABS
BOOLEAN_OR
XOR

Function Documentation

core::Real protocols::simple_filters::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 numeric::xyzVector< class >::distance(), and core::conformation::Residue::xyz().

Referenced by protocols::simple_filters::CircularPermutationFinder::circular_permutation(), and 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
	)

References core::pose::Pose::conformation(), numeric::xyzVector< class >::distance(), core::conformation::Conformation::residue(), and core::conformation::Residue::xyz().

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

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

Referenced by protocols::simple_filters::CircularPermutationFinder::circular_permutation().

core::Real protocols::simple_filters::coord_rmsd	(	vector< numeric::xyzVector< core::Real > > const &	c1,
		vector< numeric::xyzVector< core::Real > > const &	c2
	)

References distance_squared(), and runtime_assert.

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::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(), bb_coords(), protocols::simple_moves::Ca_coord(), 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(), protocols::environment::com_calc(), protocols::loops::loop_closure::ccd::compute_single_direction_deviation(), protocols::ligand_docking::Transform::dump_conformer(), 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::FragmentChunkCrms::fill_bb_coords(), 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(), 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::toolbox::InteratomicVarianceMatrix::init(), protocols::loops::loop_closure::ccd::load_coords_and_torsions(), protocols::match::downstream::SecondaryMatcherToDownstreamResidue::prepare_for_hit_generation_at_target_build_point(), protocols::qsar::scoring_grid::ShapeGrid::refresh(), protocols::features::ProteinResidueConformationFeatures::report_features(), protocols::features::ResidueConformationFeatures::report_features(), 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(), protocols::topology_broker::CoordConstraintClaimer::superimpose(), protocols::simple_filters::SSMotifFinder::superimpose_pose_on_template(), protocols::toolbox::superposition_transform(), protocols::match::output::SingleDownstreamResidueWriter::write_downstream_coordinates(), and protocols::qsar::RenderGridsToKinemage::write_points().

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().

int protocols::simple_filters::determinant_sign

(

const bnu::permutation_matrix< std::size_t > &

pm

)

References size().

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::seeded_abinitio::GrowPeptides::apply(), protocols::simple_filters::StemFinder::apply(), protocols::seeded_abinitio::SegmentHybridizer::apply(), protocols::moves::DsspMover::apply(), protocols::protein_interface_design::movers::LoopMoverFromCommandLine::apply(), protocols::protein_interface_design::movers::LoopRemodel::apply(), protocols::flxbb::InterlockAroma::apply(), protocols::fldsgn::filters::SheetTopologyFilter::apply(), protocols::fldsgn::filters::HelixPairingFilter::apply(), protocols::fldsgn::potentials::SetSecStructEnergies::apply(), protocols::fldsgn::filters::HSSTripletFilter::apply(), protocols::flxbb::LayerDesignOperation::apply(), protocols::fldsgn::BluePrintBDR::apply(), protocols::forge::components::BDR::apply(), protocols::forge::remodel::RemodelMover::apply(), 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(), protocols::seeded_abinitio::SegmentHybridizer::check_and_create_fragments(), protocols::forge::remodel::RemodelData::collectInsertionPose(), protocols::protein_interface_design::filters::AtomicContactCountFilter::compute(), protocols::denovo_design::filters::ExposedHydrophobicsFilter::compute(), protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter::compute(), protocols::fldsgn::filters::SecondaryStructureCountFilter::compute(), protocols::fldsgn::filters::HelixPairingFilter::compute(), protocols::fldsgn::filters::InterlockingAromaFilter::compute(), protocols::toolbox::SelectResiduesByLayer::compute(), protocols::flxbb::constraints_sheet(), protocols::hybridization::create_fragment_set(), protocols::motif_hash::dump_matching_motifs(), protocols::toolbox::pose_metric_calculators::RotamerRecovery::get_ss(), protocols::features::SmotifFeatures::get_ss_segments(), protocols::motif_hash::harvest_motifs(), protocols::loops::loopfinder(), protocols::seeded_abinitio::DefineMovableLoops::parse_my_tag(), protocols::seeded_abinitio::CloseFold::parse_my_tag(), positions_in_secstruct(), protocols::features::strand_assembly::SandwichFeatures::report_features(), protocols::sic_dock::XfoxmScore::score(), protocols::normalmode::NormalMode::set_harmonic_constant_map(), protocols::fldsgn::BluePrintBDR::set_instruction_blueprint(), protocols::features::SecondaryStructureSegmentFeatures::write_schema_to_db(), protocols::features::ResidueSecondaryStructureFeatures::write_schema_to_db(), and protocols::features::HelixCapFeatures::write_schema_to_db().

boost::dynamic_bitset protocols::simple_filters::get_contact_features	(	core::pose::Pose const &	pose,
		core::Real const	dist_threshold,
		std::string const &	atom_name,
		core::Size const	min_seqsep = 12,
		core::Size const	skip_res = 0
	)

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

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

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::pose_from_pdb(), and TR.

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

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

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

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

)

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

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

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

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

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

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

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

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

core::Real protocols::simple_filters::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
	)

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

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

core::Real protocols::simple_filters::RMSwrapper	(	utility::vector1< numeric::xyzVector< core::Real > >	chainA,
		utility::vector1< numeric::xyzVector< core::Real > >	chainB,
		numeric::xyzMatrix< core::Real > &	R,
		numeric::xyzVector< core::Real > &	preT,
		numeric::xyzVector< core::Real > &	postT
	)

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

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

core::pose::Pose protocols::simple_filters::rotate_pose	(	core::pose::Pose const &	pose,
		core::Size const	cut
	)

References create_subpose(), core::pose::Pose::fold_tree(), and core::pose::Pose::total_residue().

Referenced by superimpose_parts().

core::Real protocols::simple_filters::superimpose_parts	(	vector< numeric::xyzVector< core::Real > > &	ref_coords,
		core::Size const	cut
	)

References protocols::stepwise::sampler::rigid_body::rotate(), and rotation.

Referenced by protocols::simple_filters::CircularPermutationFinder::circular_permutation().

core::Real protocols::simple_filters::superimpose_parts	(	core::pose::Pose const &	pose,
		utility::vector1< core::Size > const &	vec,
		core::Size const	cut
	)

References core::id::BOGUS_ATOM_ID, core::pose::initialize_atomid_map(), protocols::stepwise::sampler::rigid_body::rotate(), s, and TR.

core::Real protocols::simple_filters::superimpose_parts	(	core::pose::Pose const &	pose,
		core::Size const	cut
	)

References core::id::BOGUS_ATOM_ID, core::pose::initialize_atomid_map(), rotate_pose(), core::pose::Pose::total_residue(), and TR.

void protocols::simple_filters::write_to_file	(	std::string const	filename,
		core::pose::Pose const &	pose,
		core::Size const	interface_begin,
		core::Size const	cut,
		core::Size const	interface_end,
		core::Real const	rmsd
	)

References chain, file, core::pose::Pose::pdb_info(), and runtime_assert.

Referenced by protocols::simple_filters::SSMotifFinder::apply(), protocols::simple_filters::CircularPermutationFinder::circular_permutation(), and protocols::optimize_weights::PSSMOptEPositionData::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 core::pose::Pose::pdb_info(), and runtime_assert.

Variable Documentation

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

static

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

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

static

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

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

static

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

static

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

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

static

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

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

static

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

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

static

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

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

static

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

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

static

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

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

static

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

static

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

static

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

static

basic::Tracer protocols::simple_filters::TR("protocols.simple_filters.Sigmoid")

static

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

static

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

static

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

static

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

static

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

static

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

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

static

basic::Tracer protocols::simple_filters::TR("protocols.simple_filters.MultipleSigmoids")

static

basic::Tracer protocols::simple_filters::TR("protocols.filters.SavePoseConstraintToFileFilter")

static

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

static

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

static

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

static

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

static

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

static

basic::Tracer protocols::simple_filters::TR("protocols.simple_filters.Operator")

static

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

static

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

static

basic::Tracer protocols::simple_filters::TR("protocols.simple_filters.DdgFilter")

static

basic::Tracer protocols::simple_filters::TR("protocols.simple_filters.InterfaceBindingEnergyDensityFilter")

static

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

static

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

static

basic::Tracer protocols::simple_filters::TR("protocols.simple_filters.CircularPermutationFinder")

static

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

static

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

static

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

static

basic::Tracer protocols::simple_filters::TR("protocols.simple_filters.RelativePoseFilter")

static

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

static

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

static

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

static

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

static

basic::Tracer protocols::simple_filters::TR("protocols.simple_filters.AlaScan")

static

Referenced by protocols::simple_filters::TotalSasaFilter::apply(), protocols::simple_filters::FileRemoveFilter::apply(), protocols::simple_filters::InterfaceSasaFilter::apply(), protocols::simple_filters::DdgFilter::apply(), protocols::simple_filters::GeometryFilter::apply(), protocols::simple_filters::PoseComment::apply(), protocols::simple_filters::Operator::apply(), protocols::simple_filters::TerminusDistanceFilter::apply(), protocols::simple_filters::NetChargeFilter::apply(), protocols::simple_filters::NMerPSSMEnergyFilter::apply(), protocols::simple_filters::SSMotifFinder::apply(), protocols::simple_filters::NMerSVMEnergyFilter::apply(), protocols::simple_filters::StemFinder::apply(), protocols::simple_filters::AtomicDistanceFilter::apply(), protocols::simple_filters::MutationsFilter::apply(), protocols::simple_filters::AtomicContactFilter::apply(), protocols::simple_filters::TaskAwareScoreTypeFilter::apply(), protocols::simple_filters::ResidueSetChainEnergyFilter::apply(), protocols::simple_filters::AveragePathLengthFilter::apply(), protocols::simple_filters::DisulfideEntropyFilter::apply(), protocols::simple_filters::ResidueCountFilter::apply(), protocols::simple_filters::SymmetricMotifFilter::apply(), protocols::simple_filters::InterfaceBindingEnergyDensityFilter::apply(), protocols::simple_filters::DeltaFilter::baseline(), protocols::simple_filters::ReportFilter::checkpoint_read(), protocols::simple_filters::ReportFilter::checkpoint_write(), protocols::simple_filters::CircularPermutationFinder::circular_permutation(), protocols::simple_filters::SavePoseConstraintToFileFilter::compute(), protocols::simple_filters::PoseInfoFilter::compute(), protocols::simple_filters::TotalSasaFilter::compute(), protocols::simple_filters::InterfaceSasaFilter::compute(), protocols::simple_filters::AtomicDistanceFilter::compute(), protocols::simple_filters::GeometryFilter::compute(), protocols::simple_filters::DeltaFilter::compute(), protocols::simple_filters::AtomicContactFilter::compute(), protocols::simple_filters::NetChargeFilter::compute(), protocols::simple_filters::NonSequentialNeighborsFilter::compute(), protocols::simple_filters::Operator::compute(), protocols::simple_filters::Sigmoid::compute(), protocols::simple_filters::RelativePoseFilter::compute(), protocols::simple_filters::MultipleSigmoids::compute(), protocols::simple_filters::MutationsFilter::compute(), protocols::simple_filters::TaskAwareScoreTypeFilter::compute(), protocols::simple_filters::RotamerBoltzmannWeight::compute(), protocols::simple_filters::DdgFilter::compute(), protocols::simple_filters::TaskAwareSASAFilter::compute(), protocols::simple_filters::RotamerBoltzmannWeight::compute_Boltzmann_weight(), protocols::simple_filters::SymmetricMotifFilter::compute_d2(), protocols::simple_filters::SSMotifFinder::compute_jump(), protocols::simple_filters::AlaScan::ddG_for_single_residue(), protocols::simple_filters::TaskAwareAlaScan::ddG_for_single_residue(), protocols::simple_filters::DdgFilter::DdgFilter(), protocols::simple_filters::RotamerBoltzmannWeight::first_pass_ala_scan(), load_poses(), protocols::simple_filters::Operator::modify_relative_filters_pdb_names(), protocols::simple_filters::TaskAwareAlaScan::parse_ddG_task_operations(), protocols::simple_filters::InterfaceSasaFilter::parse_def(), protocols::simple_filters::TaskAwareScoreTypeFilter::parse_def(), protocols::simple_filters::RotamerBoltzmannWeight::parse_def(), protocols::simple_filters::DdgFilter::parse_def(), protocols::simple_filters::PoseComment::parse_my_tag(), protocols::simple_filters::Operator::parse_my_tag(), protocols::simple_filters::CircularPermutationFinder::parse_my_tag(), protocols::simple_filters::SSMotifFinder::parse_my_tag(), protocols::simple_filters::StemFinder::parse_my_tag(), protocols::simple_filters::MultipleSigmoids::parse_my_tag(), protocols::simple_filters::Sigmoid::parse_my_tag(), protocols::simple_filters::DeltaFilter::parse_my_tag(), protocols::simple_filters::NonSequentialNeighborsFilter::parse_my_tag(), protocols::simple_filters::TotalSasaFilter::parse_my_tag(), protocols::simple_filters::SavePoseConstraintToFileFilter::parse_my_tag(), protocols::simple_filters::ReportFilter::parse_my_tag(), protocols::simple_filters::RelativePoseFilter::parse_my_tag(), protocols::simple_filters::TaskAwareScoreTypeFilter::parse_my_tag(), protocols::simple_filters::RotamerBoltzmannWeight::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::ResidueCountFilter::parse_my_tag(), protocols::simple_filters::DisulfideEntropyFilter::parse_my_tag(), protocols::simple_filters::SymmetricMotifFilter::parse_my_tag(), protocols::simple_filters::SymmetricMotifFilter::process_motifs(), protocols::simple_filters::SymmetricMotifFilter::report(), protocols::simple_filters::TaskAwareAlaScan::report(), protocols::simple_filters::Operator::report_sm(), protocols::simple_filters::RotamerBoltzmannWeight::report_sm(), protocols::simple_filters::Operator::reset_baseline(), protocols::simple_filters::MultipleSigmoids::reset_baseline(), protocols::simple_filters::Sigmoid::reset_baseline(), protocols::simple_filters::SaveResfileToDiskFilter::select_residues(), superimpose_parts(), and protocols::simple_filters::RelativePoseFilter::thread_seq().

basic::Tracer protocols::simple_filters::TR("protocols.simple_filters.GeometryFilter")

static

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

static