Rosetta Protocols  2014.35
Classes | Typedefs | Enumerations | Functions | Variables
protocols::simple_filters Namespace Reference

Classes

class  AbinitioBaseFilter
 
class  AlaScan
 
class  AlaScanFilterCreator
 
class  AtomicContactFilter
 detects atomic (<4Ang) contacts between any two atoms of two residues More...
 
class  AtomicContactFilterCreator
 
class  AtomicDistanceFilter
 detects atomic contacts between two atoms of two residues More...
 
class  AtomicDistanceFilterCreator
 
class  AveragePathLengthFilter
 
class  AveragePathLengthFilterCreator
 
class  BatchEvaluator
 
class  BatchNrEvaluator
 
class  BuriedRegionsFilter
 
class  BuriedUnsatHbondFilter
 filters based on an upper bound # of buried unsatisfied polar residues More...
 
class  BuriedUnsatHbondFilterCreator
 
class  CamShiftEvaluator
 
class  CamShiftEvaluatorCreator
 creator for the CamShiftEvaluatorCreator class More...
 
class  ChiWellRmsdEvaluator
 
class  ChiWellRmsdEvaluatorCreator
 creator for the ChiWellRmsdEvaluatorCreator class More...
 
class  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::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...
 
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

Enumeration Type Documentation

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 
)
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 
)
vector< numeric::xyzVector< core::Real > > protocols::simple_filters::bb_coords ( core::pose::Pose const &  pose,
utility::vector1< core::Size > const &  positions 
)
core::Real protocols::simple_filters::coord_rmsd ( vector< numeric::xyzVector< core::Real > > const &  c1,
vector< numeric::xyzVector< core::Real > > const &  c2 
)
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)
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 
)
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 
)
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 
)
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 
)
core::pose::Pose protocols::simple_filters::rotate_pose ( core::pose::Pose const &  pose,
core::Size const  cut 
)
core::Real protocols::simple_filters::superimpose_parts ( vector< numeric::xyzVector< core::Real > > &  ref_coords,
core::Size const  cut 
)
core::Real protocols::simple_filters::superimpose_parts ( core::pose::Pose const &  pose,
utility::vector1< core::Size > const &  vec,
core::Size const  cut 
)
core::Real protocols::simple_filters::superimpose_parts ( core::pose::Pose const &  pose,
core::Size const  cut 
)
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 
)
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

basic::Tracer protocols::simple_filters::buried_unsat_hbond_filter_tracer("protocols.simple_filters.BuriedUnsatHbondFilter")
static
core::scoring::methods::ResidualDipolarCouplingEnergy protocols::simple_filters::energy_evaluator
static
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
basic::Tracer protocols::simple_filters::residue_burial_filter_tracer("protocols.simple_filters.ResidueBurialFilter")
static
basic::Tracer protocols::simple_filters::residue_distance_filter_tracer("protocols.simple_filters.ResidueDistanceFilter")
static
basic::Tracer protocols::simple_filters::residues_in_interface_tracer("protocols.simple_filters.ResiduesInInterfaceFilter")
static
basic::Tracer protocols::simple_filters::score_type_filter_tracer("protocols.simple_filters.ScoreTypeFilter")
static
basic::Tracer protocols::simple_filters::sidechain_rmsd_filter_tracer("protocols.simple_filters.SidechainRmsdFilter")
static
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