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protocols::simple_moves Namespace Reference

Namespaces

 asym_fold_and_dock
 
 carbohydrates
 
 chiral
 
 hbs
 
 oop
 
 rational_mc
 
 sidechain_moves
 
 symmetry
 

Classes

class  AddCavitiesMover
 
class  AddConstraintsToCurrentConformationMover
 
class  AddConstraintsToCurrentConformationMoverCreator
 
class  BackboneMover
 
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  BBGaussianMover
 the basic class for implementing Gaussian Perturbation of bb More...
 
class  BBG8T3AMover
 a particular gaussian mover from the original paper More...
 
class  ClearConstraintsMover
 
class  ClearConstraintsMoverCreator
 
class  ConsensusDesignMover
 This mover will modify a given task according to a sequence profile and then call the PackRotamersMover. At every position that is designable in the task, AAs that have a probability > min_aa_probability_ and higher than the native in the sequence profile will be allowed. More...
 
class  ConsensusDesignMoverCreator
 
class  ConstraintFragmentMover
 
class  ConstrainToIdealMover
 
class  ConstraintSetMover
 
class  ConstraintSetMoverCreator
 
class  CutChainMover
 simple mover that sperates Fv from Fl into two seperate chains More...
 
class  CutChainMoverCreator
 
class  ddG
 
class  ddGCreator
 
class  DesignRepackMover
 a pure virtual base class for movers which redesign and repack the interface More...
 
class  DME_FilterMover
 
class  DOFHistogramRecorder
 
class  DumpPdb
 what you think this can now be assimilated into DumpPdbMover More...
 
class  DumpPdbCreator
 
class  ExtendedPoseMover
 
class  ExtendedPoseMoverCreator
 
class  FavorSequenceProfile
 
class  FavorSequenceProfileCreator
 
class  ForceDisulfidesMover
 simple mover that fixes disulfides according to a defined list and then simultaneously repacks within 6A shells around each affected cystein residue. More...
 
class  ForceDisulfidesMoverCreator
 
class  FragmentMover
 abstract base class for FragmentMovers More...
 
class  ClassicFragmentMover
 A FragmentMover that applies uniform sampling of fragments. More...
 
class  LoggedFragmentMover
 
class  GenericMonteCarloMover
 
class  GenericMonteCarloMoverCreator
 
class  MinimalRotamer
 
class  GroupDiscriminator
 Interface class used to break a pose down into a set of component "groups" where intra-group rotamer-pair energies are preserved between calls to the GreenPacker. E.g. in rigid-body docking between two proteins, chains 1 and 2 define groups 1 and 2. In rigid-body docking between two domains of the same chain, those residues upstream of jump 1 define group 1, and those downstream of jump 1 define group 2. In loop modelling, the static background is group 1, and the loop itself is group 0, since loop residues will have their bb dofs change regularly between repackings. More...
 
class  UserDefinedGroupDiscriminator
 
class  ChainGroupDiscriminator
 
class  GreenPacker
 
struct  GunnTuple
 
class  GunnCost
 
class  HelicalPeptideLengthMover
 
class  LoadPDBMover
 
class  LoadPDBMoverCreator
 
class  LoadUnboundRotMover
 
class  LoadUnboundRotMoverCreator
 
class  MakePolyXMover
 
class  MakePolyXMoverCreator
 
class  MembraneTopology
 A mover to change one torsion angle. More...
 
class  MembraneTopologyCreator
 
class  MinMover
 A protocols::moves::Mover that minimizes a Pose to a local energy minimum by performing energy minimization of a ScoreFunction over the allowable degrees of freedom, defined by a MoveMap. The minimization type, minimization tolerance, and various other options can be also be set. More...
 
class  MinMoverCreator
 
class  MinPackMover
 a mover that packs and minimizes the side-chains. It uses a ScoreFunction for packing and either a PackerTask, or a TaskFactory that generates a PackerTask for instructions on what rotamer sets are allowed at each residue position during packing. More...
 
class  MinPackMoverCreator
 
class  MissingDensityToJumpMover
 
class  ModifyVariantTypeMover
 Adds variant types to selected residues. More...
 
class  ModifyVariantTypeMoverCreator
 
class  MonteCarloRecover
 
class  MonteCarloRecoverCreator
 
class  MonteCarloTest
 
class  MonteCarloTestCreator
 
class  MutateResidue
 A mover to mutate a single residue. More...
 
class  MutateResidueCreator
 
class  O2M_MutateMover
 
class  PackRotamersMover
 A protocols::moves::Mover that packs the side-chains using a rotamer library It uses a ScoreFunction for packing and a PackerTask, or a TaskFactory that generates a PackerTask, for instructions on what rotamer sets are allowed at each residue position during packing. More...
 
class  PackRotamersMoverCreator
 
class  PackRotamersMoverLazy
 a mover that packs the side-chains using a rotamer library in a lazy fashion. More...
 
class  PackRotamersMoverLazyCreator
 
class  PDBReloadMover
 
class  PDBReloadMoverCreator
 
class  PeptideStapleMover
 
class  ProlineFixMover
 
class  RepackSidechainsMover
 A protocols::moves::Mover that packs the side-chains (very similar to pack_missing_sidechains() More...
 
class  RepackSidechainsMoverCreator
 
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  ReturnSidechainMover
 
class  RotamerTrialsMinMover
 
class  EnergyCutRotamerTrialsMinMover
 Wrapper for Rotamer Trials with Minimization, which modifies only rotamers whose energy changed by a given constant. More...
 
class  RotamerTrialsMinMoverCreator
 
class  RotamerTrialsMover
 
class  EnergyCutRotamerTrialsMover
 
class  RotamerTrialsMoverCreator
 
class  SaneMinMover
 
class  SaneMinMoverCreator
 
class  ScoreMover
 
class  ScoreMoverCreator
 
class  SequenceProfileMover
 
class  SequenceProfileMoverCreator
 
class  SetReturningPackRotamersMover
 
class  SetTorsion
 A mover to change one torsion angle. More...
 
class  SetTorsionCreator
 
class  ShakeStructureMover
 
class  FragmentCost
 
class  SmoothFragmentMover
 
class  SuperimposeMover
 
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  TaskAwareMinMover
 
class  TaskAwareMinMoverCreator
 
class  TorsionDOFMover
 TODO: De-duplicate shared code from RotateJumpAxisMover (angle picking code) More...
 
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...
 

Typedefs

typedef
utility::pointer::owning_ptr
< BackboneMover
BackboneMoverOP
 
typedef
utility::pointer::owning_ptr
< BackboneMover const > 
BackboneMoverCOP
 
typedef
utility::pointer::owning_ptr
< SmallMover
SmallMoverOP
 
typedef
utility::pointer::owning_ptr
< SmallMover const > 
SmallMoverCOP
 
typedef
utility::pointer::owning_ptr
< ShearMover
ShearMoverOP
 
typedef
utility::pointer::owning_ptr
< ShearMover const > 
ShearMoverCOP
 
typedef
utility::pointer::owning_ptr
< BBConRotMover
BBConRotMoverOP
 
typedef
utility::pointer::owning_ptr
< BBConRotMover const > 
BBConRotMoverCOP
 
typedef
utility::pointer::owning_ptr
< BBGaussianMover
BBGaussianMoverOP
 
typedef
utility::pointer::owning_ptr
< BBGaussianMover const > 
BBGaussianMoverCOP
 
typedef
utility::pointer::owning_ptr
< BBG8T3AMover
BBG8T3AMoverOP
 
typedef
utility::pointer::owning_ptr
< BBG8T3AMover const > 
BBG8T3AMoverCOP
 
typedef
utility::pointer::owning_ptr
< ConsensusDesignMover
ConsensusDesignMoverOP
 
typedef utility::vector1
< core::Real
ScoreList
 
typedef
utility::pointer::owning_ptr
< ConstrainToIdealMover
ConstrainToIdealMoverOP
 
typedef
utility::pointer::owning_ptr
< ConstrainToIdealMover const > 
ConstrainToIdealMoverCOP
 
typedef
utility::pointer::owning_ptr
< ConstraintSetMover
ConstraintSetMoverOP
 
typedef
utility::pointer::owning_ptr
< ConstraintSetMover const > 
ConstraintSetMoverCOP
 
typedef
utility::pointer::owning_ptr
< CutChainMover
CutChainMoverOP
 
typedef
utility::pointer::owning_ptr
< CutChainMover const > 
CutChainMoverCOP
 
typedef
utility::pointer::owning_ptr
< ddG
ddGOP
 
typedef
utility::pointer::owning_ptr
< ddG const > 
ddGCOP
 
typedef
utility::pointer::owning_ptr
< DesignRepackMover
DesignRepackMoverOP
 
typedef
utility::pointer::owning_ptr
< DesignRepackMover const > 
DesignRepackMoverCOP
 
typedef
utility::pointer::owning_ptr
< ExtendedPoseMover
ExtendedPoseMoverOP
 
typedef
utility::pointer::owning_ptr
< ExtendedPoseMover const > 
ExtendedPoseMoverCOP
 
typedef
utility::pointer::owning_ptr
< ForceDisulfidesMover
ForceDisulfideMoverOP
 
typedef
utility::pointer::owning_ptr
< ForceDisulfidesMover const > 
ForceDisulfideMoverCOP
 
typedef
utility::pointer::owning_ptr
< FragmentMover
FragmentMoverOP
 
typedef
utility::pointer::owning_ptr
< FragmentMover const > 
FragmentMoverCOP
 
typedef
utility::pointer::owning_ptr
< ClassicFragmentMover
ClassicFragmentMoverOP
 
typedef
utility::pointer::owning_ptr
< ClassicFragmentMover const > 
ClassicFragmentMoverCOP
 
typedef
utility::pointer::owning_ptr
< GenericMonteCarloMover
GenericMonteCarloMoverOP
 
typedef
utility::pointer::owning_ptr
< GenericMonteCarloMover const > 
GenericMonteCarloMoverCOP
 
typedef boost::function< bool(core::Size,
core::Size, const
core::pose::Pose
&, core::scoring::ScoreFunctionOP)> 
GenericMonteCarloMoverTrigger
 Trigger API definition. More...
 
typedef
utility::pointer::owning_ptr
< MinimalRotamer
MinimalRotamerOP
 
typedef
utility::pointer::owning_ptr
< MinimalRotamer const > 
MinimalRotamerCOP
 
typedef
utility::pointer::owning_ptr
< GroupDiscriminator
GroupDiscriminatorOP
 
typedef
utility::pointer::owning_ptr
< GroupDiscriminator const > 
GroupDiscriminatorCOP
 
typedef
utility::pointer::owning_ptr
< UserDefinedGroupDiscriminator
UserDefinedGroupDiscriminatorOP
 
typedef
utility::pointer::owning_ptr
< GreenPacker
GreenPackerOP
 
typedef
utility::pointer::owning_ptr
< GreenPacker const > 
GreenPackerCOP
 
typedef
utility::pointer::owning_ptr
< HelicalPeptideLengthMover
HelicalPeptideLengthMoverOP
 
typedef
utility::pointer::owning_ptr
< HelicalPeptideLengthMover
const > 
HelicalPeptideLengthMoverCOP
 
typedef
utility::pointer::owning_ptr
< LoadPDBMover
LoadPDBMoverOP
 
typedef
utility::pointer::owning_ptr
< LoadPDBMover const > 
LoadPDBMoverCOP
 
typedef
utility::pointer::owning_ptr
< LoadUnboundRotMover
LoadUnboundRotMoverOP
 
typedef
utility::pointer::owning_ptr
< LoadUnboundRotMover const > 
LoadUnboundRotMoverCOP
 
typedef
utility::pointer::owning_ptr
< MakePolyXMover
MakePolyXMoverOP
 
typedef
utility::pointer::owning_ptr
< MembraneTopology
MembraneTopologyOP
 
typedef
utility::pointer::owning_ptr
< MembraneTopology const > 
MembraneTopologyCOP
 
typedef
utility::pointer::owning_ptr
< MinMover
MinMoverOP
 
typedef
utility::pointer::owning_ptr
< MinMover const > 
MinMoverCOP
 
typedef
utility::pointer::owning_ptr
< MinPackMover
MinPackMoverOP
 
typedef
utility::pointer::owning_ptr
< MinPackMover const > 
MinPackMoverCOP
 
typedef
utility::pointer::owning_ptr
< MissingDensityToJumpMover
MissingDensityToJumpMoverOP
 
typedef
utility::pointer::owning_ptr
< MissingDensityToJumpMover
const > 
MissingDensityToJumpMoverCOP
 
typedef
utility::pointer::owning_ptr
< ModifyVariantTypeMover
ModifyVariantTypeMoverOP
 
typedef
utility::pointer::owning_ptr
< ModifyVariantTypeMover const > 
ModifyVariantTypeMoverCOP
 
typedef
utility::pointer::owning_ptr
< MonteCarloRecover
MonteCarloRecoverOP
 
typedef
utility::pointer::owning_ptr
< MonteCarloRecover const > 
MonteCarloRecoverCOP
 
typedef
utility::pointer::owning_ptr
< MonteCarloTest
MonteCarloTestOP
 
typedef
utility::pointer::owning_ptr
< MonteCarloTest const > 
MonteCarloTestCOP
 
typedef
utility::pointer::owning_ptr
< MutateResidue
MutateResidueOP
 
typedef
utility::pointer::owning_ptr
< MutateResidue const > 
MutateResidueCOP
 
typedef boost::shared_ptr
< O2M_MutateMover
O2M_MutateMoverSP
 
typedef
utility::pointer::owning_ptr
< PackRotamersMover
PackRotamersMoverOP
 
typedef
utility::pointer::owning_ptr
< PackRotamersMover const > 
PackRotamersMoverCOP
 
typedef
utility::pointer::owning_ptr
< PackRotamersMoverLazy
PackRotamersMoverLazyOP
 
typedef
utility::pointer::owning_ptr
< PackRotamersMoverLazy const > 
PackRotamersMoverLazyCOP
 
typedef
utility::pointer::owning_ptr
< PDBReloadMover
PDBReloadMoverOP
 
typedef
utility::pointer::owning_ptr
< PDBReloadMover const > 
PDBReloadMoverCOP
 
typedef
utility::pointer::owning_ptr
< PeptideStapleMover
PeptideStapleMoverOP
 
typedef
utility::pointer::owning_ptr
< PeptideStapleMover const > 
PeptideStapleMoverCOP
 
typedef
utility::pointer::owning_ptr
< ProlineFixMover
ProlineFixMoverOP
 
typedef
utility::pointer::owning_ptr
< ProlineFixMover const > 
ProlineFixMoverCOP
 
typedef
utility::pointer::owning_ptr
< RepackSidechainsMover
RepackSidechainsMoverOP
 
typedef
utility::pointer::owning_ptr
< RepackSidechainsMover const > 
RepackSidechainsMoverCOP
 
typedef
utility::pointer::owning_ptr
< RepulsiveOnlyMover
RepulsiveOnlyMoverOP
 
typedef
utility::pointer::owning_ptr
< RepulsiveOnlyMover const > 
RepulsiveOnlyMoverCOP
 
typedef
utility::pointer::owning_ptr
< ReturnSidechainMover
ReturnSidechainMoverOP
 
typedef
utility::pointer::owning_ptr
< ReturnSidechainMover const > 
ReturnSidechainMoverCOP
 
typedef
utility::pointer::owning_ptr
< RotamerTrialsMinMover
RotamerTrialsMinMoverOP
 
typedef
utility::pointer::owning_ptr
< RotamerTrialsMinMover const > 
RotamerTrialsMinMoverCOP
 
typedef
utility::pointer::owning_ptr
< EnergyCutRotamerTrialsMinMover
EnergyCutRotamerTrialsMinMoverOP
 
typedef
utility::pointer::owning_ptr
< EnergyCutRotamerTrialsMinMover
const > 
EnergyCutRotamerTrialsMinMoverCOP
 
typedef
utility::pointer::owning_ptr
< RotamerTrialsMover
RotamerTrialsMoverOP
 
typedef
utility::pointer::owning_ptr
< RotamerTrialsMover const > 
RotamerTrialsMoverCOP
 
typedef
utility::pointer::owning_ptr
< EnergyCutRotamerTrialsMover
EnergyCutRotamerTrialsMoverOP
 
typedef
utility::pointer::owning_ptr
< EnergyCutRotamerTrialsMover
const > 
EnergyCutRotamerTrialsMoverCOP
 
typedef
utility::pointer::owning_ptr
< SaneMinMover
SaneMinMoverOP
 
typedef
utility::pointer::owning_ptr
< SaneMinMover const > 
SaneMinMoverCOP
 
typedef
utility::pointer::owning_ptr
< ScoreMover
ScoreMoverOP
 
typedef
utility::pointer::owning_ptr
< ScoreMover const > 
ScoreMoverCOP
 
typedef
utility::pointer::owning_ptr
< SequenceProfileMover
SequenceProfileMoverOP
 
typedef
utility::pointer::owning_ptr
< SequenceProfileMover const > 
SequenceProfileMoverCOP
 
typedef
utility::pointer::owning_ptr
< SetReturningPackRotamersMover
SetReturningPackRotamersMoverOP
 
typedef
utility::pointer::owning_ptr
< SetReturningPackRotamersMover
const > 
SetReturningPackRotamersMoverCOP
 
typedef
utility::pointer::owning_ptr
< SetTorsion
SetTorsionOP
 
typedef
utility::pointer::owning_ptr
< SetTorsion const > 
SetTorsionCOP
 
typedef
utility::pointer::owning_ptr
< ShakeStructureMover
ShakeStructureMoverOP
 
typedef
utility::pointer::owning_ptr
< ShakeStructureMover const > 
ShakeStructureMoverCOP
 
typedef
utility::pointer::owning_ptr
< SmoothFragmentMover
SmoothFragmentMoverOP
 
typedef
utility::pointer::owning_ptr
< SmoothFragmentMover const > 
SmoothFragmentMoverCOP
 
typedef
utility::pointer::owning_ptr
< FragmentCost
FragmentCostOP
 
typedef
utility::pointer::owning_ptr
< FragmentCost const > 
FragmentCostCOP
 
typedef
utility::pointer::owning_ptr
< SuperimposeMover
SuperimposeMoverOP
 
typedef
utility::pointer::owning_ptr
< SuperimposeMover const > 
SuperimposeMoverCOP
 
typedef
utility::pointer::owning_ptr
< SwitchChainOrderMover
SwitchChainOrderMoverOP
 
typedef
utility::pointer::owning_ptr
< SwitchChainOrderMover const > 
SwitchChainOrderMoverCOP
 
typedef
utility::pointer::owning_ptr
< SwitchResidueTypeSetMover
SwitchResidueTypeSetMoverOP
 
typedef
utility::pointer::owning_ptr
< SwitchResidueTypeSetMover
const > 
SwitchResidueTypeSetMoverCOP
 
typedef
utility::pointer::owning_ptr
< SymmetricFragmentMover
SymmetricFragmentMoverOP
 
typedef
utility::pointer::owning_ptr
< SymmetricFragmentMover const > 
SymmetricFragmentMoverCOP
 
typedef
utility::pointer::owning_ptr
< TaskAwareMinMover
TaskAwareMinMoverOP
 
typedef
utility::pointer::owning_ptr
< TaskAwareMinMover const > 
TaskAwareMinMoverCOP
 
typedef
utility::pointer::owning_ptr
< TorsionDOFMover
TorsionDOFMoverOP
 
typedef
utility::pointer::owning_ptr
< TorsionDOFMover const > 
TorsionDOFMoverCOP
 
typedef
utility::pointer::owning_ptr
< WobbleMover
WobbleMoverOP
 
typedef
utility::pointer::owning_ptr
< const WobbleMover
WobbleMoverCOP
 

Enumerations

enum  residue_addition_type { append =1, prepend, insert }
 

Functions

static
numeric::random::RandomGenerator 
RG (90)
 
std::ostream & operator<< (std::ostream &os, BackboneMover const &mover)
 
void apply_ideal_coordinates_for_alternative_pucker (core::pose::Pose const &pose, core::pose::Pose &pose_reference)
 
static basic::Tracer TR ("protocols.simple_moves.CutChainMover")
 
static basic::Tracer TR ("protocols.protein_interface_design.movers.ddG")
 
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)
 
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")
 
static basic::Tracer TR ("protocols.simple_moves.FavorSequenceProfile")
 
static basic::Tracer TR ("protocols.simple_moves.ForceDisulfidesMover")
 
static
numeric::random::RandomGenerator 
RG (489)
 
static basic::Tracer tr ("protocols.simple_moves.FragmentMover")
 
std::ostream & operator<< (std::ostream &os, ClassicFragmentMover const &cfmover)
 
basic::Tracer TR ("protocols.simple_moves.GreenPacker")
 
static basic::Tracer trGunnCost ("protocols.FragmentMover.GunnCost")
 
static basic::Tracer TR ("protocols.simple_moves.MembraneTopology")
 
static basic::Tracer TR ("protocols.simple_moves.MinMover")
 
std::ostream & operator<< (std::ostream &os, MinMover const &mover)
 
static basic::Tracer TR ("protocols.simple_moves.MinPackMover")
 
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.O2M_MutateMover")
 
static basic::Tracer TR ("protocols.simple_moves.PackRotamersMover")
 
std::ostream & operator<< (std::ostream &os, PackRotamersMover const &mover)
 
static basic::Tracer TR ("protocols.simple_moves.PackRotamersMoverLazy")
 
static basic::Tracer TR ("protocols.simple_moves.PDBReloadMover")
 
static basic::Tracer TR ("protocols.simple_moves.RepackSidechainsMover")
 
static basic::Tracer TR ("protocol.mover.RepulsiveOnlyMover")
 
std::ostream & operator<< (std::ostream &os, ReturnSidechainMover const &mover)
 
std::ostream & operator<< (std::ostream &os, RotamerTrialsMinMover const &mover)
 
std::ostream & operator<< (std::ostream &os, RotamerTrialsMover const &mover)
 
static basic::Tracer TR ("protocols.simple_moves.SaneMinMover")
 
static basic::Tracer TR ("protocols.simple_moves.ScoreMover")
 
static basic::Tracer TR ("protocols.simple_moves.SetTorsion")
 
static
numeric::random::RandomGenerator 
rg (15433)
 
static
numeric::random::RandomGenerator 
RG (345)
 
static basic::Tracer TR ("protocols.simple_moves.SuperimposeMover")
 
std::ostream & operator<< (std::ostream &os, SwitchResidueTypeSetMover const &mover)
 
static
numeric::random::RandomGenerator 
RG (43389)
 
static basic::Tracer tr ("protocols.simple_moves.FragmentMover")
 
static
numeric::random::RandomGenerator 
RG (490)
 

Variables

const int VISITED = 1
 
const int PREVIOUS_HILL = 2
 
const int HILL = 3
 
const int VISITED_HILL = 4
 
const double ED = 2
 
const double KT = 15
 

Typedef Documentation

Trigger API definition.

Enumeration Type Documentation

Enumerator
append 
prepend 
insert 

Function Documentation

void protocols::simple_moves::apply_ideal_coordinates_for_alternative_pucker ( core::pose::Pose const &  pose,
core::pose::Pose pose_reference 
)
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,
ReturnSidechainMover const &  mover 
)
std::ostream& protocols::simple_moves::operator<< ( std::ostream &  os,
RotamerTrialsMinMover const &  mover 
)
std::ostream& protocols::simple_moves::operator<< ( std::ostream &  os,
RotamerTrialsMover const &  mover 
)
std::ostream& protocols::simple_moves::operator<< ( std::ostream &  os,
PackRotamersMover const &  mover 
)
std::ostream & protocols::simple_moves::operator<< ( std::ostream &  os,
MinMover const &  mover 
)
std::ostream& protocols::simple_moves::operator<< ( std::ostream &  os,
ClassicFragmentMover const &  cfmover 
)
std::ostream & protocols::simple_moves::operator<< ( std::ostream &  os,
BackboneMover const &  mover 
)
Real protocols::simple_moves::point_graph_dme ( conformation::PointGraph const &  pg,
pose::Pose const &  pose 
)
static numeric::random::RandomGenerator protocols::simple_moves::RG ( 43389  )
static
static numeric::random::RandomGenerator protocols::simple_moves::RG ( 490  )
static
static numeric::random::RandomGenerator protocols::simple_moves::RG ( 345  )
static
static numeric::random::RandomGenerator protocols::simple_moves::RG ( 489  )
static
static numeric::random::RandomGenerator protocols::simple_moves::RG ( 90  )
static

Referenced by protocols::simple_moves::BackboneMover::apply(), protocols::simple_moves::carbohydrates::RingConformationMover::apply(), protocols::simple_moves::sidechain_moves::SidechainMover::apply(), protocols::simple_moves::BBG8T3AMover::apply(), protocols::simple_moves::WobbleMover::apply_fragment(), protocols::simple_moves::TorsionDOFMover::boltzmann(), protocols::simple_moves::TorsionDOFMover::calc_angle(), protocols::simple_moves::BackboneMover::check_rama(), protocols::simple_moves::SmoothFragmentMover::choose_fragment(), protocols::simple_moves::ClassicFragmentMover::choose_fragment(), protocols::simple_moves::ClassicFragmentMover::choose_window_start(), protocols::simple_moves::ClassicFragmentMover::end_bias_check(), protocols::simple_moves::BBConRotMover::get_L_move(), protocols::simple_moves::BBG8T3AMover::get_L_move(), protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover::make_chi_move(), protocols::simple_moves::sidechain_moves::PerturbChiSidechainMover::make_chi_move(), protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMover::make_chi_move(), protocols::simple_moves::BBConRotMover::make_move(), protocols::simple_moves::sidechain_moves::SidechainMover::make_move(), protocols::simple_moves::SmallMover::make_move(), protocols::simple_moves::ShearMover::make_move(), protocols::simple_moves::sidechain_moves::SidechainMover::make_rotwell_jump(), protocols::simple_moves::sidechain_moves::SidechainMover::perturb_rot_within_well(), protocols::simple_moves::BBGaussianMover::pivot_range_randomly(), protocols::simple_moves::sidechain_moves::SidechainMover::preturb_rot_and_dunbrack_eval(), and protocols::simple_moves::sidechain_moves::SidechainMoverBase::suggest_residue_number().

static numeric::random::RandomGenerator protocols::simple_moves::rg ( 15433  )
static
conformation::PointGraphOP protocols::simple_moves::setup_dme_point_graph ( pose::Pose const &  ref_pose,
Real const  threshold 
)
static basic::Tracer protocols::simple_moves::TR ( "protocols.simple_moves.SaneMinMover"  )
static
static basic::Tracer protocols::simple_moves::TR ( "protocols.simple_moves.MembraneTopology"  )
static
static basic::Tracer protocols::simple_moves::TR ( "protocols.simple_moves.O2M_MutateMover"  )
static
static basic::Tracer protocols::simple_moves::TR ( "protocols.simple_moves.DumpPdb"  )
static
static basic::Tracer protocols::simple_moves::tr ( "protocols.simple_moves.FragmentMover"  )
static
static basic::Tracer protocols::simple_moves::TR ( "protocols.simple_moves.PDBReloadMover"  )
static
static basic::Tracer protocols::simple_moves::TR ( "protocols.simple_moves.SuperimposeMover"  )
static
static basic::Tracer protocols::simple_moves::TR ( "protocols.mover.MissingDensityToJumpMover"  )
static
static basic::Tracer protocols::simple_moves::TR ( "protocols.simple_moves.ForceDisulfidesMover"  )
static
static basic::Tracer protocols::simple_moves::TR ( "protocol.mover.RepulsiveOnlyMover"  )
static
static basic::Tracer protocols::simple_moves::TR ( "protocols.simple_moves.SetTorsion"  )
static
static basic::Tracer protocols::simple_moves::TR ( "protocols.simple_moves.PackRotamersMoverLazy"  )
static
static basic::Tracer protocols::simple_moves::TR ( "protocols.simple_moves.RepackSidechainsMover"  )
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.MutateResidue"  )
static
static basic::Tracer protocols::simple_moves::TR ( "protocols.simple_moves.MinPackMover"  )
static
static basic::Tracer protocols::simple_moves::tr ( "protocols.simple_moves.FragmentMover"  )
static
static basic::Tracer protocols::simple_moves::TR ( "protocols.simple_moves.MinMover"  )
static
basic::Tracer protocols::simple_moves::TR ( "protocols.simple_moves.GreenPacker"  )
static basic::Tracer protocols::simple_moves::TR ( "protocols.simple_moves.PackRotamersMover"  )
static
static basic::Tracer protocols::simple_moves::TR ( "protocols.simple_moves.CutChainMover"  )
static

Referenced by protocols::simple_moves::ConstrainToIdealMover::add_bond_angle_constraint(), protocols::simple_moves::ConstrainToIdealMover::add_bond_constraint(), protocols::simple_moves::HelicalPeptideLengthMover::add_residue_(), protocols::simple_moves::AddConstraintsToCurrentConformationMover::apply(), protocols::simple_moves::SequenceProfileMover::apply(), protocols::simple_moves::LoadPDBMover::apply(), protocols::simple_moves::O2M_MutateMover::apply(), protocols::simple_moves::DumpPdb::apply(), protocols::simple_moves::SuperimposeMover::apply(), protocols::simple_moves::SwitchChainOrderMover::apply(), protocols::simple_moves::PeptideStapleMover::apply(), protocols::simple_moves::SetReturningPackRotamersMover::apply(), protocols::simple_moves::HelicalPeptideLengthMover::apply(), protocols::simple_moves::MissingDensityToJumpMover::apply(), protocols::simple_moves::SetTorsion::apply(), protocols::simple_moves::RepulsiveOnlyMover::apply(), protocols::simple_moves::ModifyVariantTypeMover::apply(), protocols::simple_moves::MutateResidue::apply(), protocols::simple_moves::SaneMinMover::apply(), protocols::simple_moves::BBConRotMover::apply(), protocols::simple_moves::ddG::apply(), protocols::simple_moves::MakePolyXMover::apply(), protocols::simple_moves::DME_FilterMover::apply(), protocols::simple_moves::MonteCarloTest::apply(), protocols::simple_moves::ScoreMover::apply(), protocols::simple_moves::RotamerTrialsMover::apply(), protocols::simple_moves::carbohydrates::RingConformationMover::apply(), protocols::simple_moves::GenericMonteCarloMover::apply(), protocols::simple_moves::GreenPacker::apply(), protocols::simple_moves::WobbleMover::apply_fragment(), protocols::simple_moves::GenericMonteCarloMover::boltzmann(), protocols::simple_moves::BBConRotMover::closure(), protocols::simple_moves::ConsensusDesignMover::create_consensus_design_task(), protocols::simple_moves::ddG::ddG(), protocols::simple_moves::PeptideStapleMover::derive_staple_constraints_(), protocols::simple_moves::GreenPacker::find_reference_and_current_rotamer_correspondence(), protocols::simple_moves::BBConRotMover::get_determinant(), protocols::simple_moves::GenericMonteCarloMover::initialize(), protocols::simple_moves::GenericMonteCarloMover::load_trial_number_from_checkpoint(), protocols::simple_moves::BBConRotMover::make_move(), protocols::simple_moves::PeptideStapleMover::minimize_(), protocols::simple_moves::GenericMonteCarloMover::num_designable(), protocols::simple_moves::FavorSequenceProfile::parse_def(), protocols::simple_moves::ConstraintSetMover::parse_def(), protocols::simple_moves::MutateResidue::parse_def(), protocols::simple_moves::SequenceProfileMover::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::DesignRepackMover::parse_my_tag(), protocols::simple_moves::ConstraintSetMover::parse_my_tag(), protocols::simple_moves::ModifyVariantTypeMover::parse_my_tag(), protocols::simple_moves::TaskAwareMinMover::parse_my_tag(), protocols::simple_moves::SetTorsion::parse_my_tag(), protocols::simple_moves::MakePolyXMover::parse_my_tag(), protocols::simple_moves::MutateResidue::parse_my_tag(), protocols::simple_moves::PackRotamersMoverLazy::parse_my_tag(), protocols::simple_moves::ddG::parse_my_tag(), protocols::simple_moves::MonteCarloRecover::parse_my_tag(), protocols::simple_moves::MinPackMover::parse_my_tag(), protocols::simple_moves::MonteCarloTest::parse_my_tag(), protocols::simple_moves::RotamerTrialsMinMover::parse_my_tag(), protocols::simple_moves::GenericMonteCarloMover::parse_my_tag(), protocols::simple_moves::GenericMonteCarloMover::parse_task_operations(), protocols::simple_moves::GenericMonteCarloMover::recover_low(), protocols::simple_moves::GenericMonteCarloMover::remove_trigger(), protocols::simple_moves::GenericMonteCarloMover::reset(), protocols::simple_moves::FavorSequenceProfile::set_profile(), protocols::simple_moves::GenericMonteCarloMover::set_sampletype(), protocols::simple_moves::FavorSequenceProfile::set_sequence(), and protocols::simple_moves::oop::OopMover::update_hydrogens_().

static basic::Tracer protocols::simple_moves::TR ( "protocols.simple_moves.ScoreMover"  )
static
static basic::Tracer protocols::simple_moves::TR ( "protocols.protein_interface_design.movers.ddG"  )
static
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 double protocols::simple_moves::ED = 2
const int protocols::simple_moves::HILL = 3
const double 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