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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  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  AlignChainMover
 Align a chain in the working pose to a chain. CA superposition. More...
 
class  AlignChainMoverCreator
 
class  AtomHash
 
struct  AtomHashNode
 
class  BackboneMover
 BackboneMover class has elements of the MC temperature to do repetitions of bb moves (small, shear, wobble, etc.). More...
 
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  BBG8T3AMover
 a particular gaussian mover from the original paper More...
 
class  BBGaussianMover
 the basic class for implementing Gaussian Perturbation of bb 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  ClassicFragmentMover
 A FragmentMover that applies uniform sampling of fragments. More...
 
class  CombinePoseMover
 
class  ConcatenatePosesMover
 links supplied Poses by their termini More...
 
class  ConcatenatePosesMoverCreator
 
class  ConstrainToIdealMover
 
class  ContingentAcceptMover
 
class  ContingentAcceptMoverCreator
 
class  ConvertRealToVirtualMover
 Mover for switching a residue type to all VIRTUAL. A VIRTUAL Residue is one that is not scored or output. More...
 
class  ConvertRealToVirtualMoverCreator
 
class  ConvertVirtualToRealMover
 Mover for switching from VIRTUAL residues to REAL residues. A VIRTUAL residue is one that is not scored or output. More...
 
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  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
 
class  ExplicitWaterMover
 
class  ExplicitWaterMoverCreator
 
class  FavorSequenceProfile
 
class  FavorSequenceProfileCreator
 
class  FavorSymmetricSequence
 
class  FavorSymmetricSequenceCreator
 
class  FoldTreeFromMotif
 
class  FoldTreeFromMotifCreator
 
class  FragmentCost
 
class  FragmentMover
 abstract base class for FragmentMovers More...
 
class  GunnCost
 
struct  GunnTuple
 
struct  Hit
 
class  IonizableResidue
 
struct  less_then_match_rmsd
 
class  LoadPDBMover
 
class  LoadPDBMoverCreator
 
class  LoadUnboundRotMover
 
class  LoadUnboundRotMoverCreator
 
class  LoggedFragmentMover
 
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
 
class  PeptideStapleMover
 
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  RepeatPropagationMover
 
class  RepeatPropagationMoverCreator
 
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  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  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  ShearMoverCreator
 
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  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  SmallMoverCreator
 
class  SmoothFragmentMover
 
class  SmoothSymmetricFragmentMover
 A SymmetricFragmentMover that applies uniform sampling of fragments. More...
 
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
 
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  TailsScoreMover
 
struct  ThermodynamicData
 structure that stores data during simulation More...
 
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
 
struct  WaterRot
 
class  WaterRotsDB
 
class  WobbleMover
 A protocols::moves::Mover class for a classic-wobble analog: a smooth move followed by ccd closure 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
< 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
< 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
 
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
 
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")
 
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.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::Realuniform_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::Realrandom_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)
 
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)
 
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

typedef utility::pointer::shared_ptr< AddChainMover const > protocols::simple_moves::AddChainMoverCOP
typedef utility::pointer::shared_ptr< AddChainMover > protocols::simple_moves::AddChainMoverOP
typedef utility::pointer::shared_ptr< AddJobPairData const > protocols::simple_moves::AddJobPairDataCOP
typedef utility::pointer::shared_ptr< AddJobPairData > protocols::simple_moves::AddJobPairDataOP
typedef utility::pointer::shared_ptr< AddPDBInfoMover const > protocols::simple_moves::AddPDBInfoMoverCOP
typedef utility::pointer::shared_ptr< AddPDBInfoMover > protocols::simple_moves::AddPDBInfoMoverOP
typedef utility::pointer::shared_ptr< AddResidueLabelMover const > protocols::simple_moves::AddResidueLabelMoverCOP
typedef utility::pointer::shared_ptr<AddResidueTensorConstraint> protocols::simple_moves::AddResidueTensorConstraintOP
typedef utility::pointer::shared_ptr< AlignChainMover const > protocols::simple_moves::AlignChainMoverCOP
typedef utility::pointer::shared_ptr< AlignChainMover > protocols::simple_moves::AlignChainMoverOP
typedef utility::pointer::shared_ptr< BackboneMover const > protocols::simple_moves::BackboneMoverCOP
typedef utility::pointer::shared_ptr< BackboneMover > protocols::simple_moves::BackboneMoverOP
typedef utility::pointer::shared_ptr< BBConRotMover const > protocols::simple_moves::BBConRotMoverCOP
typedef utility::pointer::shared_ptr< BBConRotMover > protocols::simple_moves::BBConRotMoverOP
typedef utility::pointer::shared_ptr< BBDihedralSamplerMover const > protocols::simple_moves::BBDihedralSamplerMoverCOP
typedef utility::pointer::shared_ptr< BBG8T3AMover const > protocols::simple_moves::BBG8T3AMoverCOP
typedef utility::pointer::shared_ptr< BBG8T3AMover > protocols::simple_moves::BBG8T3AMoverOP
typedef utility::pointer::shared_ptr< BBGaussianMover const > protocols::simple_moves::BBGaussianMoverCOP
typedef utility::pointer::shared_ptr< BBGaussianMover > protocols::simple_moves::BBGaussianMoverOP
typedef utility::pointer::shared_ptr< ChainSplitMover const > protocols::simple_moves::ChainSplitMoverCOP
typedef utility::pointer::shared_ptr< ChainSplitMover > protocols::simple_moves::ChainSplitMoverOP
typedef utility::pointer::shared_ptr< ClassicFragmentMover const > protocols::simple_moves::ClassicFragmentMoverCOP
typedef utility::pointer::shared_ptr< CombinePoseMover const > protocols::simple_moves::CombinePoseMoverCOP
typedef utility::pointer::shared_ptr< CombinePoseMover > protocols::simple_moves::CombinePoseMoverOP
using protocols::simple_moves::ConcatenatePosesMoverCOP = typedef utility::pointer::shared_ptr< ConcatenatePosesMover const >
using protocols::simple_moves::ConcatenatePosesMoverOP = typedef utility::pointer::shared_ptr< ConcatenatePosesMover >
typedef utility::pointer::shared_ptr< ConstrainToIdealMover const > protocols::simple_moves::ConstrainToIdealMoverCOP
typedef utility::pointer::shared_ptr< ContingentAcceptMover const > protocols::simple_moves::ContingentAcceptMoverCOP
typedef utility::pointer::shared_ptr< CopyDofMover const > protocols::simple_moves::CopyDofMoverCOP
typedef utility::pointer::shared_ptr< CopyDofMover > protocols::simple_moves::CopyDofMoverOP
typedef utility::pointer::shared_ptr< CopyRotamerMover const > protocols::simple_moves::CopyRotamerMoverCOP
typedef utility::pointer::shared_ptr< CopyRotamerMover > protocols::simple_moves::CopyRotamerMoverOP
typedef utility::pointer::shared_ptr< CoupledMover const > protocols::simple_moves::CoupledMoverCOP
typedef utility::pointer::shared_ptr< CoupledMover > protocols::simple_moves::CoupledMoverOP
typedef utility::pointer::shared_ptr< CutChainMover const > protocols::simple_moves::CutChainMoverCOP
typedef utility::pointer::shared_ptr< CutChainMover > protocols::simple_moves::CutChainMoverOP
typedef utility::pointer::shared_ptr< CyclizationMover const > protocols::simple_moves::CyclizationMoverCOP
typedef utility::pointer::shared_ptr< CyclizationMover > protocols::simple_moves::CyclizationMoverOP
typedef utility::pointer::shared_ptr< DeleteChainMover const > protocols::simple_moves::DeleteChainMoverCOP
typedef utility::pointer::shared_ptr< DeleteChainMover > protocols::simple_moves::DeleteChainMoverOP
typedef utility::pointer::shared_ptr< DeleteChainsMover const > protocols::simple_moves::DeleteChainsMoverCOP
typedef utility::pointer::shared_ptr< DeleteChainsMover > protocols::simple_moves::DeleteChainsMoverOP
typedef utility::pointer::shared_ptr< DumpPdb const > protocols::simple_moves::DumpPdbCOP
typedef utility::pointer::shared_ptr< DumpPdb > protocols::simple_moves::DumpPdbOP
typedef utility::pointer::shared_ptr< ExplicitWaterMover const > protocols::simple_moves::ExplicitWaterMoverCOP
typedef utility::pointer::shared_ptr< ExplicitWaterMover > protocols::simple_moves::ExplicitWaterMoverOP
typedef utility::pointer::shared_ptr< FavorSymmetricSequence const > protocols::simple_moves::FavorSymmetricSequenceCOP
typedef utility::pointer::shared_ptr< FragmentCost const > protocols::simple_moves::FragmentCostCOP
typedef utility::pointer::shared_ptr< FragmentCost > protocols::simple_moves::FragmentCostOP
typedef utility::pointer::shared_ptr< FragmentMover const > protocols::simple_moves::FragmentMoverCOP
typedef utility::pointer::shared_ptr< FragmentMover > protocols::simple_moves::FragmentMoverOP
typedef utility::pointer::shared_ptr< LoadPDBMover const > protocols::simple_moves::LoadPDBMoverCOP
typedef utility::pointer::shared_ptr< LoadPDBMover > protocols::simple_moves::LoadPDBMoverOP
typedef utility::pointer::shared_ptr< LoadUnboundRotMover const > protocols::simple_moves::LoadUnboundRotMoverCOP
typedef utility::pointer::shared_ptr< MembraneTopology const > protocols::simple_moves::MembraneTopologyCOP
typedef utility::pointer::shared_ptr< MembraneTopology > protocols::simple_moves::MembraneTopologyOP
typedef utility::pointer::shared_ptr< ModifyVariantTypeMover const > protocols::simple_moves::ModifyVariantTypeMoverCOP
typedef utility::pointer::shared_ptr< MutateResidue const > protocols::simple_moves::MutateResidueCOP
typedef utility::pointer::shared_ptr< MutateResidue > protocols::simple_moves::MutateResidueOP
typedef utility::pointer::shared_ptr< PDBReloadMover const > protocols::simple_moves::PDBReloadMoverCOP
typedef utility::pointer::shared_ptr< PDBReloadMover > protocols::simple_moves::PDBReloadMoverOP
typedef utility::pointer::shared_ptr< PeptideStapleMover const > protocols::simple_moves::PeptideStapleMoverCOP
typedef utility::pointer::shared_ptr< PeptideStapleMover > protocols::simple_moves::PeptideStapleMoverOP
typedef utility::pointer::shared_ptr< PeriodicBoxMover const > protocols::simple_moves::PeriodicBoxMoverCOP
typedef utility::pointer::shared_ptr< PeriodicBoxMover > protocols::simple_moves::PeriodicBoxMoverOP
typedef utility::pointer::shared_ptr< ProlineFixMover const > protocols::simple_moves::ProlineFixMoverCOP
typedef utility::pointer::shared_ptr< ProlineFixMover > protocols::simple_moves::ProlineFixMoverOP
typedef utility::pointer::shared_ptr< PSSM2BfactorMover const > protocols::simple_moves::PSSM2BfactorMoverCOP
typedef utility::pointer::shared_ptr< PSSM2BfactorMover > protocols::simple_moves::PSSM2BfactorMoverOP
typedef utility::vector1< utility::vector1< core::Vector > > protocols::simple_moves::PWatRotamerCloud
typedef utility::pointer::shared_ptr< RandomOmegaFlipMover const > protocols::simple_moves::RandomOmegaFlipMoverCOP
typedef utility::pointer::shared_ptr< RandomTorsionMover const > protocols::simple_moves::RandomTorsionMoverCOP
typedef utility::pointer::shared_ptr< RandomTorsionMover > protocols::simple_moves::RandomTorsionMoverOP
typedef utility::pointer::shared_ptr< RepeatPropagationMover const > protocols::simple_moves::RepeatPropagationMoverCOP
typedef utility::pointer::shared_ptr< RepeatProteinRelax const > protocols::simple_moves::RepeatProteinRelaxCOP
typedef utility::pointer::shared_ptr< RepeatProteinRelax > protocols::simple_moves::RepeatProteinRelaxOP
typedef utility::pointer::shared_ptr< ReportXYZ const > protocols::simple_moves::ReportXYZCOP
typedef utility::pointer::shared_ptr< ReportXYZ > protocols::simple_moves::ReportXYZOP
typedef utility::pointer::shared_ptr< RepulsiveOnlyMover const > protocols::simple_moves::RepulsiveOnlyMoverCOP
typedef utility::pointer::shared_ptr< RepulsiveOnlyMover > protocols::simple_moves::RepulsiveOnlyMoverOP
typedef utility::pointer::shared_ptr< ResetFoldTree const > protocols::simple_moves::ResetFoldTreeCOP
typedef utility::pointer::shared_ptr< ResetFoldTree > protocols::simple_moves::ResetFoldTreeOP
using protocols::simple_moves::ResetFullModelInfoMoverCOP = typedef utility::pointer::shared_ptr< ResetFullModelInfoMover const >
using protocols::simple_moves::ResetFullModelInfoMoverOP = typedef utility::pointer::shared_ptr< ResetFullModelInfoMover >
typedef utility::pointer::shared_ptr< ResTypeFragmentMover const > protocols::simple_moves::ResTypeFragmentMoverCOP
typedef utility::pointer::shared_ptr< ReturnSidechainMover const > protocols::simple_moves::ReturnSidechainMoverCOP
typedef utility::pointer::shared_ptr< RingConformationMover const > protocols::simple_moves::RingConformationMoverCOP
typedef utility::vector1< core::Real > protocols::simple_moves::ScoreList
typedef utility::pointer::shared_ptr< ScoreMover const > protocols::simple_moves::ScoreMoverCOP
typedef utility::pointer::shared_ptr< ScoreMover > protocols::simple_moves::ScoreMoverOP
typedef utility::pointer::shared_ptr< SequenceProfileMover const > protocols::simple_moves::SequenceProfileMoverCOP
typedef utility::pointer::shared_ptr< SetTorsion const > protocols::simple_moves::SetTorsionCOP
typedef utility::pointer::shared_ptr< SetTorsion > protocols::simple_moves::SetTorsionOP
typedef utility::pointer::shared_ptr< SetupMetalsMover const > protocols::simple_moves::SetupMetalsMoverCOP
typedef utility::pointer::shared_ptr< SetupMetalsMover > protocols::simple_moves::SetupMetalsMoverOP
typedef utility::pointer::shared_ptr< ShakeStructureMover const > protocols::simple_moves::ShakeStructureMoverCOP
typedef utility::pointer::shared_ptr< ShearMover const > protocols::simple_moves::ShearMoverCOP
typedef utility::pointer::shared_ptr< ShearMover > protocols::simple_moves::ShearMoverOP
typedef utility::pointer::shared_ptr< ShortBackrubMover const > protocols::simple_moves::ShortBackrubMoverCOP
typedef utility::pointer::shared_ptr< ShortBackrubMover > protocols::simple_moves::ShortBackrubMoverOP
typedef utility::pointer::shared_ptr< SimpleThreadingMover const > protocols::simple_moves::SimpleThreadingMoverCOP
typedef utility::pointer::shared_ptr< SmallMover const > protocols::simple_moves::SmallMoverCOP
typedef utility::pointer::shared_ptr< SmallMover > protocols::simple_moves::SmallMoverOP
typedef utility::pointer::shared_ptr< SmoothFragmentMover const > protocols::simple_moves::SmoothFragmentMoverCOP
typedef utility::pointer::shared_ptr< StorePoseSnapshot const > protocols::simple_moves::StorePoseSnapshotCOP
typedef utility::pointer::shared_ptr< StorePoseSnapshot > protocols::simple_moves::StorePoseSnapshotOP
typedef utility::pointer::shared_ptr< StructProfileMover const > protocols::simple_moves::StructProfileMoverCOP
typedef utility::pointer::shared_ptr< StructProfileMover > protocols::simple_moves::StructProfileMoverOP
typedef utility::pointer::shared_ptr< SuperimposeMover const > protocols::simple_moves::SuperimposeMoverCOP
typedef utility::pointer::shared_ptr< SuperimposeMover > protocols::simple_moves::SuperimposeMoverOP
typedef utility::pointer::shared_ptr< SwitchChainOrderMover const > protocols::simple_moves::SwitchChainOrderMoverCOP
typedef utility::pointer::shared_ptr< SymmetricFragmentMover const > protocols::simple_moves::SymmetricFragmentMoverCOP
typedef utility::pointer::shared_ptr< TorsionDOFMover const > protocols::simple_moves::TorsionDOFMoverCOP
typedef utility::pointer::shared_ptr< TorsionDOFMover > protocols::simple_moves::TorsionDOFMoverOP
typedef utility::pointer::shared_ptr< TorsionSetMover const > protocols::simple_moves::TorsionSetMoverCOP
typedef utility::pointer::shared_ptr< TorsionSetMover > protocols::simple_moves::TorsionSetMoverOP
typedef utility::pointer::shared_ptr< UniformRotationMover const > protocols::simple_moves::UniformRotationMoverCOP
typedef utility::pointer::shared_ptr< VirtualRootMover const > protocols::simple_moves::VirtualRootMoverCOP
typedef utility::pointer::shared_ptr< VirtualRootMover > protocols::simple_moves::VirtualRootMoverOP
typedef utility::pointer::shared_ptr< ConvertVirtualToRealMover const > protocols::simple_moves::VirtualToFaMoverCOP
typedef utility::pointer::shared_ptr< const WobbleMover > protocols::simple_moves::WobbleMoverCOP
typedef utility::pointer::shared_ptr< WobbleMover > protocols::simple_moves::WobbleMoverOP
typedef utility::pointer::shared_ptr< WriteSSEMover const > protocols::simple_moves::WriteSSEMoverCOP
typedef utility::pointer::shared_ptr< WriteSSEMover > protocols::simple_moves::WriteSSEMoverOP

Enumeration Type Documentation

Enumerator
DCV_NOT_CYCLIZABLE 
DCV_CYCLIZABLE 
DCV_ALREADY_CYCLIZED 
Enumerator
perturbtorsion_uniform 
perturbtorsion_gaussian 
perturbtorsion_unknown 

Function Documentation

void protocols::simple_moves::apply_ideal_coordinates_for_alternative_pucker ( core::pose::Pose const &  pose,
core::pose::Pose pose_reference 
)
utility::vector1< numeric::xyzVector< core::Real > > protocols::simple_moves::Ca_coord ( core::pose::Pose const &  pose,
utility::vector1< core::Size > const  positions 
)
utility::vector1< numeric::xyzVector< core::Real > > protocols::simple_moves::Ca_coords ( core::pose::Pose const &  pose,
utility::vector1< core::Size > const  positions 
)
core::Size protocols::simple_moves::check_if_proton_chi_atom ( core::chemical::ResidueType const &  rsd_type,
core::Size const  j 
)
core::Size protocols::simple_moves::check_if_proton_chi_atom ( core::pose::Pose const &  pose,
core::Size const  i,
core::Size const  j 
)
std::ostream & protocols::simple_moves::operator<< ( std::ostream &  os,
BBDihedralSamplerMover const &  mover 
)
std::ostream & protocols::simple_moves::operator<< ( std::ostream &  os,
SwitchResidueTypeSetMover const &  mover 
)
std::ostream & protocols::simple_moves::operator<< ( std::ostream &  os,
DOFHistogramRecorder const &  dof_recorder 
)
std::ostream & protocols::simple_moves::operator<< ( std::ostream &  os,
ResetFullModelInfoMover const &  mover 
)
std::ostream & protocols::simple_moves::operator<< ( std::ostream &  os,
PoseFromPoseResourceMover const &  mover 
)
std::ostream & protocols::simple_moves::operator<< ( std::ostream &  os,
ConvertVirtualToRealMover const &  mover 
)
std::ostream & protocols::simple_moves::operator<< ( std::ostream &  os,
ConvertRealToVirtualMover const &  mover 
)
std::ostream & protocols::simple_moves::operator<< ( std::ostream &  os,
ReturnSidechainMover const &  mover 
)
std::ostream & protocols::simple_moves::operator<< ( std::ostream &  os,
CopyRotamerMover const &  mover 
)

Get the name of the Mover.

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

std::ostream & protocols::simple_moves::operator<< ( std::ostream &  os,
ConcatenatePosesMover const &  mover 
)
std::ostream & protocols::simple_moves::operator<< ( std::ostream &  os,
DumpSingleResidueRotamers const &  mover 
)
std::ostream & protocols::simple_moves::operator<< ( std::ostream &  output,
RingConformationMover const &  object_to_output 
)
std::ostream & protocols::simple_moves::operator<< ( std::ostream &  os,
SetupMetalsMover const &  mover 
)
std::ostream & protocols::simple_moves::operator<< ( std::ostream &  os,
BackboneMover const &  mover 
)
std::ostream & protocols::simple_moves::operator<< ( std::ostream &  os,
ClassicFragmentMover const &  cfmover 
)
Real protocols::simple_moves::point_graph_dme ( conformation::PointGraph const &  pg,
pose::Pose const &  pose 
)
numeric::xyzMatrix<core::Real> protocols::simple_moves::random_rotation ( core::Real  magnitude)
conformation::PointGraphOP protocols::simple_moves::setup_dme_point_graph ( pose::Pose const &  ref_pose,
Real const  threshold 
)
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 
)
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 
)
static basic::Tracer protocols::simple_moves::TR ( "protocols.simple_moves.FavorSymmetricSequence"  )
static
static basic::Tracer protocols::simple_moves::TR ( "protocols.simple_moves.AddJobPairData"  )
static
static basic::Tracer protocols::simple_moves::TR ( "protocols.simple_moves.DeleteChainMover"  )
static
static basic::Tracer protocols::simple_moves::TR ( "protocols.loops.FoldTreeFromMotif"  )
static
static basic::Tracer protocols::simple_moves::TR ( "protocols.simple_moves.MembraneTopology"  )
static
static basic::Tracer protocols::simple_moves::TR ( "protocols.simple_moves.VirtualRootMover"  )
static
static basic::Tracer protocols::simple_moves::tr ( "protocols.simple_moves.FragmentMover"  )
static
static basic::Tracer protocols::simple_moves::TR ( "protocols.mover.MissingDensityToJumpMover"  )
static
static basic::Tracer protocols::simple_moves::TR ( "protocols.simple_moves.CombinePoseMover"  )
static
static basic::Tracer protocols::simple_moves::TR ( "protocols.simple_moves.PDBReloadMover"  )
static
static basic::Tracer protocols::simple_moves::TR ( "protocols.simple_moves.AddPDBInfoMover"  )
static
static basic::Tracer protocols::simple_moves::TR ( "protocol.mover.RepulsiveOnlyMover"  )
static
static basic::Tracer protocols::simple_moves::TR ( "protocols.simple_moves.DumpPdb"  )
static
static basic::Tracer protocols::simple_moves::TR ( "protocols.simple_moves.DOFHistogramRecorder"  )
static
static basic::Tracer protocols::simple_moves::TR ( "protocols.simple_moves.SuperimposeMover"  )
static
static basic::Tracer protocols::simple_moves::TR ( "protocols.simple_moves.AddResidueCouplingConstraint"  )
static
static basic::Tracer protocols::simple_moves::TR ( "protocols.simple_moves.FavorSequenceProfile"  )
static
static basic::Tracer protocols::simple_moves::TR ( "protocols.simple_moves.ModifyVariantTypeMover"  )
static
static basic::Tracer protocols::simple_moves::TR ( "protocols.simple_moves.StorePoseSnapshot"  )
static
static basic::Tracer protocols::simple_moves::tr ( "protocols.simple_moves.ResTypeFragmentMover"  )
static
static basic::Tracer protocols::simple_moves::tr ( "protocols.simple_moves.FragmentMover"  )
static
static basic::Tracer protocols::simple_moves::TR ( "protocols.simple_moves.MutateResidue"  )
static
static basic::Tracer protocols::simple_moves::TR ( "protocols.simple_moves.CutChainMover"  )
static
static basic::Tracer protocols::simple_moves::TR ( "protocols.simple_moves.CyclizationMover"  )
static
static basic::Tracer protocols::simple_moves::TR ( "protocols.simple_moves.SetTorsion"  )
static
static basic::Tracer protocols::simple_moves::TR ( "protocols.simple_moves.DisulfideInsertionMover"  )
static
static basic::Tracer protocols::simple_moves::TR ( "protocols.simple_moves.ScoreMover"  )
static
static basic::Tracer protocols::simple_moves::TR ( "protocols.moves.ExplicitWaterMover"  )
static
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::PSSM2BfactorMover::apply(), protocols::simple_moves::FavorSymmetricSequence::apply(), protocols::simple_moves::ContingentAcceptMover::apply(), protocols::simple_moves::FoldTreeFromMotif::apply(), protocols::simple_moves::AddJobPairData::apply(), protocols::simple_moves::SequenceProfileMover::apply(), protocols::simple_moves::VirtualRootMover::apply(), protocols::simple_moves::AlignChainMover::apply(), protocols::simple_moves::AddResidueLabelMover::apply(), protocols::simple_moves::LoadPDBMover::apply(), protocols::simple_moves::DeleteChainMover::apply(), protocols::simple_moves::SwitchChainOrderMover::apply(), protocols::simple_moves::DumpPdb::apply(), protocols::simple_moves::PeptideStapleMover::apply(), protocols::simple_moves::CombinePoseMover::apply(), protocols::simple_moves::SuperimposeMover::apply(), protocols::simple_moves::AddResidueCouplingConstraint::apply(), protocols::simple_moves::BBConRotMover::apply(), protocols::simple_moves::RepulsiveOnlyMover::apply(), protocols::simple_moves::ModifyVariantTypeMover::apply(), protocols::simple_moves::FavorSequenceProfile::apply(), protocols::simple_moves::MissingDensityToJumpMover::apply(), protocols::simple_moves::BBDihedralSamplerMover::apply(), protocols::simple_moves::SetTorsion::apply(), protocols::simple_moves::DisulfideInsertionMover::apply(), protocols::simple_moves::CopyRotamerMover::apply(), protocols::simple_moves::TorsionDOFMover::apply(), protocols::simple_moves::DME_FilterMover::apply(), protocols::simple_moves::ReturnSidechainMover::apply(), protocols::simple_moves::StorePoseSnapshot::apply(), protocols::simple_moves::ScoreMover::apply(), protocols::simple_moves::BackboneMover::apply(), protocols::simple_moves::ConvertVirtualToRealMover::apply(), protocols::simple_moves::ConvertRealToVirtualMover::apply(), protocols::simple_moves::ReportEffectivePKA::apply(), protocols::simple_moves::CoupledMover::apply(), protocols::simple_moves::RingConformationMover::apply(), protocols::simple_moves::SimpleThreadingMover::apply(), protocols::simple_moves::PeriodicBoxMover::apply(), protocols::simple_moves::ChangeAndResetFoldTreeMover::apply(), protocols::simple_moves::ExplicitWaterMover::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::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::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::AddChainMover::load_pose(), protocols::simple_moves::BBConRotMover::make_move(), protocols::simple_moves::MutateResidue::make_mutation(), protocols::simple_moves::PeptideStapleMover::minimize_(), protocols::simple_moves::SmallMover::move_with_scorefxn(), protocols::simple_moves::FavorSymmetricSequence::parse_my_tag(), protocols::simple_moves::ResetFoldTree::parse_my_tag(), protocols::simple_moves::PSSM2BfactorMover::parse_my_tag(), protocols::simple_moves::AddChainMover::parse_my_tag(), protocols::simple_moves::SequenceProfileMover::parse_my_tag(), protocols::simple_moves::CutChainMover::parse_my_tag(), protocols::simple_moves::AddJobPairData::parse_my_tag(), protocols::simple_moves::AlignChainMover::parse_my_tag(), protocols::simple_moves::AddResidueLabelMover::parse_my_tag(), protocols::simple_moves::LoadPDBMover::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::PoseFromPoseResourceMover::parse_my_tag(), protocols::simple_moves::CopyRotamerMover::parse_my_tag(), protocols::simple_moves::StorePoseSnapshot::parse_my_tag(), protocols::simple_moves::ReportEffectivePKA::parse_my_tag(), protocols::simple_moves::BBGaussianMover::parse_my_tag(), 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::CopyRotamerMover::set_copy_identity(), protocols::simple_moves::CopyRotamerMover::set_copy_torsions(), 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::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().

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

Variable Documentation

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