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protocols::simple_moves Namespace Reference

Namespaces

 a3b_hbs
 
 asym_fold_and_dock
 
 bb_sampler
 
 bin_transitions
 
 chiral
 
 hbs
 
 oop
 
 rational_mc
 
 sidechain_moves
 
 symmetry
 
 triazolamer
 

Classes

class  PeptideStapleMover
 
class  LoadPDBMover
 
class  LoadPDBMoverCreator
 
class  RepeatPropagationMover
 
class  RepeatPropagationMoverCreator
 
class  AddCavitiesMover
 
class  AddChainMover
 
class  AddChainMoverCreator
 
class  AddJobPairData
 Add an arbitrary piece of data to the current Job, which will be output in the silent file, database, etc. This is useful for adding metadata to keep track of data generated using multiple experimental conditions. Currently ONLY RosettaScript interface supported. More...
 
class  AddJobPairDataCreator
 
class  AddPDBInfoMover
 
class  AddPDBInfoMoverCreator
 
class  AddResidueCouplingConstraint
 
class  AddResidueCouplingConstraintCreator
 
class  AddResidueLabelMover
 
class  AddResidueLabelMoverCreator
 
class  AddSapConstraintMover
 Adds variant types to selected residues. More...
 
class  AddSapConstraintMoverCreator
 
class  AddSapMathConstraintMover
 Adds variant types to selected residues. More...
 
class  AddSapMathConstraintMoverCreator
 
class  AlignChainMover
 Align a chain in the working pose to a chain. CA superposition. More...
 
class  AlignChainMoverCreator
 
class  BackboneMover
 BackboneMover class has elements of the MC temperature to do repetitions of bb moves (small, shear, wobble, etc.). More...
 
class  SmallMover
 A mover that makes independent random perturbations of the phi and psi torsion angles of residue i. It selects residue i at random among movable residues (set by its MoveMap), and the final torsion angle is subject to a metropolis criterion using the rama score to ensure that only favorable backbone torsion angles are being selected. The number of perturbations, and the magnitude of perturbations, and the temperature in the rama check, can all be modified. More...
 
class  ShearMover
 A mover that perturbs the phi of residue i and the psi of residue i-1 such that they create a 'shearing' effect, minimizing the downstream consequences of this torsional perturbation. The final torsion angle is subject to a metropolis criterion using the rama score to ensure that only favorable backbone torsion angles are being selected. The number of perturbations, and the magnitude of perturbations, and the temperature in the rama check, can all be modified. More...
 
class  SmallMoverCreator
 
class  ShearMoverCreator
 
class  BBConRotMover
 
class  BBDihedralSamplerMover
 Mover interface to BBDihedralSampler ( 1D ). Samples using BBDihedralSamplers randomly using residues set in the movemap. If multiple samplers are given, will randomly sample on them. More...
 
class  BBDihedralSamplerMoverCreator
 
class  BBGaussianMover
 the basic class for implementing Gaussian Perturbation of bb More...
 
class  BBG8T3AMover
 a particular gaussian mover from the original paper More...
 
class  BBGaussianMoverCreator
 
class  ChainSplitMover
 ChainSplitMover splits a pose into two chains given a cutpoint. This may be necessary for evaluating a domain interface using classes such as the InterfaceAnalyzerMover. More...
 
class  ChangeAndResetFoldTreeMover
 Basic mover used primarily for setting up atomic protocols, especially in generator functions. More...
 
class  ChangeAndResetFoldTreeMoverCreator
 
class  CombinePoseMover
 
class  ConcatenatePosesMover
 links supplied Poses by their termini More...
 
class  ConcatenatePosesMoverCreator
 
class  ConstrainToIdealMover
 
class  ContingentAcceptMover
 
class  ContingentAcceptMoverCreator
 
class  ConvertRealToVirtualMover
 
class  ConvertRealToVirtualMoverCreator
 
class  ConvertVirtualToRealMover
 
class  ConvertVirtualToRealMoverCreator
 
class  CopyDofMover
 
class  CopyRotamerMover
 A mover to copy a rotamer (residue identity and conformation) from one position in a pose to another. More...
 
class  CopyRotamerMoverCreator
 
class  CoupledMover
 This mover is called by CoupledMovesProtocol to make a single coupled move. More...
 
class  CoupledMoverCreator
 This is used by CoupledMover.cc. More...
 
class  CutChainMover
 simple mover that sperates Fv from Fl into two seperate chains More...
 
class  CutChainMoverCreator
 
class  CyclizationMover
 
class  DeclareBond
 
class  DeclareBondCreator
 
class  DEEROptimizeCoordsMover
 
class  DEEROptimizeCoordsMoverCreator
 
class  DeleteChainMover
 
class  DeleteChainMoverCreator
 
class  DeleteChainsMover
 Delete a chain from a Pose, or a set of chains. More...
 
class  DeleteChainsMoverCreator
 
class  DisulfideInsertionMover
 
class  DisulfideInsertionMoverCreator
 
class  DME_FilterMover
 
class  DOFHistogramRecorder
 
class  DumpPdb
 what you think this can now be assimilated into DumpPdbMover More...
 
class  DumpPdbCreator
 
class  DumpSingleResidueRotamers
 Given a residue index, dump all of the rotamers to individual PDB files within 0-1 sd of the mean. More...
 
class  DumpSingleResidueRotamersCreator
 
struct  WaterRot
 
class  WaterRotsDB
 
struct  AtomHashNode
 
class  AtomHash
 
class  ExplicitWaterMover
 
class  ExplicitWaterMoverCreator
 
class  FavorSequenceProfile
 
class  FavorSequenceProfileCreator
 
class  FavorSymmetricSequence
 
class  FavorSymmetricSequenceCreator
 
class  FoldTreeFromMotif
 
class  FoldTreeFromMotifCreator
 
class  FragmentMover
 abstract base class for FragmentMovers More...
 
class  ClassicFragmentMover
 A FragmentMover that applies uniform sampling of fragments. More...
 
class  LoggedFragmentMover
 
struct  GunnTuple
 
class  GunnCost
 
class  LoadUnboundRotMover
 
class  LoadUnboundRotMoverCreator
 
class  MembraneTopology
 A mover to change one torsion angle. More...
 
class  MembraneTopologyCreator
 
class  MissingDensityToJumpMover
 
class  ModifyVariantTypeMover
 Adds variant types to selected residues. More...
 
class  ModifyVariantTypeMoverCreator
 
class  MutateResidue
 A mover to mutate a single residue. More...
 
class  MutateResidueCreator
 
class  PDBReloadMover
 
class  PDBReloadMoverCreator
 
struct  ThermodynamicData
 structure that stores data during simulation More...
 
class  PeriodicBoxMover
 
class  PeriodicBoxMoverCreator
 
class  PoseFromPoseResourceMover
 Mover that shuttles a Pose from a PoseResource into the DataMap when its parse_my_tag method is invoked. More...
 
class  PoseFromPoseResourceMoverCreator
 
class  ProlineFixMover
 
class  PSSM2BfactorMover
 
class  PSSM2BfactorMoverCreator
 
class  RandomOmegaFlipMover
 
class  RandomOmegaFlipMoverCreator
 
class  RandomTorsionMover
 
class  RandomTorsionMoverCreator
 
class  IonizableResidue
 
class  ReportEffectivePKA
 scale density map intensities to match a pose's More...
 
class  ReportEffectivePKACreator
 
class  ReportXYZ
 
class  ReportXYZCreator
 
class  RepulsiveOnlyMover
 this mover replace designated residues with glycines, and then assigns a "REPLONLY" residue type to those glycines. Those "REPLONLY" residues will make only repulsive contributions to the overall energy. More...
 
class  ResetFoldTree
 
class  ResetFoldTreeCreator
 
class  ResetFullModelInfoMover
 Ensure synchronized full model info. More...
 
class  ResetFullModelInfoMoverCreator
 
class  ResTypeFragmentMover
 
class  ReturnSidechainMover
 
class  RingConformationMover
 
class  RingConformationMoverCreator
 MoverCreator allowing the MoverFactory to create a RingConformationMover. More...
 
class  SampleSequenceFromProbabilities
 A class to sample sequences from a PerResidueProbabilitiesMetric and thread them onto the pose. More...
 
class  SampleSequenceFromProbabilitiesCreator
 
class  SaveProbabilitiesMetricMover
 A class to save a PerResidueProbabilitiesMetric to a weight file. More...
 
class  SaveProbabilitiesMetricMoverCreator
 
class  SaveSequenceToCommentsMover
 
class  SaveSequenceToCommentsMoverCreator
 
class  ScoreMover
 
class  ScoreMoverCreator
 
class  SequenceProfileMover
 
class  SequenceProfileMoverCreator
 
class  SetTorsion
 A mover to change one torsion angle. More...
 
class  SetTorsionCreator
 
class  SetupMetalsMover
 A protocols::moves::Mover that. More...
 
class  SetupMetalsMoverCreator
 
class  ShakeStructureMover
 
class  ShortBackrubMover
 
class  ShortBackrubMoverCreator
 
class  SimpleThreadingMover
 This mover functions to thread the sequence of a region onto the given pose. Nothing fancy here. For more fancy things see protocols/comparative_modeling. More...
 
class  SimpleThreadingMoverCreator
 
class  SixDoFGridDockMover
 Class for enumerating docked orientations (3 translations and 3 rotations) between two chains. More...
 
class  SixDoFGridDockMoverCreator
 
class  FragmentCost
 
class  SmoothFragmentMover
 
class  StorePoseSnapshot
 A mover to store current residue indices in a map that will be updated as residues are added or deleted, permitting residue indices from the current state to be used to set up movers applied in the future. More...
 
class  StorePoseSnapshotCreator
 
struct  Hit
 
struct  less_then_match_rmsd
 
class  StructProfileMover
 
class  StructProfileMoverCreator
 
class  SuperimposeMover
 Superimpose pose onto reference pose. Default CA only. All residues. Optionally set to superimpose regions or backbone only (N, C, CA, O) More...
 
class  SuperimposeMoverCreator
 
class  SwitchChainOrderMover
 
class  SwitchChainOrderMoverCreator
 
class  SwitchResidueTypeSetMover
 A mover that switches a pose between residue type sets (e.g. centroid and fullatom) More...
 
class  SwitchResidueTypeSetMoverCreator
 
class  SymmetricFragmentMover
 A SymmetricFragmentMover that applies uniform sampling of fragments. More...
 
class  SmoothSymmetricFragmentMover
 A SymmetricFragmentMover that applies uniform sampling of fragments. More...
 
class  TailsScoreMover
 
class  TorsionDOFMover
 TODO: De-duplicate shared code from RotateJumpAxisMover (angle picking code) More...
 
class  TorsionSetMover
 
class  Tumble
 
class  TumbleCreator
 
class  UniformRotationMover
 Uniform Rotation Mover. More...
 
class  UniformTranslationMover
 Uniform Translation Mover. More...
 
class  VirtualRootMover
 
class  VirtualRootMoverCreator
 
class  WobbleMover
 A protocols::moves::Mover class for a classic-wobble analog: a smooth move followed by ccd closure @detail a smooth fragment is chosen according to the FragmentCost Functor; a cutpoint is inserted just in front of or just after the fragment a loop is defined around the fragment and cutpoint to be closed with ccd: a cut_Cterm insertion: -—lfff bbb-— f: fragment_res b: buffer_res -: immovable residues a !cut_Cterm insertion: —bbb fffl— the number of b resiudes is controlled by buffer_length_ (default 3); the move is used by apply() (inherited from FragmentMover). the insertion and loop closure is implemented in the virtual method apply_fragment(). More...
 
class  WriteFiltersToPose
 Writes the results from all filters to the pose file. More...
 
class  WriteFiltersToPoseCreator
 
class  WriteSSEMover
 Writes SSE assignation from DSSP or prediction from PSIPRED as REMARK. More...
 
class  WriteSSEMoverCreator
 

Typedefs

typedef utility::pointer::shared_ptr< PeptideStapleMover > PeptideStapleMoverOP
 
typedef utility::pointer::shared_ptr< PeptideStapleMover const > PeptideStapleMoverCOP
 
typedef utility::pointer::shared_ptr< LoadPDBMover > LoadPDBMoverOP
 
typedef utility::pointer::shared_ptr< LoadPDBMover const > LoadPDBMoverCOP
 
typedef utility::pointer::shared_ptr< RepeatPropagationMover > RepeatPropagationMoverOP
 
typedef utility::pointer::shared_ptr< RepeatPropagationMover const > RepeatPropagationMoverCOP
 
typedef utility::pointer::shared_ptr< RepeatProteinRelax > RepeatProteinRelaxOP
 
typedef utility::pointer::shared_ptr< RepeatProteinRelax const > RepeatProteinRelaxCOP
 
typedef utility::pointer::shared_ptr< AddChainMover > AddChainMoverOP
 
typedef utility::pointer::shared_ptr< AddChainMover const > AddChainMoverCOP
 
typedef utility::pointer::shared_ptr< AddJobPairData > AddJobPairDataOP
 
typedef utility::pointer::shared_ptr< AddJobPairData const > AddJobPairDataCOP
 
typedef utility::pointer::shared_ptr< AddPDBInfoMover > AddPDBInfoMoverOP
 
typedef utility::pointer::shared_ptr< AddPDBInfoMover const > AddPDBInfoMoverCOP
 
typedef utility::pointer::shared_ptr< AddResidueTensorConstraint > AddResidueTensorConstraintOP
 
typedef utility::pointer::shared_ptr< AddResidueLabelMover > AddResidueLabelMoverOP
 
typedef utility::pointer::shared_ptr< AddResidueLabelMover const > AddResidueLabelMoverCOP
 
typedef utility::pointer::shared_ptr< AddSapConstraintMover > AddSapConstraintMoverOP
 
typedef utility::pointer::shared_ptr< AddSapConstraintMover const > AddSapConstraintMoverCOP
 
typedef utility::pointer::shared_ptr< AddSapMathConstraintMover > AddSapMathConstraintMoverOP
 
typedef utility::pointer::shared_ptr< AddSapMathConstraintMover const > AddSapMathConstraintMoverCOP
 
typedef utility::pointer::shared_ptr< AlignChainMover > AlignChainMoverOP
 
typedef utility::pointer::shared_ptr< AlignChainMover const > AlignChainMoverCOP
 
typedef utility::pointer::shared_ptr< BackboneMover > BackboneMoverOP
 
typedef utility::pointer::shared_ptr< BackboneMover const > BackboneMoverCOP
 
typedef utility::pointer::shared_ptr< SmallMover > SmallMoverOP
 
typedef utility::pointer::shared_ptr< SmallMover const > SmallMoverCOP
 
typedef utility::pointer::shared_ptr< ShearMover > ShearMoverOP
 
typedef utility::pointer::shared_ptr< ShearMover const > ShearMoverCOP
 
typedef utility::pointer::shared_ptr< BBConRotMover > BBConRotMoverOP
 
typedef utility::pointer::shared_ptr< BBConRotMover const > BBConRotMoverCOP
 
typedef utility::pointer::shared_ptr< BBDihedralSamplerMover > BBDihedralSamplerMoverOP
 
typedef utility::pointer::shared_ptr< BBDihedralSamplerMover const > BBDihedralSamplerMoverCOP
 
typedef utility::pointer::shared_ptr< BBGaussianMover > BBGaussianMoverOP
 
typedef utility::pointer::shared_ptr< BBGaussianMover const > BBGaussianMoverCOP
 
typedef utility::pointer::shared_ptr< BBG8T3AMover > BBG8T3AMoverOP
 
typedef utility::pointer::shared_ptr< BBG8T3AMover const > BBG8T3AMoverCOP
 
typedef utility::pointer::shared_ptr< ChainSplitMover > ChainSplitMoverOP
 
typedef utility::pointer::shared_ptr< ChainSplitMover const > ChainSplitMoverCOP
 
typedef utility::pointer::shared_ptr< ChangeAndResetFoldTreeMover > ChangeAndResetFoldTreeMoverOP
 
typedef utility::pointer::shared_ptr< ChangeAndResetFoldTreeMover const > ChangeAndResetFoldTreeMoverCOP
 
typedef utility::pointer::shared_ptr< CombinePoseMover > CombinePoseMoverOP
 
typedef utility::pointer::shared_ptr< CombinePoseMover const > CombinePoseMoverCOP
 
using ConcatenatePosesMoverOP = utility::pointer::shared_ptr< ConcatenatePosesMover >
 
using ConcatenatePosesMoverCOP = utility::pointer::shared_ptr< ConcatenatePosesMover const >
 
typedef utility::pointer::shared_ptr< ConstrainToIdealMover > ConstrainToIdealMoverOP
 
typedef utility::pointer::shared_ptr< ConstrainToIdealMover const > ConstrainToIdealMoverCOP
 
typedef utility::pointer::shared_ptr< ContingentAcceptMover > ContingentAcceptMoverOP
 
typedef utility::pointer::shared_ptr< ContingentAcceptMover const > ContingentAcceptMoverCOP
 
typedef utility::pointer::shared_ptr< ConvertRealToVirtualMover > ConvertRealToVirtualMoverOP
 
typedef utility::pointer::shared_ptr< ConvertRealToVirtualMover const > ConvertRealToVirtualMoverCOP
 
typedef utility::pointer::shared_ptr< ConvertVirtualToRealMover > VirtualToFaMoverOP
 
typedef utility::pointer::shared_ptr< ConvertVirtualToRealMover const > VirtualToFaMoverCOP
 
typedef utility::pointer::shared_ptr< CopyDofMover > CopyDofMoverOP
 
typedef utility::pointer::shared_ptr< CopyDofMover const > CopyDofMoverCOP
 
typedef utility::pointer::shared_ptr< CopyRotamerMover > CopyRotamerMoverOP
 
typedef utility::pointer::shared_ptr< CopyRotamerMover const > CopyRotamerMoverCOP
 
typedef utility::pointer::shared_ptr< CoupledMover > CoupledMoverOP
 
typedef utility::pointer::shared_ptr< CoupledMover const > CoupledMoverCOP
 
typedef utility::pointer::shared_ptr< CutChainMover > CutChainMoverOP
 
typedef utility::pointer::shared_ptr< CutChainMover const > CutChainMoverCOP
 
typedef utility::pointer::shared_ptr< CyclizationMover > CyclizationMoverOP
 
typedef utility::pointer::shared_ptr< CyclizationMover const > CyclizationMoverCOP
 
typedef utility::pointer::shared_ptr< DeclareBond > DeclareBondOP
 
typedef utility::pointer::shared_ptr< DeclareBond const > DeclareBondCOP
 
typedef utility::vector1< DeclareBondOP > DeclareBondOPs
 
typedef utility::vector1< DeclareBondCOP > DeclareBondCOPs
 
typedef utility::pointer::shared_ptr< DEEROptimizeCoordsMover > DEEROptimizeCoordsMoverOP
 
typedef utility::pointer::shared_ptr< DEEROptimizeCoordsMover const > DEEROptimizeCoordsMoverCOP
 
typedef utility::pointer::shared_ptr< DeleteChainMover > DeleteChainMoverOP
 
typedef utility::pointer::shared_ptr< DeleteChainMover const > DeleteChainMoverCOP
 
typedef utility::pointer::shared_ptr< DeleteChainsMover > DeleteChainsMoverOP
 
typedef utility::pointer::shared_ptr< DeleteChainsMover const > DeleteChainsMoverCOP
 
typedef utility::pointer::shared_ptr< DisulfideInsertionMover > DisulfideInsertionMoverOP
 
typedef utility::pointer::shared_ptr< DisulfideInsertionMover const > DisulfideInsertionMoverCOP
 
typedef utility::pointer::shared_ptr< DisulfideInsertionMoverCreator > DisulfideInsertionMoverCreatorOP
 
typedef utility::pointer::shared_ptr< DisulfideInsertionMoverCreator const > DisulfideInsertionMoverCreatorCOP
 
typedef utility::pointer::shared_ptr< DumpPdb > DumpPdbOP
 
typedef utility::pointer::shared_ptr< DumpPdb const > DumpPdbCOP
 
typedef utility::pointer::shared_ptr< DumpSingleResidueRotamers > DumpSingleResidueRotamersOP
 
typedef utility::pointer::shared_ptr< DumpSingleResidueRotamers const > DumpSingleResidueRotamersCOP
 
typedef utility::pointer::shared_ptr< ExplicitWaterMover > ExplicitWaterMoverOP
 
typedef utility::pointer::shared_ptr< ExplicitWaterMover const > ExplicitWaterMoverCOP
 
typedef utility::vector1< utility::vector1< core::Vector > > PWatRotamerCloud
 
typedef utility::pointer::shared_ptr< FavorSymmetricSequence > FavorSymmetricSequenceOP
 
typedef utility::pointer::shared_ptr< FavorSymmetricSequence const > FavorSymmetricSequenceCOP
 
typedef utility::pointer::shared_ptr< FragmentMover > FragmentMoverOP
 
typedef utility::pointer::shared_ptr< FragmentMover const > FragmentMoverCOP
 
typedef utility::pointer::shared_ptr< ClassicFragmentMover > ClassicFragmentMoverOP
 
typedef utility::pointer::shared_ptr< ClassicFragmentMover const > ClassicFragmentMoverCOP
 
typedef utility::pointer::shared_ptr< LoadUnboundRotMover > LoadUnboundRotMoverOP
 
typedef utility::pointer::shared_ptr< LoadUnboundRotMover const > LoadUnboundRotMoverCOP
 
typedef utility::pointer::shared_ptr< MembraneTopology > MembraneTopologyOP
 
typedef utility::pointer::shared_ptr< MembraneTopology const > MembraneTopologyCOP
 
typedef utility::pointer::shared_ptr< MissingDensityToJumpMover > MissingDensityToJumpMoverOP
 
typedef utility::pointer::shared_ptr< MissingDensityToJumpMover const > MissingDensityToJumpMoverCOP
 
typedef utility::pointer::shared_ptr< ModifyVariantTypeMover > ModifyVariantTypeMoverOP
 
typedef utility::pointer::shared_ptr< ModifyVariantTypeMover const > ModifyVariantTypeMoverCOP
 
typedef utility::pointer::shared_ptr< MutateResidue > MutateResidueOP
 
typedef utility::pointer::shared_ptr< MutateResidue const > MutateResidueCOP
 
typedef utility::pointer::shared_ptr< PDBReloadMover > PDBReloadMoverOP
 
typedef utility::pointer::shared_ptr< PDBReloadMover const > PDBReloadMoverCOP
 
typedef utility::pointer::shared_ptr< PeriodicBoxMover > PeriodicBoxMoverOP
 
typedef utility::pointer::shared_ptr< PeriodicBoxMover const > PeriodicBoxMoverCOP
 
typedef utility::pointer::shared_ptr< PoseFromPoseResourceMover > PoseFromPoseResourceMoverOP
 
typedef utility::pointer::shared_ptr< PoseFromPoseResourceMover const > PoseFromPoseResourceMoverCOP
 
typedef utility::pointer::shared_ptr< ProlineFixMover > ProlineFixMoverOP
 
typedef utility::pointer::shared_ptr< ProlineFixMover const > ProlineFixMoverCOP
 
typedef utility::pointer::shared_ptr< PSSM2BfactorMover > PSSM2BfactorMoverOP
 
typedef utility::pointer::shared_ptr< PSSM2BfactorMover const > PSSM2BfactorMoverCOP
 
typedef utility::pointer::shared_ptr< RandomOmegaFlipMover > RandomOmegaFlipMoverOP
 
typedef utility::pointer::shared_ptr< RandomOmegaFlipMover const > RandomOmegaFlipMoverCOP
 
typedef utility::pointer::shared_ptr< RandomTorsionMover > RandomTorsionMoverOP
 
typedef utility::pointer::shared_ptr< RandomTorsionMover const > RandomTorsionMoverCOP
 
typedef utility::pointer::shared_ptr< ReportXYZ > ReportXYZOP
 
typedef utility::pointer::shared_ptr< ReportXYZ const > ReportXYZCOP
 
typedef utility::pointer::shared_ptr< RepulsiveOnlyMover > RepulsiveOnlyMoverOP
 
typedef utility::pointer::shared_ptr< RepulsiveOnlyMover const > RepulsiveOnlyMoverCOP
 
typedef utility::pointer::shared_ptr< ResetFoldTree > ResetFoldTreeOP
 
typedef utility::pointer::shared_ptr< ResetFoldTree const > ResetFoldTreeCOP
 
using ResetFullModelInfoMoverOP = utility::pointer::shared_ptr< ResetFullModelInfoMover >
 
using ResetFullModelInfoMoverCOP = utility::pointer::shared_ptr< ResetFullModelInfoMover const >
 
typedef utility::pointer::shared_ptr< ResTypeFragmentMover > ResTypeFragmentMoverOP
 
typedef utility::pointer::shared_ptr< ResTypeFragmentMover const > ResTypeFragmentMoverCOP
 
typedef utility::pointer::shared_ptr< ReturnSidechainMover > ReturnSidechainMoverOP
 
typedef utility::pointer::shared_ptr< ReturnSidechainMover const > ReturnSidechainMoverCOP
 
typedef utility::pointer::shared_ptr< RingConformationMover > RingConformationMoverOP
 
typedef utility::pointer::shared_ptr< RingConformationMover const > RingConformationMoverCOP
 
using SampleSequenceFromProbabilitiesOP = utility::pointer::shared_ptr< SampleSequenceFromProbabilities >
 
using SampleSequenceFromProbabilitiesCOP = utility::pointer::shared_ptr< SampleSequenceFromProbabilities const >
 
using SaveProbabilitiesMetricMoverOP = utility::pointer::shared_ptr< SaveProbabilitiesMetricMover >
 
using SaveProbabilitiesMetricMoverCOP = utility::pointer::shared_ptr< SaveProbabilitiesMetricMover const >
 
typedef utility::pointer::shared_ptr< ScoreMover > ScoreMoverOP
 
typedef utility::pointer::shared_ptr< ScoreMover const > ScoreMoverCOP
 
typedef utility::pointer::shared_ptr< SequenceProfileMover > SequenceProfileMoverOP
 
typedef utility::pointer::shared_ptr< SequenceProfileMover const > SequenceProfileMoverCOP
 
typedef utility::pointer::shared_ptr< SetTorsion > SetTorsionOP
 
typedef utility::pointer::shared_ptr< SetTorsion const > SetTorsionCOP
 
typedef utility::pointer::shared_ptr< SetupMetalsMover > SetupMetalsMoverOP
 
typedef utility::pointer::shared_ptr< SetupMetalsMover const > SetupMetalsMoverCOP
 
typedef utility::pointer::shared_ptr< ShakeStructureMover > ShakeStructureMoverOP
 
typedef utility::pointer::shared_ptr< ShakeStructureMover const > ShakeStructureMoverCOP
 
typedef utility::pointer::shared_ptr< ShortBackrubMover > ShortBackrubMoverOP
 
typedef utility::pointer::shared_ptr< ShortBackrubMover const > ShortBackrubMoverCOP
 
typedef utility::pointer::shared_ptr< SimpleThreadingMover > SimpleThreadingMoverOP
 
typedef utility::pointer::shared_ptr< SimpleThreadingMover const > SimpleThreadingMoverCOP
 
using SixDoFGridDockMoverOP = utility::pointer::shared_ptr< SixDoFGridDockMover >
 
using SixDoFGridDockMoverCOP = utility::pointer::shared_ptr< SixDoFGridDockMover const >
 
typedef utility::pointer::shared_ptr< SmoothFragmentMover > SmoothFragmentMoverOP
 
typedef utility::pointer::shared_ptr< SmoothFragmentMover const > SmoothFragmentMoverCOP
 
typedef utility::pointer::shared_ptr< FragmentCost > FragmentCostOP
 
typedef utility::pointer::shared_ptr< FragmentCost const > FragmentCostCOP
 
typedef utility::vector1< core::Real > ScoreList
 
typedef utility::pointer::shared_ptr< StorePoseSnapshot > StorePoseSnapshotOP
 
typedef utility::pointer::shared_ptr< StorePoseSnapshot const > StorePoseSnapshotCOP
 
typedef utility::pointer::shared_ptr< StructProfileMover > StructProfileMoverOP
 
typedef utility::pointer::shared_ptr< StructProfileMover const > StructProfileMoverCOP
 
typedef core::Real Probability
 
typedef utility::pointer::shared_ptr< SuperimposeMover > SuperimposeMoverOP
 
typedef utility::pointer::shared_ptr< SuperimposeMover const > SuperimposeMoverCOP
 
typedef utility::pointer::shared_ptr< SwitchChainOrderMover > SwitchChainOrderMoverOP
 
typedef utility::pointer::shared_ptr< SwitchChainOrderMover const > SwitchChainOrderMoverCOP
 
typedef utility::pointer::shared_ptr< SwitchResidueTypeSetMover > SwitchResidueTypeSetMoverOP
 
typedef utility::pointer::shared_ptr< SwitchResidueTypeSetMover const > SwitchResidueTypeSetMoverCOP
 
typedef utility::pointer::shared_ptr< SymmetricFragmentMover > SymmetricFragmentMoverOP
 
typedef utility::pointer::shared_ptr< SymmetricFragmentMover const > SymmetricFragmentMoverCOP
 
typedef utility::pointer::shared_ptr< SmoothSymmetricFragmentMover > SmoothSymmetricFragmentMoverOP
 
typedef utility::pointer::shared_ptr< SmoothSymmetricFragmentMover const > SmoothSymmetricFragmentMoverCOP
 
typedef utility::pointer::shared_ptr< TorsionDOFMover > TorsionDOFMoverOP
 
typedef utility::pointer::shared_ptr< TorsionDOFMover const > TorsionDOFMoverCOP
 
typedef utility::pointer::shared_ptr< TorsionSetMover > TorsionSetMoverOP
 
typedef utility::pointer::shared_ptr< TorsionSetMover const > TorsionSetMoverCOP
 
typedef utility::pointer::shared_ptr< UniformRotationMover > UniformRotationMoverOP
 
typedef utility::pointer::shared_ptr< UniformRotationMover const > UniformRotationMoverCOP
 
typedef utility::pointer::shared_ptr< UniformTranslationMover > UniformTranslationMoverOP
 
typedef utility::pointer::shared_ptr< UniformTranslationMover const > UniformTranslationMoverCOP
 
typedef utility::pointer::shared_ptr< VirtualRootMover > VirtualRootMoverOP
 
typedef utility::pointer::shared_ptr< VirtualRootMover const > VirtualRootMoverCOP
 
typedef utility::pointer::shared_ptr< WobbleMover > WobbleMoverOP
 
typedef utility::pointer::shared_ptr< const WobbleMover > WobbleMoverCOP
 
typedef utility::pointer::shared_ptr< WriteSSEMover > WriteSSEMoverOP
 
typedef utility::pointer::shared_ptr< WriteSSEMover const > WriteSSEMoverCOP
 

Enumerations

enum  DisulfideCyclizationViability { DCV_NOT_CYCLIZABLE , DCV_CYCLIZABLE , DCV_ALREADY_CYCLIZED }
 
enum  TorsionPerturbType { perturbtorsion_uniform =1 , perturbtorsion_gaussian , perturbtorsion_unknown }
 

Functions

static basic::Tracer TR ("protocols.simple_moves.RepeatPropagationMover")
 
utility::vector1< numeric::xyzVector< core::Real > > Ca_coords (core::pose::Pose const &pose, utility::vector1< core::Size > const positions)
 
static basic::Tracer TR ("protocols.simple_moves.AddJobPairData")
 
static basic::Tracer TR ("protocols.simple_moves.AddPDBInfoMover")
 
static basic::Tracer TR ("protocols.simple_moves.AddResidueCouplingConstraint")
 
static basic::Tracer TR ("protocols.simple_moves.AddSapConstraintMover")
 
static basic::Tracer TR ("protocols.simple_moves.AddSapMathConstraintMover")
 
bool has_option (utility::tag::TagCOP const &tag, std::string const &key)
 
utility::vector1< numeric::xyzVector< core::Real > > Ca_coord (core::pose::Pose const &pose, utility::vector1< core::Size > const positions)
 
std::ostream & operator<< (std::ostream &os, BackboneMover const &mover)
 
std::ostream & operator<< (std::ostream &os, BBDihedralSamplerMover const &mover)
 
static basic::Tracer TR ("protocols.simple_moves.CombinePoseMover")
 
std::ostream & operator<< (std::ostream &os, ConcatenatePosesMover const &mover)
 private methods /// More...
 
core::Size check_if_proton_chi_atom (core::chemical::ResidueType const &rsd_type, core::Size const j)
 
core::Size check_if_proton_chi_atom (core::pose::Pose const &pose, core::Size const i, core::Size const j)
 
void apply_ideal_coordinates_for_alternative_pucker (core::pose::Pose const &pose, core::pose::Pose &pose_reference)
 
void setup_vary_rna_bond_geometry (core::kinematics::MoveMap &mm, core::pose::Pose &pose, core::pose::toolbox::AtomLevelDomainMapCOP atom_level_domain_map, core::scoring::ScoreType score_type)
 
void setup_vary_polar_hydrogen_geometry (core::kinematics::MoveMap &mm, core::pose::Pose &pose, core::pose::toolbox::AtomLevelDomainMapCOP atom_level_domain_map)
 
std::ostream & operator<< (std::ostream &os, ConvertRealToVirtualMover const &mover)
 
std::ostream & operator<< (std::ostream &os, ConvertVirtualToRealMover const &mover)
 
std::ostream & operator<< (std::ostream &os, CopyRotamerMover const &mover)
 Get the name of the Mover. More...
 
static basic::Tracer TR ("protocols.simple_moves.CutChainMover")
 
static basic::Tracer TR ("protocols.simple_moves.CyclizationMover")
 
static basic::Tracer TR ("protocols.simple_moves.DEEROptimizeCoordsMover")
 
static basic::Tracer TR ("protocols.simple_moves.DeleteChainMover")
 
static basic::Tracer TR ("protocols.simple_moves.DisulfideInsertionMover")
 
conformation::PointGraphOP setup_dme_point_graph (pose::Pose const &ref_pose, Real const threshold)
 
Real point_graph_dme (conformation::PointGraph const &pg, pose::Pose const &pose)
 
static basic::Tracer TR ("protocols.simple_moves.DOFHistogramRecorder")
 
std::ostream & operator<< (std::ostream &os, DOFHistogramRecorder const &dof_recorder)
 
utility::vector1< core::Real > uniform_dof_distribution (core::id::DOF_Type dof_type, core::Size num_bins, core::Real min, core::Real max)
 
static basic::Tracer TR ("protocols.simple_moves.DumpPdb")
 
std::ostream & operator<< (std::ostream &os, DumpSingleResidueRotamers const &mover)
 private methods /// More...
 
static basic::Tracer TR ("protocols.moves.ExplicitWaterMover")
 
static basic::Tracer TR ("protocols.simple_moves.FavorSequenceProfile")
 
static basic::Tracer TR ("protocols.simple_moves.FavorSymmetricSequence")
 
static basic::Tracer TR ("protocols.loops.FoldTreeFromMotif")
 
static basic::Tracer tr ("protocols.simple_moves.FragmentMover")
 
std::ostream & operator<< (std::ostream &os, ClassicFragmentMover const &cfmover)
 
static basic::Tracer trGunnCost ("protocols.FragmentMover.GunnCost")
 
static basic::Tracer TR ("protocols.simple_moves.MembraneTopology")
 
static basic::Tracer TR ("protocols.mover.MissingDensityToJumpMover")
 
static basic::Tracer TR ("protocols.simple_moves.ModifyVariantTypeMover")
 
static basic::Tracer TR ("protocols.simple_moves.MutateResidue")
 
static basic::Tracer TR ("protocols.simple_moves.PDBReloadMover")
 
numeric::xyzMatrix< core::Real > random_rotation (core::Real magnitude)
 
std::ostream & operator<< (std::ostream &os, PoseFromPoseResourceMover const &mover)
 private methods /// More...
 
static basic::Tracer TR ("protocol.mover.RepulsiveOnlyMover")
 
std::ostream & operator<< (std::ostream &os, ResetFullModelInfoMover const &mover)
 private methods /// More...
 
static basic::Tracer tr ("protocols.simple_moves.ResTypeFragmentMover")
 
std::ostream & operator<< (std::ostream &os, ReturnSidechainMover const &mover)
 
std::ostream & operator<< (std::ostream &output, RingConformationMover const &object_to_output)
 
std::ostream & operator<< (std::ostream &os, SampleSequenceFromProbabilities const &mover)
 
std::ostream & operator<< (std::ostream &os, SaveProbabilitiesMetricMover const &mover)
 private methods /// More...
 
static basic::Tracer TR ("protocols.simple_moves.ScoreMover")
 
static basic::Tracer TR ("protocols.simple_moves.SetTorsion")
 
std::ostream & operator<< (std::ostream &os, SetupMetalsMover const &mover)
 
std::ostream & operator<< (std::ostream &os, SixDoFGridDockMover const &mover)
 private methods /// More...
 
static basic::Tracer TR ("protocols.simple_moves.StorePoseSnapshot")
 
static basic::Tracer TR ("protocols.simple_moves.SuperimposeMover")
 
std::ostream & operator<< (std::ostream &os, SwitchResidueTypeSetMover const &mover)
 
static basic::Tracer tr ("protocols.simple_moves.FragmentMover")
 
static basic::Tracer TR ("protocols.simple_moves.VirtualRootMover")
 

Variables

const int VISITED = 1
 
const int PREVIOUS_HILL = 2
 
const int HILL = 3
 
const int VISITED_HILL = 4
 
const core::Real ED = 2
 
const core::Real KT = 15
 

Typedef Documentation

◆ AddChainMoverCOP

typedef utility::pointer::shared_ptr< AddChainMover const > protocols::simple_moves::AddChainMoverCOP

◆ AddChainMoverOP

typedef utility::pointer::shared_ptr< AddChainMover > protocols::simple_moves::AddChainMoverOP

◆ AddJobPairDataCOP

typedef utility::pointer::shared_ptr< AddJobPairData const > protocols::simple_moves::AddJobPairDataCOP

◆ AddJobPairDataOP

typedef utility::pointer::shared_ptr< AddJobPairData > protocols::simple_moves::AddJobPairDataOP

◆ AddPDBInfoMoverCOP

typedef utility::pointer::shared_ptr< AddPDBInfoMover const > protocols::simple_moves::AddPDBInfoMoverCOP

◆ AddPDBInfoMoverOP

typedef utility::pointer::shared_ptr< AddPDBInfoMover > protocols::simple_moves::AddPDBInfoMoverOP

◆ AddResidueLabelMoverCOP

typedef utility::pointer::shared_ptr< AddResidueLabelMover const > protocols::simple_moves::AddResidueLabelMoverCOP

◆ AddResidueLabelMoverOP

typedef utility::pointer::shared_ptr< AddResidueLabelMover > protocols::simple_moves::AddResidueLabelMoverOP

◆ AddResidueTensorConstraintOP

typedef utility::pointer::shared_ptr<AddResidueTensorConstraint> protocols::simple_moves::AddResidueTensorConstraintOP

◆ AddSapConstraintMoverCOP

typedef utility::pointer::shared_ptr< AddSapConstraintMover const > protocols::simple_moves::AddSapConstraintMoverCOP

◆ AddSapConstraintMoverOP

typedef utility::pointer::shared_ptr< AddSapConstraintMover > protocols::simple_moves::AddSapConstraintMoverOP

◆ AddSapMathConstraintMoverCOP

typedef utility::pointer::shared_ptr< AddSapMathConstraintMover const > protocols::simple_moves::AddSapMathConstraintMoverCOP

◆ AddSapMathConstraintMoverOP

typedef utility::pointer::shared_ptr< AddSapMathConstraintMover > protocols::simple_moves::AddSapMathConstraintMoverOP

◆ AlignChainMoverCOP

typedef utility::pointer::shared_ptr< AlignChainMover const > protocols::simple_moves::AlignChainMoverCOP

◆ AlignChainMoverOP

typedef utility::pointer::shared_ptr< AlignChainMover > protocols::simple_moves::AlignChainMoverOP

◆ BackboneMoverCOP

typedef utility::pointer::shared_ptr< BackboneMover const > protocols::simple_moves::BackboneMoverCOP

◆ BackboneMoverOP

typedef utility::pointer::shared_ptr< BackboneMover > protocols::simple_moves::BackboneMoverOP

◆ BBConRotMoverCOP

typedef utility::pointer::shared_ptr< BBConRotMover const > protocols::simple_moves::BBConRotMoverCOP

◆ BBConRotMoverOP

typedef utility::pointer::shared_ptr< BBConRotMover > protocols::simple_moves::BBConRotMoverOP

◆ BBDihedralSamplerMoverCOP

typedef utility::pointer::shared_ptr< BBDihedralSamplerMover const > protocols::simple_moves::BBDihedralSamplerMoverCOP

◆ BBDihedralSamplerMoverOP

typedef utility::pointer::shared_ptr< BBDihedralSamplerMover > protocols::simple_moves::BBDihedralSamplerMoverOP

◆ BBG8T3AMoverCOP

typedef utility::pointer::shared_ptr< BBG8T3AMover const > protocols::simple_moves::BBG8T3AMoverCOP

◆ BBG8T3AMoverOP

typedef utility::pointer::shared_ptr< BBG8T3AMover > protocols::simple_moves::BBG8T3AMoverOP

◆ BBGaussianMoverCOP

typedef utility::pointer::shared_ptr< BBGaussianMover const > protocols::simple_moves::BBGaussianMoverCOP

◆ BBGaussianMoverOP

typedef utility::pointer::shared_ptr< BBGaussianMover > protocols::simple_moves::BBGaussianMoverOP

◆ ChainSplitMoverCOP

typedef utility::pointer::shared_ptr< ChainSplitMover const > protocols::simple_moves::ChainSplitMoverCOP

◆ ChainSplitMoverOP

typedef utility::pointer::shared_ptr< ChainSplitMover > protocols::simple_moves::ChainSplitMoverOP

◆ ChangeAndResetFoldTreeMoverCOP

typedef utility::pointer::shared_ptr< ChangeAndResetFoldTreeMover const > protocols::simple_moves::ChangeAndResetFoldTreeMoverCOP

◆ ChangeAndResetFoldTreeMoverOP

typedef utility::pointer::shared_ptr< ChangeAndResetFoldTreeMover > protocols::simple_moves::ChangeAndResetFoldTreeMoverOP

◆ ClassicFragmentMoverCOP

typedef utility::pointer::shared_ptr< ClassicFragmentMover const > protocols::simple_moves::ClassicFragmentMoverCOP

◆ ClassicFragmentMoverOP

typedef utility::pointer::shared_ptr< ClassicFragmentMover > protocols::simple_moves::ClassicFragmentMoverOP

◆ CombinePoseMoverCOP

typedef utility::pointer::shared_ptr< CombinePoseMover const > protocols::simple_moves::CombinePoseMoverCOP

◆ CombinePoseMoverOP

typedef utility::pointer::shared_ptr< CombinePoseMover > protocols::simple_moves::CombinePoseMoverOP

◆ ConcatenatePosesMoverCOP

using protocols::simple_moves::ConcatenatePosesMoverCOP = typedef utility::pointer::shared_ptr< ConcatenatePosesMover const >

◆ ConcatenatePosesMoverOP

using protocols::simple_moves::ConcatenatePosesMoverOP = typedef utility::pointer::shared_ptr< ConcatenatePosesMover >

◆ ConstrainToIdealMoverCOP

typedef utility::pointer::shared_ptr< ConstrainToIdealMover const > protocols::simple_moves::ConstrainToIdealMoverCOP

◆ ConstrainToIdealMoverOP

typedef utility::pointer::shared_ptr< ConstrainToIdealMover > protocols::simple_moves::ConstrainToIdealMoverOP

◆ ContingentAcceptMoverCOP

typedef utility::pointer::shared_ptr< ContingentAcceptMover const > protocols::simple_moves::ContingentAcceptMoverCOP

◆ ContingentAcceptMoverOP

typedef utility::pointer::shared_ptr< ContingentAcceptMover > protocols::simple_moves::ContingentAcceptMoverOP

◆ ConvertRealToVirtualMoverCOP

typedef utility::pointer::shared_ptr< ConvertRealToVirtualMover const > protocols::simple_moves::ConvertRealToVirtualMoverCOP

◆ ConvertRealToVirtualMoverOP

typedef utility::pointer::shared_ptr< ConvertRealToVirtualMover > protocols::simple_moves::ConvertRealToVirtualMoverOP

◆ CopyDofMoverCOP

typedef utility::pointer::shared_ptr< CopyDofMover const > protocols::simple_moves::CopyDofMoverCOP

◆ CopyDofMoverOP

typedef utility::pointer::shared_ptr< CopyDofMover > protocols::simple_moves::CopyDofMoverOP

◆ CopyRotamerMoverCOP

typedef utility::pointer::shared_ptr< CopyRotamerMover const > protocols::simple_moves::CopyRotamerMoverCOP

◆ CopyRotamerMoverOP

typedef utility::pointer::shared_ptr< CopyRotamerMover > protocols::simple_moves::CopyRotamerMoverOP

◆ CoupledMoverCOP

typedef utility::pointer::shared_ptr< CoupledMover const > protocols::simple_moves::CoupledMoverCOP

◆ CoupledMoverOP

typedef utility::pointer::shared_ptr< CoupledMover > protocols::simple_moves::CoupledMoverOP

◆ CutChainMoverCOP

typedef utility::pointer::shared_ptr< CutChainMover const > protocols::simple_moves::CutChainMoverCOP

◆ CutChainMoverOP

typedef utility::pointer::shared_ptr< CutChainMover > protocols::simple_moves::CutChainMoverOP

◆ CyclizationMoverCOP

typedef utility::pointer::shared_ptr< CyclizationMover const > protocols::simple_moves::CyclizationMoverCOP

◆ CyclizationMoverOP

typedef utility::pointer::shared_ptr< CyclizationMover > protocols::simple_moves::CyclizationMoverOP

◆ DeclareBondCOP

typedef utility::pointer::shared_ptr< DeclareBond const > protocols::simple_moves::DeclareBondCOP

◆ DeclareBondCOPs

typedef utility::vector1<DeclareBondCOP> protocols::simple_moves::DeclareBondCOPs

◆ DeclareBondOP

typedef utility::pointer::shared_ptr< DeclareBond > protocols::simple_moves::DeclareBondOP

◆ DeclareBondOPs

typedef utility::vector1<DeclareBondOP> protocols::simple_moves::DeclareBondOPs

◆ DEEROptimizeCoordsMoverCOP

typedef utility::pointer::shared_ptr< DEEROptimizeCoordsMover const > protocols::simple_moves::DEEROptimizeCoordsMoverCOP

◆ DEEROptimizeCoordsMoverOP

typedef utility::pointer::shared_ptr< DEEROptimizeCoordsMover > protocols::simple_moves::DEEROptimizeCoordsMoverOP

◆ DeleteChainMoverCOP

typedef utility::pointer::shared_ptr< DeleteChainMover const > protocols::simple_moves::DeleteChainMoverCOP

◆ DeleteChainMoverOP

typedef utility::pointer::shared_ptr< DeleteChainMover > protocols::simple_moves::DeleteChainMoverOP

◆ DeleteChainsMoverCOP

typedef utility::pointer::shared_ptr< DeleteChainsMover const > protocols::simple_moves::DeleteChainsMoverCOP

◆ DeleteChainsMoverOP

typedef utility::pointer::shared_ptr< DeleteChainsMover > protocols::simple_moves::DeleteChainsMoverOP

◆ DisulfideInsertionMoverCOP

typedef utility::pointer::shared_ptr< DisulfideInsertionMover const > protocols::simple_moves::DisulfideInsertionMoverCOP

◆ DisulfideInsertionMoverCreatorCOP

typedef utility::pointer::shared_ptr< DisulfideInsertionMoverCreator const > protocols::simple_moves::DisulfideInsertionMoverCreatorCOP

◆ DisulfideInsertionMoverCreatorOP

typedef utility::pointer::shared_ptr< DisulfideInsertionMoverCreator > protocols::simple_moves::DisulfideInsertionMoverCreatorOP

◆ DisulfideInsertionMoverOP

typedef utility::pointer::shared_ptr< DisulfideInsertionMover > protocols::simple_moves::DisulfideInsertionMoverOP

◆ DumpPdbCOP

typedef utility::pointer::shared_ptr< DumpPdb const > protocols::simple_moves::DumpPdbCOP

◆ DumpPdbOP

typedef utility::pointer::shared_ptr< DumpPdb > protocols::simple_moves::DumpPdbOP

◆ DumpSingleResidueRotamersCOP

typedef utility::pointer::shared_ptr< DumpSingleResidueRotamers const > protocols::simple_moves::DumpSingleResidueRotamersCOP

◆ DumpSingleResidueRotamersOP

typedef utility::pointer::shared_ptr< DumpSingleResidueRotamers > protocols::simple_moves::DumpSingleResidueRotamersOP

◆ ExplicitWaterMoverCOP

typedef utility::pointer::shared_ptr< ExplicitWaterMover const > protocols::simple_moves::ExplicitWaterMoverCOP

◆ ExplicitWaterMoverOP

typedef utility::pointer::shared_ptr< ExplicitWaterMover > protocols::simple_moves::ExplicitWaterMoverOP

◆ FavorSymmetricSequenceCOP

typedef utility::pointer::shared_ptr< FavorSymmetricSequence const > protocols::simple_moves::FavorSymmetricSequenceCOP

◆ FavorSymmetricSequenceOP

typedef utility::pointer::shared_ptr< FavorSymmetricSequence > protocols::simple_moves::FavorSymmetricSequenceOP

◆ FragmentCostCOP

typedef utility::pointer::shared_ptr< FragmentCost const > protocols::simple_moves::FragmentCostCOP

◆ FragmentCostOP

typedef utility::pointer::shared_ptr< FragmentCost > protocols::simple_moves::FragmentCostOP

◆ FragmentMoverCOP

typedef utility::pointer::shared_ptr< FragmentMover const > protocols::simple_moves::FragmentMoverCOP

◆ FragmentMoverOP

typedef utility::pointer::shared_ptr< FragmentMover > protocols::simple_moves::FragmentMoverOP

◆ LoadPDBMoverCOP

typedef utility::pointer::shared_ptr< LoadPDBMover const > protocols::simple_moves::LoadPDBMoverCOP

◆ LoadPDBMoverOP

typedef utility::pointer::shared_ptr< LoadPDBMover > protocols::simple_moves::LoadPDBMoverOP

◆ LoadUnboundRotMoverCOP

typedef utility::pointer::shared_ptr< LoadUnboundRotMover const > protocols::simple_moves::LoadUnboundRotMoverCOP

◆ LoadUnboundRotMoverOP

typedef utility::pointer::shared_ptr< LoadUnboundRotMover > protocols::simple_moves::LoadUnboundRotMoverOP

◆ MembraneTopologyCOP

typedef utility::pointer::shared_ptr< MembraneTopology const > protocols::simple_moves::MembraneTopologyCOP

◆ MembraneTopologyOP

typedef utility::pointer::shared_ptr< MembraneTopology > protocols::simple_moves::MembraneTopologyOP

◆ MissingDensityToJumpMoverCOP

typedef utility::pointer::shared_ptr< MissingDensityToJumpMover const > protocols::simple_moves::MissingDensityToJumpMoverCOP

◆ MissingDensityToJumpMoverOP

typedef utility::pointer::shared_ptr< MissingDensityToJumpMover > protocols::simple_moves::MissingDensityToJumpMoverOP

◆ ModifyVariantTypeMoverCOP

typedef utility::pointer::shared_ptr< ModifyVariantTypeMover const > protocols::simple_moves::ModifyVariantTypeMoverCOP

◆ ModifyVariantTypeMoverOP

typedef utility::pointer::shared_ptr< ModifyVariantTypeMover > protocols::simple_moves::ModifyVariantTypeMoverOP

◆ MutateResidueCOP

typedef utility::pointer::shared_ptr< MutateResidue const > protocols::simple_moves::MutateResidueCOP

◆ MutateResidueOP

typedef utility::pointer::shared_ptr< MutateResidue > protocols::simple_moves::MutateResidueOP

◆ PDBReloadMoverCOP

typedef utility::pointer::shared_ptr< PDBReloadMover const > protocols::simple_moves::PDBReloadMoverCOP

◆ PDBReloadMoverOP

typedef utility::pointer::shared_ptr< PDBReloadMover > protocols::simple_moves::PDBReloadMoverOP

◆ PeptideStapleMoverCOP

typedef utility::pointer::shared_ptr< PeptideStapleMover const > protocols::simple_moves::PeptideStapleMoverCOP

◆ PeptideStapleMoverOP

typedef utility::pointer::shared_ptr< PeptideStapleMover > protocols::simple_moves::PeptideStapleMoverOP

◆ PeriodicBoxMoverCOP

typedef utility::pointer::shared_ptr< PeriodicBoxMover const > protocols::simple_moves::PeriodicBoxMoverCOP

◆ PeriodicBoxMoverOP

typedef utility::pointer::shared_ptr< PeriodicBoxMover > protocols::simple_moves::PeriodicBoxMoverOP

◆ PoseFromPoseResourceMoverCOP

typedef utility::pointer::shared_ptr< PoseFromPoseResourceMover const > protocols::simple_moves::PoseFromPoseResourceMoverCOP

◆ PoseFromPoseResourceMoverOP

typedef utility::pointer::shared_ptr< PoseFromPoseResourceMover > protocols::simple_moves::PoseFromPoseResourceMoverOP

◆ Probability

typedef core::Real protocols::simple_moves::Probability

◆ ProlineFixMoverCOP

typedef utility::pointer::shared_ptr< ProlineFixMover const > protocols::simple_moves::ProlineFixMoverCOP

◆ ProlineFixMoverOP

typedef utility::pointer::shared_ptr< ProlineFixMover > protocols::simple_moves::ProlineFixMoverOP

◆ PSSM2BfactorMoverCOP

typedef utility::pointer::shared_ptr< PSSM2BfactorMover const > protocols::simple_moves::PSSM2BfactorMoverCOP

◆ PSSM2BfactorMoverOP

typedef utility::pointer::shared_ptr< PSSM2BfactorMover > protocols::simple_moves::PSSM2BfactorMoverOP

◆ PWatRotamerCloud

typedef utility::vector1< utility::vector1< core::Vector > > protocols::simple_moves::PWatRotamerCloud

◆ RandomOmegaFlipMoverCOP

typedef utility::pointer::shared_ptr< RandomOmegaFlipMover const > protocols::simple_moves::RandomOmegaFlipMoverCOP

◆ RandomOmegaFlipMoverOP

typedef utility::pointer::shared_ptr< RandomOmegaFlipMover > protocols::simple_moves::RandomOmegaFlipMoverOP

◆ RandomTorsionMoverCOP

typedef utility::pointer::shared_ptr< RandomTorsionMover const > protocols::simple_moves::RandomTorsionMoverCOP

◆ RandomTorsionMoverOP

typedef utility::pointer::shared_ptr< RandomTorsionMover > protocols::simple_moves::RandomTorsionMoverOP

◆ RepeatPropagationMoverCOP

typedef utility::pointer::shared_ptr< RepeatPropagationMover const > protocols::simple_moves::RepeatPropagationMoverCOP

◆ RepeatPropagationMoverOP

typedef utility::pointer::shared_ptr< RepeatPropagationMover > protocols::simple_moves::RepeatPropagationMoverOP

◆ RepeatProteinRelaxCOP

typedef utility::pointer::shared_ptr< RepeatProteinRelax const > protocols::simple_moves::RepeatProteinRelaxCOP

◆ RepeatProteinRelaxOP

typedef utility::pointer::shared_ptr< RepeatProteinRelax > protocols::simple_moves::RepeatProteinRelaxOP

◆ ReportXYZCOP

typedef utility::pointer::shared_ptr< ReportXYZ const > protocols::simple_moves::ReportXYZCOP

◆ ReportXYZOP

typedef utility::pointer::shared_ptr< ReportXYZ > protocols::simple_moves::ReportXYZOP

◆ RepulsiveOnlyMoverCOP

typedef utility::pointer::shared_ptr< RepulsiveOnlyMover const > protocols::simple_moves::RepulsiveOnlyMoverCOP

◆ RepulsiveOnlyMoverOP

typedef utility::pointer::shared_ptr< RepulsiveOnlyMover > protocols::simple_moves::RepulsiveOnlyMoverOP

◆ ResetFoldTreeCOP

typedef utility::pointer::shared_ptr< ResetFoldTree const > protocols::simple_moves::ResetFoldTreeCOP

◆ ResetFoldTreeOP

typedef utility::pointer::shared_ptr< ResetFoldTree > protocols::simple_moves::ResetFoldTreeOP

◆ ResetFullModelInfoMoverCOP

using protocols::simple_moves::ResetFullModelInfoMoverCOP = typedef utility::pointer::shared_ptr< ResetFullModelInfoMover const >

◆ ResetFullModelInfoMoverOP

using protocols::simple_moves::ResetFullModelInfoMoverOP = typedef utility::pointer::shared_ptr< ResetFullModelInfoMover >

◆ ResTypeFragmentMoverCOP

typedef utility::pointer::shared_ptr< ResTypeFragmentMover const > protocols::simple_moves::ResTypeFragmentMoverCOP

◆ ResTypeFragmentMoverOP

typedef utility::pointer::shared_ptr< ResTypeFragmentMover > protocols::simple_moves::ResTypeFragmentMoverOP

◆ ReturnSidechainMoverCOP

typedef utility::pointer::shared_ptr< ReturnSidechainMover const > protocols::simple_moves::ReturnSidechainMoverCOP

◆ ReturnSidechainMoverOP

typedef utility::pointer::shared_ptr< ReturnSidechainMover > protocols::simple_moves::ReturnSidechainMoverOP

◆ RingConformationMoverCOP

typedef utility::pointer::shared_ptr< RingConformationMover const > protocols::simple_moves::RingConformationMoverCOP

◆ RingConformationMoverOP

typedef utility::pointer::shared_ptr< RingConformationMover > protocols::simple_moves::RingConformationMoverOP

◆ SampleSequenceFromProbabilitiesCOP

using protocols::simple_moves::SampleSequenceFromProbabilitiesCOP = typedef utility::pointer::shared_ptr< SampleSequenceFromProbabilities const >

◆ SampleSequenceFromProbabilitiesOP

using protocols::simple_moves::SampleSequenceFromProbabilitiesOP = typedef utility::pointer::shared_ptr< SampleSequenceFromProbabilities >

◆ SaveProbabilitiesMetricMoverCOP

using protocols::simple_moves::SaveProbabilitiesMetricMoverCOP = typedef utility::pointer::shared_ptr< SaveProbabilitiesMetricMover const >

◆ SaveProbabilitiesMetricMoverOP

using protocols::simple_moves::SaveProbabilitiesMetricMoverOP = typedef utility::pointer::shared_ptr< SaveProbabilitiesMetricMover >

◆ ScoreList

typedef utility::vector1< core::Real > protocols::simple_moves::ScoreList

◆ ScoreMoverCOP

typedef utility::pointer::shared_ptr< ScoreMover const > protocols::simple_moves::ScoreMoverCOP

◆ ScoreMoverOP

typedef utility::pointer::shared_ptr< ScoreMover > protocols::simple_moves::ScoreMoverOP

◆ SequenceProfileMoverCOP

typedef utility::pointer::shared_ptr< SequenceProfileMover const > protocols::simple_moves::SequenceProfileMoverCOP

◆ SequenceProfileMoverOP

typedef utility::pointer::shared_ptr< SequenceProfileMover > protocols::simple_moves::SequenceProfileMoverOP

◆ SetTorsionCOP

typedef utility::pointer::shared_ptr< SetTorsion const > protocols::simple_moves::SetTorsionCOP

◆ SetTorsionOP

typedef utility::pointer::shared_ptr< SetTorsion > protocols::simple_moves::SetTorsionOP

◆ SetupMetalsMoverCOP

typedef utility::pointer::shared_ptr< SetupMetalsMover const > protocols::simple_moves::SetupMetalsMoverCOP

◆ SetupMetalsMoverOP

typedef utility::pointer::shared_ptr< SetupMetalsMover > protocols::simple_moves::SetupMetalsMoverOP

◆ ShakeStructureMoverCOP

typedef utility::pointer::shared_ptr< ShakeStructureMover const > protocols::simple_moves::ShakeStructureMoverCOP

◆ ShakeStructureMoverOP

typedef utility::pointer::shared_ptr< ShakeStructureMover > protocols::simple_moves::ShakeStructureMoverOP

◆ ShearMoverCOP

typedef utility::pointer::shared_ptr< ShearMover const > protocols::simple_moves::ShearMoverCOP

◆ ShearMoverOP

typedef utility::pointer::shared_ptr< ShearMover > protocols::simple_moves::ShearMoverOP

◆ ShortBackrubMoverCOP

typedef utility::pointer::shared_ptr< ShortBackrubMover const > protocols::simple_moves::ShortBackrubMoverCOP

◆ ShortBackrubMoverOP

typedef utility::pointer::shared_ptr< ShortBackrubMover > protocols::simple_moves::ShortBackrubMoverOP

◆ SimpleThreadingMoverCOP

typedef utility::pointer::shared_ptr< SimpleThreadingMover const > protocols::simple_moves::SimpleThreadingMoverCOP

◆ SimpleThreadingMoverOP

typedef utility::pointer::shared_ptr< SimpleThreadingMover > protocols::simple_moves::SimpleThreadingMoverOP

◆ SixDoFGridDockMoverCOP

using protocols::simple_moves::SixDoFGridDockMoverCOP = typedef utility::pointer::shared_ptr< SixDoFGridDockMover const >

◆ SixDoFGridDockMoverOP

using protocols::simple_moves::SixDoFGridDockMoverOP = typedef utility::pointer::shared_ptr< SixDoFGridDockMover >

◆ SmallMoverCOP

typedef utility::pointer::shared_ptr< SmallMover const > protocols::simple_moves::SmallMoverCOP

◆ SmallMoverOP

typedef utility::pointer::shared_ptr< SmallMover > protocols::simple_moves::SmallMoverOP

◆ SmoothFragmentMoverCOP

typedef utility::pointer::shared_ptr< SmoothFragmentMover const > protocols::simple_moves::SmoothFragmentMoverCOP

◆ SmoothFragmentMoverOP

typedef utility::pointer::shared_ptr< SmoothFragmentMover > protocols::simple_moves::SmoothFragmentMoverOP

◆ SmoothSymmetricFragmentMoverCOP

typedef utility::pointer::shared_ptr< SmoothSymmetricFragmentMover const > protocols::simple_moves::SmoothSymmetricFragmentMoverCOP

◆ SmoothSymmetricFragmentMoverOP

typedef utility::pointer::shared_ptr< SmoothSymmetricFragmentMover > protocols::simple_moves::SmoothSymmetricFragmentMoverOP

◆ StorePoseSnapshotCOP

typedef utility::pointer::shared_ptr< StorePoseSnapshot const > protocols::simple_moves::StorePoseSnapshotCOP

◆ StorePoseSnapshotOP

typedef utility::pointer::shared_ptr< StorePoseSnapshot > protocols::simple_moves::StorePoseSnapshotOP

◆ StructProfileMoverCOP

typedef utility::pointer::shared_ptr< StructProfileMover const > protocols::simple_moves::StructProfileMoverCOP

◆ StructProfileMoverOP

typedef utility::pointer::shared_ptr< StructProfileMover > protocols::simple_moves::StructProfileMoverOP

◆ SuperimposeMoverCOP

typedef utility::pointer::shared_ptr< SuperimposeMover const > protocols::simple_moves::SuperimposeMoverCOP

◆ SuperimposeMoverOP

typedef utility::pointer::shared_ptr< SuperimposeMover > protocols::simple_moves::SuperimposeMoverOP

◆ SwitchChainOrderMoverCOP

typedef utility::pointer::shared_ptr< SwitchChainOrderMover const > protocols::simple_moves::SwitchChainOrderMoverCOP

◆ SwitchChainOrderMoverOP

typedef utility::pointer::shared_ptr< SwitchChainOrderMover > protocols::simple_moves::SwitchChainOrderMoverOP

◆ SwitchResidueTypeSetMoverCOP

typedef utility::pointer::shared_ptr< SwitchResidueTypeSetMover const > protocols::simple_moves::SwitchResidueTypeSetMoverCOP

◆ SwitchResidueTypeSetMoverOP

typedef utility::pointer::shared_ptr< SwitchResidueTypeSetMover > protocols::simple_moves::SwitchResidueTypeSetMoverOP

◆ SymmetricFragmentMoverCOP

typedef utility::pointer::shared_ptr< SymmetricFragmentMover const > protocols::simple_moves::SymmetricFragmentMoverCOP

◆ SymmetricFragmentMoverOP

typedef utility::pointer::shared_ptr< SymmetricFragmentMover > protocols::simple_moves::SymmetricFragmentMoverOP

◆ TorsionDOFMoverCOP

typedef utility::pointer::shared_ptr< TorsionDOFMover const > protocols::simple_moves::TorsionDOFMoverCOP

◆ TorsionDOFMoverOP

typedef utility::pointer::shared_ptr< TorsionDOFMover > protocols::simple_moves::TorsionDOFMoverOP

◆ TorsionSetMoverCOP

typedef utility::pointer::shared_ptr< TorsionSetMover const > protocols::simple_moves::TorsionSetMoverCOP

◆ TorsionSetMoverOP

typedef utility::pointer::shared_ptr< TorsionSetMover > protocols::simple_moves::TorsionSetMoverOP

◆ UniformRotationMoverCOP

typedef utility::pointer::shared_ptr< UniformRotationMover const > protocols::simple_moves::UniformRotationMoverCOP

◆ UniformRotationMoverOP

typedef utility::pointer::shared_ptr< UniformRotationMover > protocols::simple_moves::UniformRotationMoverOP

◆ UniformTranslationMoverCOP

typedef utility::pointer::shared_ptr< UniformTranslationMover const > protocols::simple_moves::UniformTranslationMoverCOP

◆ UniformTranslationMoverOP

typedef utility::pointer::shared_ptr< UniformTranslationMover > protocols::simple_moves::UniformTranslationMoverOP

◆ VirtualRootMoverCOP

typedef utility::pointer::shared_ptr< VirtualRootMover const > protocols::simple_moves::VirtualRootMoverCOP

◆ VirtualRootMoverOP

typedef utility::pointer::shared_ptr< VirtualRootMover > protocols::simple_moves::VirtualRootMoverOP

◆ VirtualToFaMoverCOP

typedef utility::pointer::shared_ptr< ConvertVirtualToRealMover const > protocols::simple_moves::VirtualToFaMoverCOP

◆ VirtualToFaMoverOP

typedef utility::pointer::shared_ptr< ConvertVirtualToRealMover > protocols::simple_moves::VirtualToFaMoverOP

◆ WobbleMoverCOP

typedef utility::pointer::shared_ptr< const WobbleMover > protocols::simple_moves::WobbleMoverCOP

◆ WobbleMoverOP

typedef utility::pointer::shared_ptr< WobbleMover > protocols::simple_moves::WobbleMoverOP

◆ WriteSSEMoverCOP

typedef utility::pointer::shared_ptr< WriteSSEMover const > protocols::simple_moves::WriteSSEMoverCOP

◆ WriteSSEMoverOP

typedef utility::pointer::shared_ptr< WriteSSEMover > protocols::simple_moves::WriteSSEMoverOP

Enumeration Type Documentation

◆ DisulfideCyclizationViability

enum protocols::simple_moves::DisulfideCyclizationViability
Enumerator
DCV_NOT_CYCLIZABLE 
DCV_CYCLIZABLE 
DCV_ALREADY_CYCLIZED 

◆ TorsionPerturbType

enum protocols::simple_moves::TorsionPerturbType
Enumerator
perturbtorsion_uniform 
perturbtorsion_gaussian 
perturbtorsion_unknown 

Function Documentation

◆ apply_ideal_coordinates_for_alternative_pucker()

void protocols::simple_moves::apply_ideal_coordinates_for_alternative_pucker ( core::pose::Pose const &  pose,
core::pose::Pose &  pose_reference 
)

References core::pose::rna::apply_ideal_c2endo_sugar_coords(), core::pose::rna::apply_pucker(), core::chemical::rna::DELTA, core::chemical::rna::RNA_FittedTorsionInfo::delta_cutoff(), core::chemical::ResidueTypeBase::is_RNA(), core::conformation::Residue::mainchain_torsion(), core::chemical::rna::NORTH, core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::size(), and core::chemical::rna::SOUTH.

Referenced by protocols::simple_moves::ConstrainToIdealMover::create_pose_reference().

◆ Ca_coord()

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

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

Referenced by protocols::simple_moves::AlignChainMover::apply().

◆ Ca_coords()

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

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

Referenced by protocols::simple_moves::AddChainMover::swap_chain().

◆ check_if_proton_chi_atom() [1/2]

core::Size protocols::simple_moves::check_if_proton_chi_atom ( core::chemical::ResidueType const &  rsd_type,
core::Size const  j 
)

References core::chemical::ResidueType::chi_atoms(), core::chemical::ResidueType::n_proton_chi(), and core::chemical::ResidueType::proton_chi_2_chi().

Referenced by check_if_proton_chi_atom(), protocols::simple_moves::ConstrainToIdealMover::i_want_this_atom_to_move(), and protocols::simple_moves::ConstrainToIdealMover::vary_bond_geometry().

◆ check_if_proton_chi_atom() [2/2]

core::Size protocols::simple_moves::check_if_proton_chi_atom ( core::pose::Pose const &  pose,
core::Size const  i,
core::Size const  j 
)

References check_if_proton_chi_atom(), and core::pose::Pose::residue_type().

◆ has_option()

bool protocols::simple_moves::has_option ( utility::tag::TagCOP const &  tag,
std::string const &  key 
)

Referenced by protocols::simple_moves::AddSapMathConstraintMover::parse_my_tag().

◆ operator<<() [1/18]

std::ostream & protocols::simple_moves::operator<< ( std::ostream &  os,
BackboneMover const &  mover 
)

References protocols::simple_moves::BackboneMover::show().

◆ operator<<() [2/18]

std::ostream & protocols::simple_moves::operator<< ( std::ostream &  os,
BBDihedralSamplerMover const &  mover 
)

References protocols::simple_moves::BBDihedralSamplerMover::show().

◆ operator<<() [3/18]

std::ostream & protocols::simple_moves::operator<< ( std::ostream &  os,
ClassicFragmentMover const &  cfmover 
)

References protocols::simple_moves::ClassicFragmentMover::show().

◆ operator<<() [4/18]

std::ostream & protocols::simple_moves::operator<< ( std::ostream &  os,
ConcatenatePosesMover const &  mover 
)

private methods ///

References protocols::simple_moves::ConcatenatePosesMover::show().

◆ operator<<() [5/18]

std::ostream & protocols::simple_moves::operator<< ( std::ostream &  os,
ConvertRealToVirtualMover const &  mover 
)

References protocols::simple_moves::ConvertRealToVirtualMover::show().

◆ operator<<() [6/18]

std::ostream & protocols::simple_moves::operator<< ( std::ostream &  os,
ConvertVirtualToRealMover const &  mover 
)

References protocols::simple_moves::ConvertVirtualToRealMover::show().

◆ operator<<() [7/18]

std::ostream & protocols::simple_moves::operator<< ( std::ostream &  os,
CopyRotamerMover const &  mover 
)

Get the name of the Mover.

References protocols::simple_moves::CopyRotamerMover::show().

◆ operator<<() [8/18]

std::ostream & protocols::simple_moves::operator<< ( std::ostream &  os,
DOFHistogramRecorder const &  dof_recorder 
)

References protocols::simple_moves::DOFHistogramRecorder::histograms().

◆ operator<<() [9/18]

std::ostream & protocols::simple_moves::operator<< ( std::ostream &  os,
DumpSingleResidueRotamers const &  mover 
)

private methods ///

References protocols::simple_moves::DumpSingleResidueRotamers::show().

◆ operator<<() [10/18]

std::ostream & protocols::simple_moves::operator<< ( std::ostream &  os,
PoseFromPoseResourceMover const &  mover 
)

private methods ///

References protocols::simple_moves::PoseFromPoseResourceMover::show().

◆ operator<<() [11/18]

std::ostream & protocols::simple_moves::operator<< ( std::ostream &  os,
ResetFullModelInfoMover const &  mover 
)

private methods ///

References protocols::simple_moves::ResetFullModelInfoMover::show().

◆ operator<<() [12/18]

std::ostream & protocols::simple_moves::operator<< ( std::ostream &  os,
ReturnSidechainMover const &  mover 
)

References protocols::simple_moves::ReturnSidechainMover::show().

◆ operator<<() [13/18]

std::ostream & protocols::simple_moves::operator<< ( std::ostream &  os,
SampleSequenceFromProbabilities const &  mover 
)

References protocols::simple_moves::SampleSequenceFromProbabilities::show().

◆ operator<<() [14/18]

std::ostream & protocols::simple_moves::operator<< ( std::ostream &  os,
SaveProbabilitiesMetricMover const &  mover 
)

private methods ///

References protocols::moves::Mover::show().

◆ operator<<() [15/18]

std::ostream & protocols::simple_moves::operator<< ( std::ostream &  os,
SetupMetalsMover const &  mover 
)

References protocols::simple_moves::SetupMetalsMover::show().

◆ operator<<() [16/18]

std::ostream & protocols::simple_moves::operator<< ( std::ostream &  os,
SixDoFGridDockMover const &  mover 
)

private methods ///

References protocols::simple_moves::SixDoFGridDockMover::show().

◆ operator<<() [17/18]

std::ostream & protocols::simple_moves::operator<< ( std::ostream &  os,
SwitchResidueTypeSetMover const &  mover 
)

References protocols::simple_moves::SwitchResidueTypeSetMover::show().

◆ operator<<() [18/18]

std::ostream & protocols::simple_moves::operator<< ( std::ostream &  output,
RingConformationMover const &  object_to_output 
)

References protocols::simple_moves::RingConformationMover::show().

◆ point_graph_dme()

Real protocols::simple_moves::point_graph_dme ( conformation::PointGraph const &  pg,
pose::Pose const &  pose 
)

Calculate the dme using a pointgraph

References core::conformation::Residue::nbr_atom_xyz(), core::pose::Pose::residue(), core::pose::Pose::size(), and protocols::analysis::total.

Referenced by protocols::simple_moves::DME_FilterMover::apply().

◆ random_rotation()

numeric::xyzMatrix<core::Real> protocols::simple_moves::random_rotation ( core::Real  magnitude)

References core::scoring::rg.

Referenced by protocols::simple_moves::PeriodicBoxMover::perturb_molecule_move().

◆ setup_dme_point_graph()

conformation::PointGraphOP protocols::simple_moves::setup_dme_point_graph ( pose::Pose const &  ref_pose,
Real const  threshold 
)

Setup a pointgraph for later use in dma calcs

References core::pose::Pose::conformation(), and core::conformation::residue_point_graph_from_conformation().

Referenced by protocols::simple_moves::DME_FilterMover::apply().

◆ setup_vary_polar_hydrogen_geometry()

void protocols::simple_moves::setup_vary_polar_hydrogen_geometry ( core::kinematics::MoveMap &  mm,
core::pose::Pose &  pose,
core::pose::toolbox::AtomLevelDomainMapCOP  atom_level_domain_map 
)

References protocols::simple_moves::ConstrainToIdealMover::apply(), core::scoring::bond_geometry, protocols::simple_moves::ConstrainToIdealMover::set_atom_level_domain_map(), protocols::simple_moves::ConstrainToIdealMover::set_just_polar_hydrogens(), and protocols::simple_moves::ConstrainToIdealMover::set_score_type().

Referenced by protocols::stepwise::modeler::StepWiseMinimizer::setup_vary_bond_geometry().

◆ setup_vary_rna_bond_geometry()

void protocols::simple_moves::setup_vary_rna_bond_geometry ( core::kinematics::MoveMap &  mm,
core::pose::Pose &  pose,
core::pose::toolbox::AtomLevelDomainMapCOP  atom_level_domain_map,
core::scoring::ScoreType  score_type 
)

References protocols::simple_moves::ConstrainToIdealMover::apply(), protocols::simple_moves::ConstrainToIdealMover::set_atom_level_domain_map(), protocols::simple_moves::ConstrainToIdealMover::set_just_rna_backbone(), and protocols::simple_moves::ConstrainToIdealMover::set_score_type().

Referenced by protocols::stepwise::modeler::StepWiseMinimizer::setup_vary_bond_geometry().

◆ TR() [1/29]

static basic::Tracer protocols::simple_moves::TR ( "protocol.mover.RepulsiveOnlyMover"  )
static

◆ TR() [2/29]

static basic::Tracer protocols::simple_moves::TR ( "protocols.loops.FoldTreeFromMotif"  )
static

◆ TR() [3/29]

static basic::Tracer protocols::simple_moves::TR ( "protocols.mover.MissingDensityToJumpMover"  )
static

◆ TR() [4/29]

static basic::Tracer protocols::simple_moves::TR ( "protocols.moves.ExplicitWaterMover"  )
static

◆ TR() [5/29]

static basic::Tracer protocols::simple_moves::TR ( "protocols.simple_moves.AddJobPairData"  )
static

◆ TR() [6/29]

static basic::Tracer protocols::simple_moves::TR ( "protocols.simple_moves.AddPDBInfoMover"  )
static

◆ TR() [7/29]

static basic::Tracer protocols::simple_moves::TR ( "protocols.simple_moves.AddResidueCouplingConstraint"  )
static

◆ TR() [8/29]

static basic::Tracer protocols::simple_moves::TR ( "protocols.simple_moves.AddSapConstraintMover"  )
static

◆ TR() [9/29]

static basic::Tracer protocols::simple_moves::TR ( "protocols.simple_moves.AddSapMathConstraintMover"  )
static

◆ TR() [10/29]

static basic::Tracer protocols::simple_moves::TR ( "protocols.simple_moves.CombinePoseMover"  )
static

◆ TR() [11/29]

static basic::Tracer protocols::simple_moves::TR ( "protocols.simple_moves.CutChainMover"  )
static

◆ TR() [12/29]

static basic::Tracer protocols::simple_moves::TR ( "protocols.simple_moves.CyclizationMover"  )
static

◆ TR() [13/29]

static basic::Tracer protocols::simple_moves::TR ( "protocols.simple_moves.DEEROptimizeCoordsMover"  )
static

◆ TR() [14/29]

static basic::Tracer protocols::simple_moves::TR ( "protocols.simple_moves.DeleteChainMover"  )
static

◆ TR() [15/29]

static basic::Tracer protocols::simple_moves::TR ( "protocols.simple_moves.DisulfideInsertionMover"  )
static

◆ TR() [16/29]

static basic::Tracer protocols::simple_moves::TR ( "protocols.simple_moves.DOFHistogramRecorder"  )
static

◆ TR() [17/29]

static basic::Tracer protocols::simple_moves::TR ( "protocols.simple_moves.DumpPdb"  )
static

◆ TR() [18/29]

static basic::Tracer protocols::simple_moves::TR ( "protocols.simple_moves.FavorSequenceProfile"  )
static

◆ TR() [19/29]

static basic::Tracer protocols::simple_moves::TR ( "protocols.simple_moves.FavorSymmetricSequence"  )
static

◆ tr() [1/3]

static basic::Tracer protocols::simple_moves::tr ( "protocols.simple_moves.FragmentMover"  )
static

Referenced by protocols::simple_moves::ClassicFragmentMover::apply(), protocols::simple_moves::SymmetricFragmentMover::apply_fragment(), protocols::simple_moves::ClassicFragmentMover::apply_frames(), protocols::simple_moves::ResTypeFragmentMover::apply_frames(), protocols::simple_moves::ClassicFragmentMover::choose_window_start(), protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMover::compute_rotdensities(), protocols::simple_moves::ClassicFragmentMover::end_bias_check(), protocols::simple_moves::FragmentMover::set_fragments(), and protocols::simple_moves::ClassicFragmentMover::valid_ss().

◆ tr() [2/3]

static basic::Tracer protocols::simple_moves::tr ( "protocols.simple_moves.FragmentMover"  )
static

◆ TR() [20/29]

static basic::Tracer protocols::simple_moves::TR ( "protocols.simple_moves.MembraneTopology"  )
static

◆ TR() [21/29]

static basic::Tracer protocols::simple_moves::TR ( "protocols.simple_moves.ModifyVariantTypeMover"  )
static

◆ TR() [22/29]

static basic::Tracer protocols::simple_moves::TR ( "protocols.simple_moves.MutateResidue"  )
static

◆ TR() [23/29]

static basic::Tracer protocols::simple_moves::TR ( "protocols.simple_moves.PDBReloadMover"  )
static

◆ TR() [24/29]

static basic::Tracer protocols::simple_moves::TR ( "protocols.simple_moves.RepeatPropagationMover"  )
static

Referenced by protocols::simple_moves::ConstrainToIdealMover::add_bond_angle_constraint(), protocols::simple_moves::ConstrainToIdealMover::add_bond_dihedral_constraint(), protocols::simple_moves::ConstrainToIdealMover::add_bond_length_constraint(), protocols::simple_moves::AddChainMover::add_new_chain(), protocols::simple_moves::BackboneMover::apply(), protocols::simple_moves::ReportEffectivePKA::apply(), protocols::simple_moves::RingConformationMover::apply(), protocols::simple_moves::PeptideStapleMover::apply(), protocols::simple_moves::LoadPDBMover::apply(), protocols::simple_moves::AddResidueCouplingConstraint::apply(), protocols::simple_moves::AddResidueLabelMover::apply(), protocols::simple_moves::AlignChainMover::apply(), protocols::simple_moves::BBDihedralSamplerMover::apply(), protocols::simple_moves::ChangeAndResetFoldTreeMover::apply(), protocols::simple_moves::ContingentAcceptMover::apply(), protocols::simple_moves::ConvertRealToVirtualMover::apply(), protocols::simple_moves::ConvertVirtualToRealMover::apply(), protocols::simple_moves::CopyRotamerMover::apply(), protocols::simple_moves::CoupledMover::apply(), protocols::simple_moves::DeleteChainMover::apply(), protocols::simple_moves::DisulfideInsertionMover::apply(), protocols::simple_moves::DME_FilterMover::apply(), protocols::simple_moves::DumpPdb::apply(), protocols::simple_moves::FavorSequenceProfile::apply(), protocols::simple_moves::FavorSymmetricSequence::apply(), protocols::simple_moves::MissingDensityToJumpMover::apply(), protocols::simple_moves::ModifyVariantTypeMover::apply(), protocols::simple_moves::PSSM2BfactorMover::apply(), protocols::simple_moves::RepulsiveOnlyMover::apply(), protocols::simple_moves::ReturnSidechainMover::apply(), protocols::simple_moves::SampleSequenceFromProbabilities::apply(), protocols::simple_moves::SaveProbabilitiesMetricMover::apply(), protocols::simple_moves::SequenceProfileMover::apply(), protocols::simple_moves::SetTorsion::apply(), protocols::simple_moves::SimpleThreadingMover::apply(), protocols::simple_moves::SixDoFGridDockMover::apply(), protocols::simple_moves::StorePoseSnapshot::apply(), protocols::simple_moves::SuperimposeMover::apply(), protocols::simple_moves::SwitchChainOrderMover::apply(), protocols::simple_moves::TorsionDOFMover::apply(), protocols::simple_moves::CombinePoseMover::apply(), protocols::simple_moves::AddJobPairData::apply(), protocols::simple_moves::BBConRotMover::apply(), protocols::simple_moves::DeclareBond::apply(), protocols::simple_moves::ExplicitWaterMover::apply(), protocols::simple_moves::FoldTreeFromMotif::apply(), protocols::simple_moves::PeriodicBoxMover::apply(), protocols::simple_moves::ScoreMover::apply(), protocols::simple_moves::VirtualRootMover::apply(), protocols::simple_moves::WobbleMover::apply_fragment(), protocols::simple_moves::CopyRotamerMover::apply_from_template_pose(), protocols::simple_moves::ExplicitWaterMover::attach_rotamer_clouds_to_pose_and_rotset(), protocols::simple_moves::MutateResidue::break_a_disulfide(), protocols::simple_moves::ExplicitWaterMover::build_backbone_rotamer_clouds(), protocols::simple_moves::ExplicitWaterMover::build_lkboverlap_rotamer_clouds(), protocols::simple_moves::SampleSequenceFromProbabilities::calculate_position_diffs(), protocols::simple_moves::CutChainMover::chain_cut(), protocols::simple_moves::PeriodicBoxMover::change_volume_move(), protocols::simple_moves::PeriodicBoxMover::check_virial_pressure(), protocols::simple_moves::BBConRotMover::closure(), protocols::simple_moves::ExplicitWaterMover::cluster_rotset(), protocols::simple_moves::ConcatenatePosesMover::concatenate_poses(), protocols::simple_moves::PeptideStapleMover::derive_staple_constraints_(), protocols::simple_moves::DisulfideInsertionMover::determine_cyclization_viability(), protocols::simple_moves::SimpleThreadingMover::determine_mutations_comma_separated(), protocols::simple_moves::SimpleThreadingMover::determine_mutations_oneletter(), protocols::simple_moves::ExplicitWaterMover::find_closest(), protocols::simple_moves::CutChainMover::foldTree(), protocols::simple_moves::BBConRotMover::get_determinant(), protocols::simple_moves::bb_sampler::SugarBBSampler::get_torsion(), protocols::simple_moves::ExplicitWaterMover::get_water_recovery(), protocols::simple_moves::BBGaussianMover::init_kic_loop(), protocols::simple_moves::WaterRotsDB::initialize(), protocols::simple_moves::SixDoFGridDockMover::lex_position(), protocols::simple_moves::AddChainMover::load_pose(), protocols::simple_moves::BBConRotMover::make_move(), protocols::simple_moves::MutateResidue::make_mutation(), protocols::simple_moves::DEEROptimizeCoordsMover::minimize(), protocols::simple_moves::PeptideStapleMover::minimize_(), protocols::simple_moves::SmallMover::move_with_scorefxn(), protocols::simple_moves::AddJobPairData::parse_my_tag(), protocols::simple_moves::AddResidueLabelMover::parse_my_tag(), protocols::simple_moves::BBGaussianMover::parse_my_tag(), protocols::simple_moves::ReportEffectivePKA::parse_my_tag(), protocols::simple_moves::DumpPdb::parse_my_tag(), protocols::simple_moves::FavorSequenceProfile::parse_my_tag(), protocols::simple_moves::ModifyVariantTypeMover::parse_my_tag(), protocols::simple_moves::MutateResidue::parse_my_tag(), protocols::simple_moves::SequenceProfileMover::parse_my_tag(), protocols::simple_moves::StorePoseSnapshot::parse_my_tag(), protocols::simple_moves::LoadPDBMover::parse_my_tag(), protocols::simple_moves::AddChainMover::parse_my_tag(), protocols::simple_moves::AlignChainMover::parse_my_tag(), protocols::simple_moves::CopyRotamerMover::parse_my_tag(), protocols::simple_moves::FavorSymmetricSequence::parse_my_tag(), protocols::simple_moves::PoseFromPoseResourceMover::parse_my_tag(), protocols::simple_moves::PSSM2BfactorMover::parse_my_tag(), protocols::simple_moves::SixDoFGridDockMover::parse_my_tag(), protocols::simple_moves::CutChainMover::parse_my_tag(), protocols::simple_moves::ResetFoldTree::parse_my_tag(), protocols::simple_moves::SixDoFGridDockMover::parse_range(), protocols::simple_moves::DEEROptimizeCoordsMover::print_coords(), protocols::simple_moves::RepeatPropagationMover::repeat_ligand(), protocols::simple_moves::RepeatPropagationMover::repeat_ligand_constraints(), protocols::simple_moves::PeriodicBoxMover::report_thermodynamics(), protocols::simple_moves::ExplicitWaterMover::run_pack(), protocols::simple_moves::SampleSequenceFromProbabilities::sample_amino_acid(), protocols::simple_moves::SampleSequenceFromProbabilities::sample_mutations(), protocols::simple_moves::DEEROptimizeCoordsMover::score(), protocols::simple_moves::CopyRotamerMover::set_copy_identity(), protocols::simple_moves::CopyRotamerMover::set_copy_torsions(), protocols::simple_moves::BBDihedralSamplerMover::set_dihedral_mask(), protocols::simple_moves::BBGaussianMover::set_preserve_detailed_balance(), protocols::simple_moves::FavorSequenceProfile::set_profile(), protocols::simple_moves::FavorSequenceProfile::set_sequence(), protocols::simple_moves::CopyRotamerMover::set_target_res_index(), protocols::simple_moves::CopyRotamerMover::set_template_res_index(), protocols::simple_moves::bb_sampler::SmallBBSampler::set_torsion_to_pose(), protocols::simple_moves::bb_sampler::SugarBBSampler::set_torsion_to_pose(), protocols::simple_moves::SampleSequenceFromProbabilities::set_use_cached_data(), protocols::simple_moves::SaveProbabilitiesMetricMover::set_use_cached_data(), protocols::simple_moves::BBDihedralSamplerMover::setup_all_bb_residues(), protocols::simple_moves::CyclizationMover::setup_connections(), protocols::simple_moves::CyclizationMover::setup_constraints(), protocols::simple_moves::BBGaussianMover::setup_list(), protocols::simple_moves::PeriodicBoxMover::setup_LJcorrection(), protocols::simple_moves::CyclizationMover::setup_minimizer(), protocols::simple_moves::ExplicitWaterMover::setup_pack(), protocols::simple_moves::PeriodicBoxMover::setup_pose(), protocols::simple_moves::BBDihedralSamplerMover::setup_samplers(), protocols::simple_moves::CyclizationMover::setup_scorefunction(), protocols::simple_moves::AddChainMover::swap_chain(), uniform_dof_distribution(), protocols::simple_moves::BBGaussianMover::update_counting_last_PDR(), protocols::simple_moves::oop::OopMover::update_hydrogens_(), protocols::simple_moves::triazolamer::TriazolamerMover::update_hydrogens_(), and protocols::simple_moves::BBGaussianMover::~BBGaussianMover().

◆ tr() [3/3]

static basic::Tracer protocols::simple_moves::tr ( "protocols.simple_moves.ResTypeFragmentMover"  )
static

◆ TR() [25/29]

static basic::Tracer protocols::simple_moves::TR ( "protocols.simple_moves.ScoreMover"  )
static

◆ TR() [26/29]

static basic::Tracer protocols::simple_moves::TR ( "protocols.simple_moves.SetTorsion"  )
static

◆ TR() [27/29]

static basic::Tracer protocols::simple_moves::TR ( "protocols.simple_moves.StorePoseSnapshot"  )
static

◆ TR() [28/29]

static basic::Tracer protocols::simple_moves::TR ( "protocols.simple_moves.SuperimposeMover"  )
static

◆ TR() [29/29]

static basic::Tracer protocols::simple_moves::TR ( "protocols.simple_moves.VirtualRootMover"  )
static

◆ trGunnCost()

static basic::Tracer protocols::simple_moves::trGunnCost ( "protocols.FragmentMover.GunnCost"  )
static

◆ uniform_dof_distribution()

utility::vector1< core::Real > protocols::simple_moves::uniform_dof_distribution ( core::id::DOF_Type  dof_type,
core::Size  num_bins,
core::Real  min,
core::Real  max 
)

References protocols::mean_field::max(), protocols::mean_field::min(), core::id::PHI, core::id::THETA, and TR().

Referenced by protocols::simple_moves::DOFHistogramRecorder::write_mse_summary().

Variable Documentation

◆ ED

const core::Real protocols::simple_moves::ED = 2

◆ HILL

const int protocols::simple_moves::HILL = 3

Referenced by protocols::simple_moves::TailsScoreMover::score_mode3(), and protocols::simple_moves::TailsScoreMover::visit().

◆ KT

const core::Real protocols::simple_moves::KT = 15

Referenced by protocols::simple_moves::TailsScoreMover::score_mode2(), and protocols::simple_moves::TailsScoreMover::score_mode3().

◆ PREVIOUS_HILL

const int protocols::simple_moves::PREVIOUS_HILL = 2

Referenced by protocols::simple_moves::TailsScoreMover::score_mode3(), and protocols::simple_moves::TailsScoreMover::visit().

◆ VISITED

const int protocols::simple_moves::VISITED = 1

Referenced by protocols::simple_moves::TailsScoreMover::visit().

◆ VISITED_HILL

const int protocols::simple_moves::VISITED_HILL = 4

Referenced by protocols::simple_moves::TailsScoreMover::score_mode3(), and protocols::simple_moves::TailsScoreMover::visit().

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