Rosetta 3.5
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Namespaces | Classes | Typedefs | Enumerations | Functions | Variables
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::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")
 
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

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

Definition at line 26 of file BackboneMover.fwd.hh.

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

Definition at line 24 of file BackboneMover.fwd.hh.

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

Definition at line 20 of file BBConRotMover.fwd.hh.

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

Definition at line 18 of file BBConRotMover.fwd.hh.

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

Definition at line 30 of file BBGaussianMover.fwd.hh.

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

Definition at line 28 of file BBGaussianMover.fwd.hh.

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

Definition at line 26 of file BBGaussianMover.fwd.hh.

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

Definition at line 24 of file BBGaussianMover.fwd.hh.

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

Definition at line 36 of file FragmentMover.fwd.hh.

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

Definition at line 33 of file FragmentMover.fwd.hh.

typedef utility::pointer::owning_ptr< ConsensusDesignMover > protocols::simple_moves::ConsensusDesignMoverOP

Definition at line 23 of file ConsensusDesignMover.fwd.hh.

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

Definition at line 27 of file ConstrainToIdealMover.fwd.hh.

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

Definition at line 25 of file ConstrainToIdealMover.fwd.hh.

typedef utility::pointer::owning_ptr< ConstraintSetMover const > protocols::simple_moves::ConstraintSetMoverCOP

Definition at line 24 of file ConstraintSetMover.fwd.hh.

typedef utility::pointer::owning_ptr< ConstraintSetMover > protocols::simple_moves::ConstraintSetMoverOP

Definition at line 22 of file ConstraintSetMover.fwd.hh.

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

Definition at line 26 of file CutChainMover.fwd.hh.

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

Definition at line 24 of file CutChainMover.fwd.hh.

typedef utility::pointer::owning_ptr< ddG const > protocols::simple_moves::ddGCOP

Definition at line 26 of file ddG.fwd.hh.

typedef utility::pointer::owning_ptr< ddG > protocols::simple_moves::ddGOP

Definition at line 23 of file ddG.fwd.hh.

typedef utility::pointer::owning_ptr< DesignRepackMover const > protocols::simple_moves::DesignRepackMoverCOP

Definition at line 28 of file DesignRepackMover.fwd.hh.

typedef utility::pointer::owning_ptr< DesignRepackMover > protocols::simple_moves::DesignRepackMoverOP

Definition at line 25 of file DesignRepackMover.fwd.hh.

typedef utility::pointer::owning_ptr< EnergyCutRotamerTrialsMinMover const > protocols::simple_moves::EnergyCutRotamerTrialsMinMoverCOP

Definition at line 28 of file RotamerTrialsMinMover.fwd.hh.

typedef utility::pointer::owning_ptr< EnergyCutRotamerTrialsMinMover > protocols::simple_moves::EnergyCutRotamerTrialsMinMoverOP

Definition at line 26 of file RotamerTrialsMinMover.fwd.hh.

typedef utility::pointer::owning_ptr< EnergyCutRotamerTrialsMover const > protocols::simple_moves::EnergyCutRotamerTrialsMoverCOP

Definition at line 29 of file RotamerTrialsMover.fwd.hh.

typedef utility::pointer::owning_ptr< EnergyCutRotamerTrialsMover > protocols::simple_moves::EnergyCutRotamerTrialsMoverOP

Definition at line 27 of file RotamerTrialsMover.fwd.hh.

typedef utility::pointer::owning_ptr<ExtendedPoseMover const> protocols::simple_moves::ExtendedPoseMoverCOP

Definition at line 23 of file ExtendedPoseMover.fwd.hh.

typedef utility::pointer::owning_ptr<ExtendedPoseMover> protocols::simple_moves::ExtendedPoseMoverOP

Definition at line 21 of file ExtendedPoseMover.fwd.hh.

typedef utility::pointer::owning_ptr< ForceDisulfidesMover const > protocols::simple_moves::ForceDisulfideMoverCOP

Definition at line 26 of file ForceDisulfidesMover.fwd.hh.

typedef utility::pointer::owning_ptr< ForceDisulfidesMover > protocols::simple_moves::ForceDisulfideMoverOP

Definition at line 24 of file ForceDisulfidesMover.fwd.hh.

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

Definition at line 35 of file SmoothFragmentMover.fwd.hh.

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

Definition at line 32 of file SmoothFragmentMover.fwd.hh.

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

Definition at line 30 of file FragmentMover.fwd.hh.

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

Definition at line 27 of file FragmentMover.fwd.hh.

typedef utility::pointer::owning_ptr< GenericMonteCarloMover const > protocols::simple_moves::GenericMonteCarloMoverCOP

Definition at line 27 of file GenericMonteCarloMover.fwd.hh.

typedef utility::pointer::owning_ptr< GenericMonteCarloMover > protocols::simple_moves::GenericMonteCarloMoverOP

Definition at line 25 of file GenericMonteCarloMover.fwd.hh.

typedef boost::function<bool(core::Size, core::Size, const core::pose::Pose&, core::scoring::ScoreFunctionOP)> protocols::simple_moves::GenericMonteCarloMoverTrigger

Trigger API definition.

Definition at line 58 of file GenericMonteCarloMover.hh.

typedef utility::pointer::owning_ptr< GreenPacker const > protocols::simple_moves::GreenPackerCOP

Definition at line 38 of file GreenPacker.fwd.hh.

typedef utility::pointer::owning_ptr< GreenPacker > protocols::simple_moves::GreenPackerOP

Definition at line 37 of file GreenPacker.fwd.hh.

typedef utility::pointer::owning_ptr< GroupDiscriminator const > protocols::simple_moves::GroupDiscriminatorCOP

Definition at line 35 of file GreenPacker.fwd.hh.

typedef utility::pointer::owning_ptr< GroupDiscriminator > protocols::simple_moves::GroupDiscriminatorOP

Definition at line 34 of file GreenPacker.fwd.hh.

typedef utility::pointer::owning_ptr< HelicalPeptideLengthMover const > protocols::simple_moves::HelicalPeptideLengthMoverCOP

Definition at line 27 of file HelicalPeptideLengthMover.fwd.hh.

typedef utility::pointer::owning_ptr< HelicalPeptideLengthMover > protocols::simple_moves::HelicalPeptideLengthMoverOP

Definition at line 25 of file HelicalPeptideLengthMover.fwd.hh.

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

Definition at line 24 of file LoadPDBMover.fwd.hh.

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

Definition at line 22 of file LoadPDBMover.fwd.hh.

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

Definition at line 28 of file LoadUnboundRotMover.fwd.hh.

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

Definition at line 26 of file LoadUnboundRotMover.fwd.hh.

typedef utility::pointer::owning_ptr< MakePolyXMover > protocols::simple_moves::MakePolyXMoverOP

Definition at line 23 of file MakePolyXMover.fwd.hh.

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

Definition at line 26 of file MembraneTopology.fwd.hh.

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

Definition at line 24 of file MembraneTopology.fwd.hh.

typedef utility::pointer::owning_ptr< MinimalRotamer const > protocols::simple_moves::MinimalRotamerCOP

Definition at line 33 of file GreenPacker.fwd.hh.

typedef utility::pointer::owning_ptr< MinimalRotamer > protocols::simple_moves::MinimalRotamerOP

Definition at line 30 of file GreenPacker.fwd.hh.

typedef utility::pointer::owning_ptr< MinMover const > protocols::simple_moves::MinMoverCOP

Definition at line 26 of file MinMover.fwd.hh.

typedef utility::pointer::owning_ptr< MinMover > protocols::simple_moves::MinMoverOP

Definition at line 24 of file MinMover.fwd.hh.

typedef utility::pointer::owning_ptr< MinPackMover const > protocols::simple_moves::MinPackMoverCOP

Definition at line 24 of file MinPackMover.fwd.hh.

typedef utility::pointer::owning_ptr< MinPackMover > protocols::simple_moves::MinPackMoverOP

Definition at line 22 of file MinPackMover.fwd.hh.

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

Definition at line 27 of file MissingDensityToJumpMover.fwd.hh.

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

Definition at line 25 of file MissingDensityToJumpMover.fwd.hh.

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

Definition at line 28 of file ModifyVariantTypeMover.fwd.hh.

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

Definition at line 26 of file ModifyVariantTypeMover.fwd.hh.

typedef utility::pointer::owning_ptr< MonteCarloRecover const > protocols::simple_moves::MonteCarloRecoverCOP

Definition at line 25 of file MonteCarloRecover.fwd.hh.

typedef utility::pointer::owning_ptr< MonteCarloRecover > protocols::simple_moves::MonteCarloRecoverOP

Definition at line 23 of file MonteCarloRecover.fwd.hh.

typedef utility::pointer::owning_ptr< MonteCarloTest const > protocols::simple_moves::MonteCarloTestCOP

Definition at line 25 of file MonteCarloTest.fwd.hh.

typedef utility::pointer::owning_ptr< MonteCarloTest > protocols::simple_moves::MonteCarloTestOP

Definition at line 23 of file MonteCarloTest.fwd.hh.

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

Definition at line 27 of file MutateResidue.fwd.hh.

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

Definition at line 25 of file MutateResidue.fwd.hh.

typedef boost::shared_ptr<O2M_MutateMover> protocols::simple_moves::O2M_MutateMoverSP

Definition at line 23 of file O2M_MutateMover.fwd.hh.

typedef utility::pointer::owning_ptr< PackRotamersMover const > protocols::simple_moves::PackRotamersMoverCOP

Definition at line 25 of file PackRotamersMover.fwd.hh.

typedef utility::pointer::owning_ptr< PackRotamersMoverLazy const > protocols::simple_moves::PackRotamersMoverLazyCOP

Definition at line 23 of file PackRotamersMoverLazy.fwd.hh.

typedef utility::pointer::owning_ptr< PackRotamersMoverLazy > protocols::simple_moves::PackRotamersMoverLazyOP

Definition at line 21 of file PackRotamersMoverLazy.fwd.hh.

typedef utility::pointer::owning_ptr< PackRotamersMover > protocols::simple_moves::PackRotamersMoverOP

Definition at line 23 of file PackRotamersMover.fwd.hh.

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

Definition at line 26 of file PDBReloadMover.fwd.hh.

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

Definition at line 24 of file PDBReloadMover.fwd.hh.

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

Definition at line 27 of file PeptideStapleMover.fwd.hh.

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

Definition at line 25 of file PeptideStapleMover.fwd.hh.

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

Definition at line 27 of file ProlineFixMover.fwd.hh.

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

Definition at line 25 of file ProlineFixMover.fwd.hh.

typedef utility::pointer::owning_ptr< RepackSidechainsMover const > protocols::simple_moves::RepackSidechainsMoverCOP

Definition at line 25 of file RepackSidechainsMover.fwd.hh.

typedef utility::pointer::owning_ptr< RepackSidechainsMover > protocols::simple_moves::RepackSidechainsMoverOP

Definition at line 23 of file RepackSidechainsMover.fwd.hh.

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

Definition at line 39 of file RepulsiveOnlyMover.fwd.hh.

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

Definition at line 37 of file RepulsiveOnlyMover.fwd.hh.

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

Definition at line 28 of file ReturnSidechainMover.fwd.hh.

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

Definition at line 26 of file ReturnSidechainMover.fwd.hh.

typedef utility::pointer::owning_ptr< RotamerTrialsMinMover const > protocols::simple_moves::RotamerTrialsMinMoverCOP

Definition at line 24 of file RotamerTrialsMinMover.fwd.hh.

typedef utility::pointer::owning_ptr< RotamerTrialsMinMover > protocols::simple_moves::RotamerTrialsMinMoverOP

Definition at line 22 of file RotamerTrialsMinMover.fwd.hh.

typedef utility::pointer::owning_ptr< RotamerTrialsMover const > protocols::simple_moves::RotamerTrialsMoverCOP

Definition at line 25 of file RotamerTrialsMover.fwd.hh.

typedef utility::pointer::owning_ptr< RotamerTrialsMover > protocols::simple_moves::RotamerTrialsMoverOP

Definition at line 23 of file RotamerTrialsMover.fwd.hh.

typedef utility::pointer::owning_ptr< SaneMinMover const > protocols::simple_moves::SaneMinMoverCOP

Definition at line 26 of file SaneMinMover.fwd.hh.

typedef utility::pointer::owning_ptr< SaneMinMover > protocols::simple_moves::SaneMinMoverOP

Definition at line 24 of file SaneMinMover.fwd.hh.

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

Definition at line 41 of file ConstraintFragmentMover.hh.

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

Definition at line 26 of file ScoreMover.fwd.hh.

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

Definition at line 24 of file ScoreMover.fwd.hh.

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

Definition at line 29 of file SequenceProfileMover.fwd.hh.

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

Definition at line 26 of file SequenceProfileMover.fwd.hh.

typedef utility::pointer::owning_ptr< SetReturningPackRotamersMover const > protocols::simple_moves::SetReturningPackRotamersMoverCOP

Definition at line 26 of file SetReturningPackRotamersMover.fwd.hh.

typedef utility::pointer::owning_ptr< SetReturningPackRotamersMover > protocols::simple_moves::SetReturningPackRotamersMoverOP

Definition at line 24 of file SetReturningPackRotamersMover.fwd.hh.

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

Definition at line 26 of file SetTorsion.fwd.hh.

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

Definition at line 24 of file SetTorsion.fwd.hh.

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

Definition at line 26 of file ShakeStructureMover.fwd.hh.

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

Definition at line 24 of file ShakeStructureMover.fwd.hh.

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

Definition at line 34 of file BackboneMover.fwd.hh.

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

Definition at line 32 of file BackboneMover.fwd.hh.

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

Definition at line 30 of file BackboneMover.fwd.hh.

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

Definition at line 28 of file BackboneMover.fwd.hh.

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

Definition at line 30 of file SmoothFragmentMover.fwd.hh.

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

Definition at line 27 of file SmoothFragmentMover.fwd.hh.

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

Definition at line 26 of file SuperimposeMover.fwd.hh.

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

Definition at line 24 of file SuperimposeMover.fwd.hh.

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

Definition at line 24 of file SwitchChainOrderMover.fwd.hh.

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

Definition at line 22 of file SwitchChainOrderMover.fwd.hh.

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

Definition at line 24 of file SwitchResidueTypeSetMover.fwd.hh.

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

Definition at line 22 of file SwitchResidueTypeSetMover.fwd.hh.

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

Definition at line 30 of file SymmetricFragmentMover.fwd.hh.

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

Definition at line 27 of file SymmetricFragmentMover.fwd.hh.

typedef utility::pointer::owning_ptr< TaskAwareMinMover const > protocols::simple_moves::TaskAwareMinMoverCOP

Definition at line 28 of file TaskAwareMinMover.fwd.hh.

typedef utility::pointer::owning_ptr< TaskAwareMinMover > protocols::simple_moves::TaskAwareMinMoverOP

Definition at line 26 of file TaskAwareMinMover.fwd.hh.

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

Definition at line 26 of file TorsionDOFMover.fwd.hh.

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

Definition at line 24 of file TorsionDOFMover.fwd.hh.

typedef utility::pointer::owning_ptr< UserDefinedGroupDiscriminator > protocols::simple_moves::UserDefinedGroupDiscriminatorOP

Definition at line 36 of file GreenPacker.fwd.hh.

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

Definition at line 45 of file WobbleMover.hh.

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

Definition at line 43 of file WobbleMover.hh.

Enumeration Type Documentation

enum protocols::simple_moves::residue_addition_type
Enumerator
append 
prepend 
insert 

Definition at line 36 of file HelicalPeptideLengthMover.hh.

Function Documentation

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

Definition at line 495 of file ConstrainToIdealMover.cc.

References core::scoring::rna::apply_ideal_c2endo_sugar_coords(), core::scoring::dna::DELTA, core::conformation::Residue::mainchain_torsion(), core::pose::Pose::residue(), and core::pose::Pose::total_residue().

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

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

Definition at line 111 of file SwitchResidueTypeSetMover.cc.

References protocols::simple_moves::SwitchResidueTypeSetMover::get_residue_type_set(), and protocols::moves::operator<<().

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

Definition at line 157 of file DOFHistogramRecorder.cc.

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

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

Definition at line 174 of file ReturnSidechainMover.cc.

References protocols::simple_moves::ReturnSidechainMover::get_end_res(), protocols::simple_moves::ReturnSidechainMover::get_start_res(), and protocols::moves::operator<<().

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

Definition at line 178 of file RotamerTrialsMinMover.cc.

References protocols::moves::operator<<(), and protocols::simple_moves::RotamerTrialsMinMover::scorefxn().

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

Definition at line 185 of file RotamerTrialsMover.cc.

References protocols::moves::operator<<(), and protocols::simple_moves::RotamerTrialsMover::scorefxn().

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

Definition at line 349 of file PackRotamersMover.cc.

References protocols::moves::operator<<(), and protocols::simple_moves::PackRotamersMover::score_function().

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

Definition at line 459 of file MinMover.cc.

References protocols::simple_moves::MinMover::deriv_check(), protocols::simple_moves::MinMover::min_type(), protocols::simple_moves::MinMover::movemap(), protocols::simple_moves::MinMover::nb_list(), protocols::moves::operator<<(), protocols::simple_moves::MinMover::score_function(), and protocols::simple_moves::MinMover::tolerance().

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

Definition at line 510 of file FragmentMover.cc.

References protocols::simple_moves::ClassicFragmentMover::bApplyEndBias_, protocols::simple_moves::ClassicFragmentMover::check_ss_, protocols::simple_moves::ClassicFragmentMover::end_bias_, protocols::simple_moves::ClassicFragmentMover::min_frag_length_, protocols::simple_moves::ClassicFragmentMover::min_overlap_, protocols::simple_moves::FragmentMover::movemap(), protocols::moves::operator<<(), protocols::simple_moves::ClassicFragmentMover::predefined_window_start_, and protocols::simple_moves::ClassicFragmentMover::use_predefined_window_start_.

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

Definition at line 583 of file BackboneMover.cc.

References protocols::simple_moves::BackboneMover::get_angle_max(), protocols::simple_moves::BackboneMover::movemap(), protocols::simple_moves::BackboneMover::nmoves(), protocols::moves::operator<<(), and protocols::simple_moves::BackboneMover::temperature().

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

Calculate the dme using a pointgraph

Definition at line 59 of file DME_FilterMover.cc.

References core::graph::UEVertex< V, E >::const_upper_edge_list_begin(), core::graph::UEVertex< V, E >::const_upper_edge_list_end(), core::graph::UpperEdgeGraph< V, E >::get_vertex(), core::conformation::Residue::nbr_atom_xyz(), core::pose::Pose::residue(), and core::pose::Pose::total_residue().

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

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

Referenced by protocols::simple_moves::symmetry::SymmetrySlider::dofmover_compresses(), and protocols::simple_moves::symmetry::SymmetrySlider::rg().

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

Definition at line 49 of file DME_FilterMover.cc.

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

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

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

Referenced by protocols::simple_moves::ClassicFragmentMover::apply(), protocols::simple_moves::SymmetricFragmentMover::apply_fragment(), protocols::simple_moves::ClassicFragmentMover::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::sidechain_moves::SidechainMoverBase::make_move(), and protocols::simple_moves::ClassicFragmentMover::valid_ss().

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 
)

Definition at line 187 of file DOFHistogramRecorder.cc.

References core::id::PHI, and core::id::THETA.

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

Variable Documentation

const double protocols::simple_moves::ED = 2

Definition at line 55 of file TailsScoreMover.cc.

Referenced by protocols::simple_moves::TailsScoreMover::score_mode1(), protocols::simple_moves::TailsScoreMover::score_mode2(), and protocols::simple_moves::TailsScoreMover::visit().

const int protocols::simple_moves::HILL = 3

Definition at line 53 of file TailsScoreMover.cc.

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

const double protocols::simple_moves::KT = 15

Definition at line 56 of file TailsScoreMover.cc.

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

const int protocols::simple_moves::PREVIOUS_HILL = 2

Definition at line 52 of file TailsScoreMover.cc.

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

const int protocols::simple_moves::VISITED = 1

Definition at line 51 of file TailsScoreMover.cc.

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

const int protocols::simple_moves::VISITED_HILL = 4

Definition at line 54 of file TailsScoreMover.cc.

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

Generated on Sat Jun 1 2013 12:53:30 for Rosetta 3.5 by   doxygen 1.8.4