Rosetta
Classes | Typedefs | Enumerations | Functions | Variables
protocols::protein_interface_design::movers Namespace Reference

Classes

class  AddChainBreak
 a mover that sets a chainbreak in a specified position More...
 
class  AddChainBreakCreator
 
class  AddSidechainConstraintsToHotspots
 
class  AddSidechainConstraintsToHotspotsCreator
 
class  BackrubDDMover
 
class  BackrubDDMoverCreator
 
class  BestHotspotCstMover
 remove all HotspotCst's from the pose except the best X More...
 
class  BestHotspotCstMoverCreator
 
class  BuildAlaPose
 designs alanine residues in place of the residue identities at the interface. Retains interface glycines and prolines. More...
 
class  BuildAlaPoseCreator
 
class  DesignMinimizeHbonds
 used to design a protein to hbond preferentially to a set of target residues on the partner. Hbonds involving backbone or sidechain on the target can be counted, and whether to design donors or acceptors can also be defined. More...
 
class  DesignMinimizeHbondsCreator
 
class  DisulfideMover
 
class  DisulfideMoverCreator
 
class  DockAndRetrieveSidechains
 
class  DockAndRetrieveSidechainsCreator
 
class  DockWithHotspotMover
 A mover to mutate a single residue. More...
 
class  DockWithHotspotMoverCreator
 
class  FavorNativeResiduePreCycle
 
class  FavorNativeResiduePreCycleCreator
 
class  FavorNonNativeResiduePreCycle
 
class  FavorNonNativeResiduePreCycleCreator
 
class  HotspotDisjointedFoldTreeMover
 
class  HotspotDisjointedFoldTreeMoverCreator
 
class  HotspotHasherMover
 
class  HotspotHasherMoverCreator
 
class  InterfaceRecapitulationMover
 a pure virtual base class for movers which redesign and repack the interface More...
 
class  InterfaceRecapitulationMoverCreator
 
class  LoopFinder
 
class  LoopFinderCreator
 
class  LoopLengthChange
 designs alanine residues in place of the residue identities at the interface. Retains interface glycines and prolines. More...
 
class  LoopLengthChangeCreator
 
class  LoopMoverFromCommandLine
 
class  LoopMoverFromCommandLineCreator
 
class  LoopOver
 essentially the same as the WhileMover but allows parsing and cloning. Will be removed at a future point. This should now be incorporated into WhileMover More...
 
class  LoopOverCreator
 
class  LoopRemodel
 
class  LoopRemodelCreator
 
class  MapHotspot
 
class  MapHotspotCreator
 
class  PatchdockTransform
 wrapper around protocols::protein_interface_design::PatchdockReader class. That class is derived from JobInputter and handles input situations that involve patchdock output files. Here, we provide an entry point for a patchdock transformation within the RosettaScripts trajectory. More...
 
class  PatchdockTransformCreator
 
class  PeptideStapleDesignMover
 Introduces a peptide staple (ala G. Verdine) to the pose. More...
 
class  PeptideStapleDesignMoverCreator
 
class  PlacementAuctionMover
 
class  PlacementAuctionMoverCreator
 
class  PlacementMinimizationMover
 a simple rb-minimization in a bb-stub constraint biased forcefield. Note that this mover is dependent on a placement mover for setting its stubsets More...
 
class  PlacementMinimizationMoverCreator
 
class  PlaceOnLoop
 
class  PlaceOnLoopCreator
 
class  PlaceSimultaneouslyMover
 choose a stub based on mc sampling, and place it on the pose. Iterates over stubs until one matches criteria. More...
 
class  PlaceSimultaneouslyMoverCreator
 
class  CoordinateConstraintStack
 
class  PlaceStubMover
 choose a stub based on mc sampling, and place it on the pose. Iterates over stubs until one matches criteria. More...
 
class  PlaceStubMoverCreator
 
class  PrepackMover
 
class  PrepackMoverCreator
 
class  ProteinInterfaceMultiStateDesignMover
 wraps protein-interface specific considerations around the general multistate design / genetic algorithm framework More...
 
class  ProteinInterfaceMultiStateDesignMoverCreator
 
class  RandomMutation
 designs alanine residues in place of the residue identities at the interface. Retains interface glycines and prolines. More...
 
class  RandomMutationCreator
 
class  RepackMinimize
 One round of design/repacking followed by interface sc/bb and rigid-body minimization. More...
 
class  RepackMinimizeCreator
 
class  SaveAndRetrieveSidechains
 saves a pose and reapplies its sequence and rotamers at a later stage. The constructor saves the initial pose, and then any calls to apply replace the residues on the input pose with that saved pose. Notice, that only ALA positions will be replaced, so this is meant to work strictly along with BuildAlaPose moves. This way, if in the design process an interface residue is designed, that will not be reverted to w/t More...
 
class  SaveAndRetrieveSidechainsCreator
 
class  SecretionOptimizationMover
 
class  SecretionOptimizationMoverCreator
 
class  SetAtomTree
 a mover that sets a user-defined atom tree More...
 
class  SetAtomTreeCreator
 
class  SetTemperatureFactor
 Set the temperature (b-)factor column in the PDB according to som filter's value. The filter needs to be ResId-compatible, i.e. to report values on a per-residue basis. More...
 
class  SetTemperatureFactorCreator
 
class  SetupHotspotConstraintsLoopsMover
 
class  SetupHotspotConstraintsLoopsMoverCreator
 
class  SetupHotspotConstraintsMover
 
class  SetupHotspotConstraintsMoverCreator
 
class  ShoveResidueMover
 
class  ShoveResidueMoverCreator
 
class  SpinMover
 
class  SpinMoverCreator
 
class  SubroutineMover
 
class  SubroutineMoverCreator
 
class  TaskAwareCsts
 applies csts (currently only coordinate csts) to every designable position in pose according to taskoperations More...
 
class  TaskAwareCstsCreator
 
class  TopologyBrokerMover
 designs alanine residues in place of the residue identities at the interface. Retains interface glycines and prolines. More...
 
class  TopologyBrokerMoverCreator
 
class  TryRotamers
 
class  TryRotamersCreator
 
struct  VLBInstruction
 
class  VLB
 user interface for YAB's Variable Length Build. More...
 
class  VLBCreator
 

Typedefs

using Real = core::Real
 
using Pose = core::pose::Pose
 
typedef utility::pointer::shared_ptr< BuildAlaPose > BuildAlaPoseOP
 
typedef utility::pointer::shared_ptr< BuildAlaPose const > BuildAlaPoseCOP
 
typedef utility::pointer::shared_ptr< DockWithHotspotMover > DockWithHotspotMoverOP
 
typedef utility::pointer::shared_ptr< DockWithHotspotMover const > DockWithHotspotMoverCOP
 
typedef utility::pointer::shared_ptr< LoopLengthChange > LoopLengthChangeOP
 
typedef utility::pointer::shared_ptr< LoopLengthChange const > LoopLengthChangeCOP
 
typedef utility::pointer::shared_ptr< LoopMoverFromCommandLine > LoopMoverFromCommandLineOP
 
typedef utility::pointer::shared_ptr< LoopMoverFromCommandLine const > LoopMoverFromCommandLineCOP
 
typedef utility::pointer::shared_ptr< LoopRemodel > LoopRemodelOP
 
typedef utility::pointer::shared_ptr< LoopRemodel const > LoopRemodelCOP
 
typedef utility::pointer::shared_ptr< PatchdockTransform > PatchdockTransformOP
 
typedef utility::pointer::shared_ptr< PatchdockTransform const > PatchdockTransformCOP
 
typedef utility::pointer::shared_ptr< PlacementAuctionMover > PlacementAuctionMoverOP
 
typedef utility::pointer::shared_ptr< PlacementAuctionMover const > PlacementAuctionMoverCOP
 
typedef utility::pointer::shared_ptr< PlacementMinimizationMover > PlacementMinimizationMoverOP
 
typedef utility::pointer::shared_ptr< PlacementMinimizationMover const > PlacementMinimizationMoverCOP
 
typedef utility::pointer::shared_ptr< PlaceOnLoop > PlaceOnLoopOP
 
typedef utility::pointer::shared_ptr< PlaceOnLoop const > PlaceOnLoopCOP
 
typedef utility::pointer::shared_ptr< PlaceStubMover > PlaceStubMoverOP
 
typedef utility::pointer::shared_ptr< PlaceStubMover const > PlaceStubMoverCOP
 
typedef utility::pointer::shared_ptr< CoordinateConstraintStack > CoordinateConstraintStackOP
 
typedef utility::pointer::shared_ptr< RandomMutation > RandomMutationOP
 
typedef utility::pointer::shared_ptr< RandomMutation const > RandomMutationCOP
 
typedef utility::pointer::shared_ptr< SaveAndRetrieveSidechains > SaveAndRetrieveSidechainsOP
 
typedef utility::pointer::shared_ptr< SaveAndRetrieveSidechains const > SaveAndRetrieveSidechainsCOP
 
typedef utility::pointer::shared_ptr< SecretionOptimizationMover > SecretionOptimizationMoverOP
 
typedef utility::pointer::shared_ptr< SecretionOptimizationMover const > SecretionOptimizationMoverCOP
 
typedef utility::pointer::shared_ptr< SetTemperatureFactor > SetTemperatureFactorOP
 
typedef utility::pointer::shared_ptr< SetTemperatureFactor const > SetTemperatureFactorCOP
 
typedef utility::pointer::shared_ptr< SetupHotspotConstraintsLoopsMover > SetupHotspotConstraintsLoopsMoverOP
 
typedef utility::pointer::shared_ptr< SetupHotspotConstraintsLoopsMover const > SetupHotspotConstraintsLoopsMoverCOP
 
typedef utility::pointer::shared_ptr< SetupHotspotConstraintsMover > SetupHotspotConstraintsMoverOP
 
typedef utility::pointer::shared_ptr< SetupHotspotConstraintsMover const > SetupHotspotConstraintsMoverCOP
 
typedef utility::pointer::shared_ptr< SubroutineMover > SubroutineMoverOP
 
typedef utility::pointer::shared_ptr< SubroutineMover const > SubroutineMoverCOP
 
typedef utility::pointer::shared_ptr< TaskAwareCsts > TaskAwareCstsOP
 
typedef utility::pointer::shared_ptr< TaskAwareCsts const > TaskAwareCstsCOP
 
typedef utility::pointer::shared_ptr< TopologyBrokerMover > TopologyBrokerMoverOP
 
typedef utility::pointer::shared_ptr< TopologyBrokerMover const > TopologyBrokerMoverCOP
 

Enumerations

enum class  VLBInstructionType {
  Bridge , ConnectRight , GrowLeft , GrowRight ,
  SegmentInsert , SegmentRebuild , SegmentSwap
}
 

Functions

static basic::Tracer TR ("protocols.protein_interface_design.movers.AddChainBreak")
 
static basic::Tracer TR ("protocols.protein_interface_design.movers.AddSidechainConstraintsToHotspots")
 
static basic::Tracer TR_cst ("protocols.protein_interface_design.movers.AddSidechainConstraintsToHotspots_csts")
 
static basic::Tracer TR ("protocols.protein_interface_design.BackrubDDMover")
 
std::string subtag_for_backrubdd (std::string const &subtag)
 
static basic::Tracer TR ("protocols.protein_interface_design.movers.BestHotspotCstMover")
 
static basic::Tracer TR ("protocols.protein_interface_design.movers.BuildAlaPose")
 
static basic::Tracer TR ("protocols.protein_interface_design.movers.DesignMinimizeHbonds")
 
static basic::Tracer TR ("protocols.protein_interface_design.movers.DisulfideMover")
 
static basic::Tracer TR ("protocols.protein_interface_design.movers.DockAndRetrieveSidechains")
 
static basic::Tracer TR ("protocols.protein_interface_design.movers.DockWithHotspotMover")
 
std::string dock_with_hotspot_subtag_naming_func (std::string const &foo)
 
std::string dock_with_hotspot_subsubtag_naming_func (std::string const &foo)
 
static basic::Tracer TR ("protocols.protein_interface_design.movers.FavorNativeResiduePreCycle")
 
static basic::Tracer favor_nonnative_residue_tracer ("protocols.protein_interface_design.movers.FavorNonNativeResiduePreCycle")
 
static basic::Tracer TR ("protocols.protein_interface_design.movers.HotspotDisjointedFoldTreeMover")
 
static basic::Tracer TR ("protocols.protein_interface_design.movers.HotspotHasherMover")
 
std::string subtag_for_hotspothasher (std::string const &tag)
 
static basic::Tracer TR ("protocols.protein_interface_design.movers.LoopFinder")
 
static basic::Tracer TR ("protocols.protein_interface_design.movers.LoopLengthChange")
 
static basic::Tracer TR ("protocols.moves.LoopRemodelFromCommandLine")
 
static basic::Tracer TR_report ("protocols.moves.LoopRemodelFromCommandLine.REPORT")
 
static basic::Tracer TR ("protocols.protein_interface_design.movers.LoopOver")
 
static basic::Tracer TR ("protocols.protein_interface_design.movers.LoopRemodel")
 
static basic::Tracer TR ("protocols.protein_interface_design.movers.MapHotspot")
 
void copy_hotspot_to_pose (core::pose::Pose const &src, core::pose::Pose &dest, core::Size const src_resi, core::chemical::ResidueType const &restype, core::Size const jump)
 
std::string jumpfunc (std::string const &manglee)
 
std::string jumpsfunc (std::string const &manglee)
 
static basic::Tracer TR ("protocols.protein_interface_design.movers.PatchdockTransform")
 
static basic::Tracer TR ("protocols.protein_interface_design.movers.PeptideStapleDesignMover")
 
static basic::Tracer TR ("protocols.protein_interface_design.movers.PlaceOnLoop")
 
std::string PlaceSimultaneously_subelement_mangler (std::string const &element)
 
std::string PlaceSimultaneously_StubMinimize_subelement_mangler (std::string const &element)
 
std::string PlaceSimultaneously_DesignMovers_subelement_mangler (std::string const &element)
 
std::string PlaceSimultaneously_NotifyMovers_subelement_mangler (std::string const &element)
 
std::string PlaceSimultaneously_StubSets_subelement_mangler (std::string const &element)
 
std::string PlaceStub_subelement_mangler (std::string const &element)
 
std::string PlaceStub_StubMinimize_subelement_mangler (std::string const &element)
 
std::string PlaceStub_DesignMovers_subelement_mangler (std::string const &element)
 
std::string PlaceStub_NotifyMovers_subelement_mangler (std::string const &element)
 
bool test_res_res_aln (core::conformation::Residue const &res1, core::conformation::Residue const &res2, core::Real &C_N_angle, core::Real &CB_CA_angle)
 
core::scoring::constraints::ConstraintCOPs add_coordinate_constraints (pose::Pose &pose, core::Size const resnum, core::conformation::Residue const &rsd_i, core::scoring::func::HarmonicFuncOP coord_cst_func, core::id::AtomID const &anchor_atom)
 
core::Size find_nearest_residue_to_coord (core::pose::Pose const &pose, numeric::xyzVector< core::Real > const &coord, core::Size const host_chain)
 find the nearest residue to a coordinate More...
 
std::string nearest_atom_for_constraint (core::conformation::Residue const &residue)
 
core::scoring::constraints::ConstraintCOPs add_coordinate_constraints (pose::Pose &pose, core::conformation::Residue const &source, core::Size const host_chain, core::Size const resnum, core::Real const coord_sdev, core::scoring::func::HarmonicFuncOP &coord_cst_func)
 
void generate_taskfactory_and_add_task_awareness (utility::tag::TagCOP tag, basic::datacache::DataMap &data, core::pack::task::TaskFactoryOP &task_factory)
 
core::scoring::ScoreFunctionOP make_stub_scorefxn ()
 
std::string legolas_what_do_your_elf_eyes_see (std::string const &foo)
 
void add_subelement_for_parse_stub_sets (utility::tag::XMLSchemaSimpleSubelementList &ssl, utility::tag::XMLSchemaDefinition &xsd)
 
utility::vector1< std::pair< protocols::hotspot_hashing::HotspotStubSetOP, std::pair< protocols::hotspot_hashing::HotspotStubOP, core::Size > > > parse_stub_sets (utility::tag::TagCOP tag, basic::datacache::DataMap data)
 a utility function for parsing stubset information from a tag You will need to call finalize_stub_sets() with the reference pose prior to using them. More...
 
void finalize_stub_set (protocols::hotspot_hashing::HotspotStubSetOP stubset, core::pose::Pose const &pose, core::Size const host_chain)
 Update a stubset with the reference pose information. More...
 
void finalize_stub_sets (utility::vector1< std::pair< protocols::hotspot_hashing::HotspotStubSetOP, std::pair< protocols::hotspot_hashing::HotspotStubOP, core::Size > > > &stubsets, core::pose::Pose const &refpose, core::Size const host_chain)
 Update the stubsets created with parse_stub_sets with the reference pose information. More...
 
static basic::Tracer TR ("protocols.protein_interface_design.movers.PrepackMover")
 
static basic::Tracer TR ("protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover", t_info)
 
void part_complex (core::pose::PoseOP pose, core::Size const rb_jump)
 
void unfold_complex (core::pose::PoseOP pose)
 
std::string subtag_for_msd (std::string const &name)
 
static basic::Tracer TR ("protocols.protein_interface_design.movers.RandomMutation")
 
static basic::Tracer TR ("protocols.protein_interface_design.movers.RepackMinimize")
 
static basic::Tracer TR ("protocols.protein_interface_design.movers.SaveAndRetrieveSidechains")
 
static basic::Tracer TR ("protocols.protein_interface_design.movers.SecretionOptimizationMover")
 
static basic::Tracer TR ("protocols.protein_interface_design.movers.SetAtomTree")
 
std::string connect_from ("")
 
std::string connect_to ("")
 
static basic::Tracer TR ("protocols.protein_interface_design.movers.SetTemperatureFactor")
 
static basic::Tracer tr ("protocols.protein_interface_design.movers.SetupHotspotConstraintsLoopsMover")
 
std::string subtag_for_SetupHotspotConstraintsLoopsMover (std::string const &foo)
 
static basic::Tracer TR ("protocols.protein_interface_design.movers.SetupHotspotConstraintsMover")
 
std::string subtag_for_SetupHotspotConstraintsMover (std::string const &foo)
 
static basic::Tracer TR ("protocols.protein_interface_design.movers.ShoveResidueMover")
 
static basic::Tracer TR ("protocols.protein_interface_design.movers.SpinMover")
 
static basic::Tracer TR ("protocols.protein_interface_design.movers.TaskAwareCsts")
 
static basic::Tracer TR ("protocols.protein_interface_design.movers.TopologyBrokerMover")
 
static basic::Tracer TR ("protocols.protein_interface_design.movers.TryRotamers")
 
static basic::Tracer TR ("protocols.protein_interface_design.movers.VLB")
 
std::string mangled_name_for_VLB (std::string const &foo)
 

Variables

core::Size anchor_num = 0
 

Typedef Documentation

◆ BuildAlaPoseCOP

typedef utility::pointer::shared_ptr< BuildAlaPose const > protocols::protein_interface_design::movers::BuildAlaPoseCOP

◆ BuildAlaPoseOP

typedef utility::pointer::shared_ptr< BuildAlaPose > protocols::protein_interface_design::movers::BuildAlaPoseOP

◆ CoordinateConstraintStackOP

typedef utility::pointer::shared_ptr< CoordinateConstraintStack > protocols::protein_interface_design::movers::CoordinateConstraintStackOP

◆ DockWithHotspotMoverCOP

typedef utility::pointer::shared_ptr< DockWithHotspotMover const > protocols::protein_interface_design::movers::DockWithHotspotMoverCOP

◆ DockWithHotspotMoverOP

typedef utility::pointer::shared_ptr< DockWithHotspotMover > protocols::protein_interface_design::movers::DockWithHotspotMoverOP

◆ LoopLengthChangeCOP

typedef utility::pointer::shared_ptr< LoopLengthChange const > protocols::protein_interface_design::movers::LoopLengthChangeCOP

◆ LoopLengthChangeOP

typedef utility::pointer::shared_ptr< LoopLengthChange > protocols::protein_interface_design::movers::LoopLengthChangeOP

◆ LoopMoverFromCommandLineCOP

typedef utility::pointer::shared_ptr< LoopMoverFromCommandLine const > protocols::protein_interface_design::movers::LoopMoverFromCommandLineCOP

◆ LoopMoverFromCommandLineOP

typedef utility::pointer::shared_ptr< LoopMoverFromCommandLine > protocols::protein_interface_design::movers::LoopMoverFromCommandLineOP

◆ LoopRemodelCOP

typedef utility::pointer::shared_ptr< LoopRemodel const > protocols::protein_interface_design::movers::LoopRemodelCOP

◆ LoopRemodelOP

typedef utility::pointer::shared_ptr< LoopRemodel > protocols::protein_interface_design::movers::LoopRemodelOP

◆ PatchdockTransformCOP

typedef utility::pointer::shared_ptr< PatchdockTransform const > protocols::protein_interface_design::movers::PatchdockTransformCOP

◆ PatchdockTransformOP

typedef utility::pointer::shared_ptr< PatchdockTransform > protocols::protein_interface_design::movers::PatchdockTransformOP

◆ PlacementAuctionMoverCOP

typedef utility::pointer::shared_ptr< PlacementAuctionMover const > protocols::protein_interface_design::movers::PlacementAuctionMoverCOP

◆ PlacementAuctionMoverOP

typedef utility::pointer::shared_ptr< PlacementAuctionMover > protocols::protein_interface_design::movers::PlacementAuctionMoverOP

◆ PlacementMinimizationMoverCOP

typedef utility::pointer::shared_ptr< PlacementMinimizationMover const > protocols::protein_interface_design::movers::PlacementMinimizationMoverCOP

◆ PlacementMinimizationMoverOP

typedef utility::pointer::shared_ptr< PlacementMinimizationMover > protocols::protein_interface_design::movers::PlacementMinimizationMoverOP

◆ PlaceOnLoopCOP

typedef utility::pointer::shared_ptr< PlaceOnLoop const > protocols::protein_interface_design::movers::PlaceOnLoopCOP

◆ PlaceOnLoopOP

typedef utility::pointer::shared_ptr< PlaceOnLoop > protocols::protein_interface_design::movers::PlaceOnLoopOP

◆ PlaceStubMoverCOP

typedef utility::pointer::shared_ptr< PlaceStubMover const > protocols::protein_interface_design::movers::PlaceStubMoverCOP

◆ PlaceStubMoverOP

typedef utility::pointer::shared_ptr< PlaceStubMover > protocols::protein_interface_design::movers::PlaceStubMoverOP

◆ Pose

using protocols::protein_interface_design::movers::Pose = typedef core::pose::Pose

◆ RandomMutationCOP

typedef utility::pointer::shared_ptr< RandomMutation const > protocols::protein_interface_design::movers::RandomMutationCOP

◆ RandomMutationOP

typedef utility::pointer::shared_ptr< RandomMutation > protocols::protein_interface_design::movers::RandomMutationOP

◆ Real

using protocols::protein_interface_design::movers::Real = typedef core::Real

◆ SaveAndRetrieveSidechainsCOP

typedef utility::pointer::shared_ptr< SaveAndRetrieveSidechains const > protocols::protein_interface_design::movers::SaveAndRetrieveSidechainsCOP

◆ SaveAndRetrieveSidechainsOP

typedef utility::pointer::shared_ptr< SaveAndRetrieveSidechains > protocols::protein_interface_design::movers::SaveAndRetrieveSidechainsOP

◆ SecretionOptimizationMoverCOP

typedef utility::pointer::shared_ptr< SecretionOptimizationMover const > protocols::protein_interface_design::movers::SecretionOptimizationMoverCOP

◆ SecretionOptimizationMoverOP

typedef utility::pointer::shared_ptr< SecretionOptimizationMover > protocols::protein_interface_design::movers::SecretionOptimizationMoverOP

◆ SetTemperatureFactorCOP

typedef utility::pointer::shared_ptr< SetTemperatureFactor const > protocols::protein_interface_design::movers::SetTemperatureFactorCOP

◆ SetTemperatureFactorOP

typedef utility::pointer::shared_ptr< SetTemperatureFactor > protocols::protein_interface_design::movers::SetTemperatureFactorOP

◆ SetupHotspotConstraintsLoopsMoverCOP

typedef utility::pointer::shared_ptr< SetupHotspotConstraintsLoopsMover const > protocols::protein_interface_design::movers::SetupHotspotConstraintsLoopsMoverCOP

◆ SetupHotspotConstraintsLoopsMoverOP

typedef utility::pointer::shared_ptr< SetupHotspotConstraintsLoopsMover > protocols::protein_interface_design::movers::SetupHotspotConstraintsLoopsMoverOP

◆ SetupHotspotConstraintsMoverCOP

typedef utility::pointer::shared_ptr< SetupHotspotConstraintsMover const > protocols::protein_interface_design::movers::SetupHotspotConstraintsMoverCOP

◆ SetupHotspotConstraintsMoverOP

typedef utility::pointer::shared_ptr< SetupHotspotConstraintsMover > protocols::protein_interface_design::movers::SetupHotspotConstraintsMoverOP

◆ SubroutineMoverCOP

typedef utility::pointer::shared_ptr< SubroutineMover const > protocols::protein_interface_design::movers::SubroutineMoverCOP

◆ SubroutineMoverOP

typedef utility::pointer::shared_ptr< SubroutineMover > protocols::protein_interface_design::movers::SubroutineMoverOP

◆ TaskAwareCstsCOP

typedef utility::pointer::shared_ptr< TaskAwareCsts const > protocols::protein_interface_design::movers::TaskAwareCstsCOP

◆ TaskAwareCstsOP

typedef utility::pointer::shared_ptr< TaskAwareCsts > protocols::protein_interface_design::movers::TaskAwareCstsOP

◆ TopologyBrokerMoverCOP

typedef utility::pointer::shared_ptr< TopologyBrokerMover const > protocols::protein_interface_design::movers::TopologyBrokerMoverCOP

◆ TopologyBrokerMoverOP

typedef utility::pointer::shared_ptr< TopologyBrokerMover > protocols::protein_interface_design::movers::TopologyBrokerMoverOP

Enumeration Type Documentation

◆ VLBInstructionType

enum protocols::protein_interface_design::movers::VLBInstructionType
strong
Enumerator
Bridge 
ConnectRight 
GrowLeft 
GrowRight 
SegmentInsert 
SegmentRebuild 
SegmentSwap 

Function Documentation

◆ add_coordinate_constraints() [1/2]

core::scoring::constraints::ConstraintCOPs protocols::protein_interface_design::movers::add_coordinate_constraints ( pose::Pose &  pose,
core::conformation::Residue const &  source,
core::Size const  host_chain,
core::Size const  resnum,
core::Real const  coord_sdev,
core::scoring::func::HarmonicFuncOP &  coord_cst_func 
)

References core::conformation::Residue::aa(), core::chemical::aa_gly, core::conformation::Residue::atom_index(), find_nearest_residue_to_coord(), nearest_atom_for_constraint(), core::pose::Pose::residue(), core::scoring::TR(), and core::conformation::Residue::xyz().

◆ add_coordinate_constraints() [2/2]

core::scoring::constraints::ConstraintCOPs protocols::protein_interface_design::movers::add_coordinate_constraints ( pose::Pose &  pose,
core::Size const  resnum,
core::conformation::Residue const &  rsd_i,
core::scoring::func::HarmonicFuncOP  coord_cst_func,
core::id::AtomID const &  anchor_atom 
)

References core::conformation::Residue::aa(), protocols::cluster::calibur::aa, core::chemical::aa_ala, core::chemical::aa_arg, core::chemical::aa_asn, core::chemical::aa_asp, core::chemical::aa_cys, core::chemical::aa_gln, core::chemical::aa_glu, core::chemical::aa_his, core::chemical::aa_ile, core::chemical::aa_leu, core::chemical::aa_lys, core::chemical::aa_met, core::chemical::aa_phe, core::chemical::aa_ser, core::chemical::aa_thr, core::chemical::aa_trp, core::chemical::aa_tyr, core::chemical::aa_val, core::pose::Pose::add_constraints(), core::chemical::ResidueType::atom_index(), core::conformation::Residue::name(), core::pose::Pose::residue(), core::scoring::TR(), core::conformation::Residue::type(), and core::conformation::Residue::xyz().

Referenced by protocols::protein_interface_design::movers::PlaceStubMover::add_coordinate_constraints_for_res_stub(), and protocols::protein_interface_design::movers::AddSidechainConstraintsToHotspots::apply().

◆ add_subelement_for_parse_stub_sets()

void protocols::protein_interface_design::movers::add_subelement_for_parse_stub_sets ( utility::tag::XMLSchemaSimpleSubelementList &  ssl,
utility::tag::XMLSchemaDefinition &  xsd 
)

References legolas_what_do_your_elf_eyes_see().

Referenced by protocols::protein_interface_design::filters::StubScoreFilter::provide_xml_schema(), protocols::protein_interface_design::movers::PlacementAuctionMover::provide_xml_schema(), and protocols::protein_interface_design::movers::PlacementMinimizationMover::provide_xml_schema().

◆ connect_from()

std::string protocols::protein_interface_design::movers::connect_from ( ""  )

Referenced by protocols::protein_interface_design::movers::SetAtomTree::apply(), and protocols::protein_interface_design::movers::SetAtomTree::create_atom_tree().

◆ connect_to()

std::string protocols::protein_interface_design::movers::connect_to ( ""  )

Referenced by protocols::protein_interface_design::movers::SetAtomTree::apply(), protocols::protein_interface_design::movers::SetAtomTree::create_atom_tree(), protocols::protein_interface_design::make_hotspot_foldtree(), and protocols::protein_interface_design::optimal_connection_point().

◆ copy_hotspot_to_pose()

void protocols::protein_interface_design::movers::copy_hotspot_to_pose ( core::pose::Pose const &  src,
core::pose::Pose &  dest,
core::Size const  src_resi,
core::chemical::ResidueType const &  restype,
core::Size const  jump 
)

Utility function to deal with all of the ugliness of copying a single residue from one pose to another while conserving the jump

References core::kinematics::FoldTree::add_edge(), core::pose::add_lower_terminus_type_to_pose_residue(), core::pose::add_upper_terminus_type_to_pose_residue(), core::pose::add_variant_type_to_pose_residue(), core::pose::Pose::append_residue_by_jump(), core::kinematics::FoldTree::clear(), core::pose::Pose::conformation(), core::conformation::ResidueFactory::create_residue(), core::pose::Pose::fold_tree(), core::pose::Pose::jump(), core::pose::Pose::set_jump(), core::chemical::SHOVE_BB, core::pose::Pose::size(), core::conformation::Conformation::update_polymeric_connection(), and core::pose::Pose::update_residue_neighbors().

Referenced by protocols::protein_interface_design::movers::MapHotspot::GenerateMap().

◆ dock_with_hotspot_subsubtag_naming_func()

std::string protocols::protein_interface_design::movers::dock_with_hotspot_subsubtag_naming_func ( std::string const &  foo)

Referenced by protocols::protein_interface_design::movers::DockWithHotspotMover::provide_xml_schema().

◆ dock_with_hotspot_subtag_naming_func()

std::string protocols::protein_interface_design::movers::dock_with_hotspot_subtag_naming_func ( std::string const &  foo)

Referenced by protocols::protein_interface_design::movers::DockWithHotspotMover::provide_xml_schema().

◆ favor_nonnative_residue_tracer()

static basic::Tracer protocols::protein_interface_design::movers::favor_nonnative_residue_tracer ( "protocols.protein_interface_design.movers.FavorNonNativeResiduePreCycle"  )
static

Referenced by protocols::protein_interface_design::movers::FavorNonNativeResiduePreCycle::parse_my_tag().

◆ finalize_stub_set()

void protocols::protein_interface_design::movers::finalize_stub_set ( protocols::hotspot_hashing::HotspotStubSetOP  stubset,
core::pose::Pose const &  pose,
core::Size const  host_chain 
)

Update a stubset with the reference pose information.

References core::chemical::aa_ala, core::chemical::aa_gly, core::chemical::aa_pro, core::pack::task::TaskFactory::create_packer_task(), core::scoring::get_score_function(), core::conformation::Residue::is_protein(), core::chemical::num_canonical_aas, core::pack::pack_rotamers(), core::pack::task::parse_resfile(), core::pose::Pose::residue(), and core::pose::Pose::size().

Referenced by protocols::protein_interface_design::movers::PlaceStubMover::apply(), and finalize_stub_sets().

◆ finalize_stub_sets()

void protocols::protein_interface_design::movers::finalize_stub_sets ( utility::vector1< std::pair< protocols::hotspot_hashing::HotspotStubSetOP, std::pair< protocols::hotspot_hashing::HotspotStubOP, core::Size > > > &  stub_sets,
core::pose::Pose const &  pose,
core::Size const  host_chain 
)

Update the stubsets created with parse_stub_sets with the reference pose information.

References finalize_stub_set().

Referenced by protocols::protein_interface_design::movers::PlacementAuctionMover::apply(), protocols::protein_interface_design::movers::PlacementMinimizationMover::apply(), and protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::apply().

◆ find_nearest_residue_to_coord()

core::Size protocols::protein_interface_design::movers::find_nearest_residue_to_coord ( pose::Pose const &  pose,
numeric::xyzVector< core::Real > const &  coord,
core::Size const  host_chain 
)

find the nearest residue to a coordinate

utility function for finding the nearest residue on a chain to a given coordinate. Useful in finding the nearest residue on the host chain to a coordinate constraint

References core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), core::kinematics::distance(), core::sequence::end, core::conformation::Residue::nbr_atom(), core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by add_coordinate_constraints(), and protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover::make_disjointed_foldtree().

◆ generate_taskfactory_and_add_task_awareness()

void protocols::protein_interface_design::movers::generate_taskfactory_and_add_task_awareness ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data,
core::pack::task::TaskFactoryOP &  task_factory 
)

common function to both grafting protocols for parsing out the movers that need to be task aware. Returns an empty task factory. If the tag is labeled TaskAware, all of the DesignRepackMovers within it will be assigned this task factory. The preceding comment about TaskAware is probaby wrong - SML @ XSDXRW Nov 2016

References protocols::rosetta_scripts::parse_mover_or_null(), and core::scoring::TR().

Referenced by protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::parse_my_tag(), and protocols::protein_interface_design::movers::PlaceStubMover::parse_my_tag().

◆ jumpfunc()

std::string protocols::protein_interface_design::movers::jumpfunc ( std::string const &  manglee)

Referenced by protocols::protein_interface_design::movers::MapHotspot::provide_xml_schema().

◆ jumpsfunc()

std::string protocols::protein_interface_design::movers::jumpsfunc ( std::string const &  manglee)

Referenced by protocols::protein_interface_design::movers::MapHotspot::provide_xml_schema().

◆ legolas_what_do_your_elf_eyes_see()

std::string protocols::protein_interface_design::movers::legolas_what_do_your_elf_eyes_see ( std::string const &  foo)

Referenced by add_subelement_for_parse_stub_sets().

◆ make_stub_scorefxn()

core::scoring::ScoreFunctionOP protocols::protein_interface_design::movers::make_stub_scorefxn ( )

utility function for setting up a scorefxn dominated by the stub constraints.

References core::scoring::backbone_stub_constraint, core::scoring::coordinate_constraint, core::scoring::fa_dun, and core::scoring::fa_rep.

Referenced by protocols::protein_interface_design::movers::PlacementMinimizationMover::apply(), protocols::protein_interface_design::filters::StubScoreFilter::compute(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::minimize_all(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::minimize_no_bb(), and protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::pair_sets_with_positions().

◆ mangled_name_for_VLB()

std::string protocols::protein_interface_design::movers::mangled_name_for_VLB ( std::string const &  foo)

Referenced by protocols::protein_interface_design::movers::VLB::provide_xml_schema().

◆ nearest_atom_for_constraint()

std::string protocols::protein_interface_design::movers::nearest_atom_for_constraint ( core::conformation::Residue const &  residue)

References core::conformation::Residue::aa(), protocols::cluster::calibur::aa, core::chemical::aa_ala, core::chemical::aa_arg, core::chemical::aa_asn, core::chemical::aa_asp, core::chemical::aa_cys, core::chemical::aa_gln, core::chemical::aa_glu, core::chemical::aa_gly, core::chemical::aa_his, core::chemical::aa_ile, core::chemical::aa_leu, core::chemical::aa_lys, core::chemical::aa_met, core::chemical::aa_phe, core::chemical::aa_pro, core::chemical::aa_ser, core::chemical::aa_thr, core::chemical::aa_trp, core::chemical::aa_tyr, and core::chemical::aa_val.

Referenced by add_coordinate_constraints(), and protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover::make_disjointed_foldtree().

◆ parse_stub_sets()

utility::vector1< std::pair< protocols::hotspot_hashing::HotspotStubSetOP, std::pair< protocols::hotspot_hashing::HotspotStubOP, core::Size > > > protocols::protein_interface_design::movers::parse_stub_sets ( utility::tag::TagCOP  tag,
basic::datacache::DataMap  data 
)

a utility function for parsing stubset information from a tag You will need to call finalize_stub_sets() with the reference pose prior to using them.

References core::scoring::TR().

Referenced by protocols::protein_interface_design::filters::StubScoreFilter::parse_my_tag(), protocols::protein_interface_design::movers::PlacementAuctionMover::parse_my_tag(), and protocols::protein_interface_design::movers::PlacementMinimizationMover::parse_my_tag().

◆ part_complex()

void protocols::protein_interface_design::movers::part_complex ( core::pose::PoseOP  pose,
core::Size const  rb_jump 
)

References protocols::toolbox::rigid_body::translate().

Referenced by protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::add_states(), and protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::restrict_sequence_profile().

◆ PlaceSimultaneously_DesignMovers_subelement_mangler()

std::string protocols::protein_interface_design::movers::PlaceSimultaneously_DesignMovers_subelement_mangler ( std::string const &  element)

Referenced by protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::provide_xml_schema().

◆ PlaceSimultaneously_NotifyMovers_subelement_mangler()

std::string protocols::protein_interface_design::movers::PlaceSimultaneously_NotifyMovers_subelement_mangler ( std::string const &  element)

Referenced by protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::provide_xml_schema().

◆ PlaceSimultaneously_StubMinimize_subelement_mangler()

std::string protocols::protein_interface_design::movers::PlaceSimultaneously_StubMinimize_subelement_mangler ( std::string const &  element)

Referenced by protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::provide_xml_schema().

◆ PlaceSimultaneously_StubSets_subelement_mangler()

std::string protocols::protein_interface_design::movers::PlaceSimultaneously_StubSets_subelement_mangler ( std::string const &  element)

Referenced by protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::provide_xml_schema().

◆ PlaceSimultaneously_subelement_mangler()

std::string protocols::protein_interface_design::movers::PlaceSimultaneously_subelement_mangler ( std::string const &  element)

Referenced by protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::provide_xml_schema().

◆ PlaceStub_DesignMovers_subelement_mangler()

std::string protocols::protein_interface_design::movers::PlaceStub_DesignMovers_subelement_mangler ( std::string const &  element)

Referenced by protocols::protein_interface_design::movers::PlaceStubMover::provide_xml_schema().

◆ PlaceStub_NotifyMovers_subelement_mangler()

std::string protocols::protein_interface_design::movers::PlaceStub_NotifyMovers_subelement_mangler ( std::string const &  element)

Referenced by protocols::protein_interface_design::movers::PlaceStubMover::provide_xml_schema().

◆ PlaceStub_StubMinimize_subelement_mangler()

std::string protocols::protein_interface_design::movers::PlaceStub_StubMinimize_subelement_mangler ( std::string const &  element)

Referenced by protocols::protein_interface_design::movers::PlaceStubMover::provide_xml_schema().

◆ PlaceStub_subelement_mangler()

std::string protocols::protein_interface_design::movers::PlaceStub_subelement_mangler ( std::string const &  element)

Referenced by protocols::protein_interface_design::movers::PlaceStubMover::provide_xml_schema().

◆ subtag_for_backrubdd()

std::string protocols::protein_interface_design::movers::subtag_for_backrubdd ( std::string const &  subtag)

Referenced by protocols::protein_interface_design::movers::BackrubDDMover::provide_xml_schema().

◆ subtag_for_hotspothasher()

std::string protocols::protein_interface_design::movers::subtag_for_hotspothasher ( std::string const &  tag)

Referenced by protocols::protein_interface_design::movers::HotspotHasherMover::provide_xml_schema().

◆ subtag_for_msd()

std::string protocols::protein_interface_design::movers::subtag_for_msd ( std::string const &  name)

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

Referenced by protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::provide_xml_schema().

◆ subtag_for_SetupHotspotConstraintsLoopsMover()

std::string protocols::protein_interface_design::movers::subtag_for_SetupHotspotConstraintsLoopsMover ( std::string const &  foo)

Referenced by protocols::protein_interface_design::movers::SetupHotspotConstraintsLoopsMover::provide_xml_schema().

◆ subtag_for_SetupHotspotConstraintsMover()

std::string protocols::protein_interface_design::movers::subtag_for_SetupHotspotConstraintsMover ( std::string const &  foo)

Referenced by protocols::protein_interface_design::movers::SetupHotspotConstraintsMover::provide_xml_schema().

◆ test_res_res_aln()

bool protocols::protein_interface_design::movers::test_res_res_aln ( core::conformation::Residue const &  res1,
core::conformation::Residue const &  res2,
core::Real &  C_N_angle,
core::Real &  CB_CA_angle 
)

a utility function that tests whether two residues are aligned properly. Useful for testing whether a single stub should be placed at a given scaffold position

References core::conformation::Residue::xyz().

Referenced by protocols::protein_interface_design::movers::PlaceStubMover::apply(), and protocols::protein_interface_design::movers::PlaceStubMover::StubMinimize().

◆ TR() [1/36]

static basic::Tracer protocols::protein_interface_design::movers::TR ( "protocols.moves.LoopRemodelFromCommandLine"  )
static

◆ TR() [2/36]

static basic::Tracer protocols::protein_interface_design::movers::TR ( "protocols.protein_interface_design.BackrubDDMover"  )
static

◆ TR() [3/36]

static basic::Tracer protocols::protein_interface_design::movers::TR ( "protocols.protein_interface_design.movers.AddChainBreak"  )
static

Referenced by protocols::protein_interface_design::movers::AddChainBreak::apply(), protocols::protein_interface_design::movers::AddSidechainConstraintsToHotspots::apply(), protocols::protein_interface_design::movers::BestHotspotCstMover::apply(), protocols::protein_interface_design::movers::DisulfideMover::apply(), protocols::protein_interface_design::movers::DockWithHotspotMover::apply(), protocols::protein_interface_design::movers::HotspotHasherMover::apply(), protocols::protein_interface_design::movers::InterfaceRecapitulationMover::apply(), protocols::protein_interface_design::movers::LoopFinder::apply(), protocols::protein_interface_design::movers::LoopMoverFromCommandLine::apply(), protocols::protein_interface_design::movers::LoopOver::apply(), protocols::protein_interface_design::movers::LoopRemodel::apply(), protocols::protein_interface_design::movers::MapHotspot::apply(), protocols::protein_interface_design::movers::PlacementAuctionMover::apply(), protocols::protein_interface_design::movers::PlaceStubMover::apply(), protocols::protein_interface_design::movers::PrepackMover::apply(), protocols::protein_interface_design::movers::SetAtomTree::apply(), protocols::protein_interface_design::movers::SpinMover::apply(), protocols::protein_interface_design::movers::TryRotamers::apply(), protocols::protein_interface_design::movers::VLB::apply(), protocols::protein_interface_design::movers::SecretionOptimizationMover::apply(), protocols::protein_interface_design::movers::BackrubDDMover::apply(), protocols::protein_interface_design::movers::DesignMinimizeHbonds::apply(), protocols::protein_interface_design::movers::LoopLengthChange::apply(), protocols::protein_interface_design::movers::PatchdockTransform::apply(), protocols::protein_interface_design::movers::RandomMutation::apply(), protocols::protein_interface_design::movers::SaveAndRetrieveSidechains::apply(), protocols::protein_interface_design::movers::TaskAwareCsts::apply(), protocols::protein_interface_design::movers::TopologyBrokerMover::apply(), protocols::protein_interface_design::movers::SetAtomTree::create_atom_tree(), protocols::protein_interface_design::movers::MapHotspot::create_rotamer_set(), protocols::protein_interface_design::movers::PlaceStubMover::cst_cleanup(), protocols::protein_interface_design::movers::PlaceStubMover::disallowed_host_pos(), protocols::protein_interface_design::movers::DisulfideMover::disulfide_list(), protocols::protein_interface_design::movers::PlaceStubMover::final_cleanup(), protocols::protein_interface_design::movers::MapHotspot::GenerateMap(), protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::initialize(), protocols::protein_interface_design::movers::PlaceOnLoop::loop_length(), protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover::make_disjointed_foldtree(), protocols::protein_interface_design::movers::PlaceOnLoop::minimize_toward_stub(), protocols::protein_interface_design::movers::MapHotspot::MinimizeHotspots(), protocols::protein_interface_design::movers::PrepackMover::mm(), protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::output_alternative_states(), protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::output_results(), protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::parse_my_tag(), protocols::protein_interface_design::movers::AddChainBreak::parse_my_tag(), protocols::protein_interface_design::movers::BackrubDDMover::parse_my_tag(), protocols::protein_interface_design::movers::BestHotspotCstMover::parse_my_tag(), protocols::protein_interface_design::movers::BuildAlaPose::parse_my_tag(), protocols::protein_interface_design::movers::DesignMinimizeHbonds::parse_my_tag(), protocols::protein_interface_design::movers::DockAndRetrieveSidechains::parse_my_tag(), protocols::protein_interface_design::movers::DockWithHotspotMover::parse_my_tag(), protocols::protein_interface_design::movers::FavorNativeResiduePreCycle::parse_my_tag(), protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover::parse_my_tag(), protocols::protein_interface_design::movers::HotspotHasherMover::parse_my_tag(), protocols::protein_interface_design::movers::LoopLengthChange::parse_my_tag(), protocols::protein_interface_design::movers::LoopOver::parse_my_tag(), protocols::protein_interface_design::movers::MapHotspot::parse_my_tag(), protocols::protein_interface_design::movers::PatchdockTransform::parse_my_tag(), protocols::protein_interface_design::movers::PlacementAuctionMover::parse_my_tag(), protocols::protein_interface_design::movers::PlaceOnLoop::parse_my_tag(), protocols::protein_interface_design::movers::PlaceStubMover::parse_my_tag(), protocols::protein_interface_design::movers::PrepackMover::parse_my_tag(), protocols::protein_interface_design::movers::RepackMinimize::parse_my_tag(), protocols::protein_interface_design::movers::SetAtomTree::parse_my_tag(), protocols::protein_interface_design::movers::SetupHotspotConstraintsMover::parse_my_tag(), protocols::protein_interface_design::movers::SpinMover::parse_my_tag(), protocols::protein_interface_design::movers::TaskAwareCsts::parse_my_tag(), protocols::protein_interface_design::movers::TopologyBrokerMover::parse_my_tag(), protocols::protein_interface_design::movers::TryRotamers::parse_my_tag(), protocols::protein_interface_design::movers::LoopFinder::parse_my_tag(), protocols::protein_interface_design::movers::LoopRemodel::parse_my_tag(), protocols::protein_interface_design::movers::VLB::parse_my_tag(), protocols::protein_interface_design::movers::LoopRemodel::pick_loop_frags(), protocols::protein_interface_design::movers::SecretionOptimizationMover::report_test(), protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::restrict_sequence_profile(), protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::run(), protocols::protein_interface_design::movers::PlaceStubMover::SelectStubIteratively(), protocols::protein_interface_design::movers::SetAtomTree::set_ab_fold_tree(), protocols::protein_interface_design::movers::TryRotamers::setup_rotamer_set(), protocols::protein_interface_design::movers::PlaceStubMover::stub_based_atom_tree(), and protocols::protein_interface_design::movers::PlaceStubMover::StubMinimize().

◆ TR() [4/36]

static basic::Tracer protocols::protein_interface_design::movers::TR ( "protocols.protein_interface_design.movers.AddSidechainConstraintsToHotspots"  )
static

◆ TR() [5/36]

static basic::Tracer protocols::protein_interface_design::movers::TR ( "protocols.protein_interface_design.movers.BestHotspotCstMover"  )
static

◆ TR() [6/36]

static basic::Tracer protocols::protein_interface_design::movers::TR ( "protocols.protein_interface_design.movers.BuildAlaPose"  )
static

◆ TR() [7/36]

static basic::Tracer protocols::protein_interface_design::movers::TR ( "protocols.protein_interface_design.movers.DesignMinimizeHbonds"  )
static

◆ TR() [8/36]

static basic::Tracer protocols::protein_interface_design::movers::TR ( "protocols.protein_interface_design.movers.DisulfideMover"  )
static

◆ TR() [9/36]

static basic::Tracer protocols::protein_interface_design::movers::TR ( "protocols.protein_interface_design.movers.DockAndRetrieveSidechains"  )
static

◆ TR() [10/36]

static basic::Tracer protocols::protein_interface_design::movers::TR ( "protocols.protein_interface_design.movers.DockWithHotspotMover"  )
static

◆ TR() [11/36]

static basic::Tracer protocols::protein_interface_design::movers::TR ( "protocols.protein_interface_design.movers.FavorNativeResiduePreCycle"  )
static

◆ TR() [12/36]

static basic::Tracer protocols::protein_interface_design::movers::TR ( "protocols.protein_interface_design.movers.HotspotDisjointedFoldTreeMover"  )
static

◆ TR() [13/36]

static basic::Tracer protocols::protein_interface_design::movers::TR ( "protocols.protein_interface_design.movers.HotspotHasherMover"  )
static

◆ TR() [14/36]

static basic::Tracer protocols::protein_interface_design::movers::TR ( "protocols.protein_interface_design.movers.LoopFinder"  )
static

◆ TR() [15/36]

static basic::Tracer protocols::protein_interface_design::movers::TR ( "protocols.protein_interface_design.movers.LoopLengthChange"  )
static

◆ TR() [16/36]

static basic::Tracer protocols::protein_interface_design::movers::TR ( "protocols.protein_interface_design.movers.LoopOver"  )
static

◆ TR() [17/36]

static basic::Tracer protocols::protein_interface_design::movers::TR ( "protocols.protein_interface_design.movers.LoopRemodel"  )
static

◆ TR() [18/36]

static basic::Tracer protocols::protein_interface_design::movers::TR ( "protocols.protein_interface_design.movers.MapHotspot"  )
static

◆ TR() [19/36]

static basic::Tracer protocols::protein_interface_design::movers::TR ( "protocols.protein_interface_design.movers.PatchdockTransform"  )
static

◆ TR() [20/36]

static basic::Tracer protocols::protein_interface_design::movers::TR ( "protocols.protein_interface_design.movers.PeptideStapleDesignMover"  )
static

◆ TR() [21/36]

static basic::Tracer protocols::protein_interface_design::movers::TR ( "protocols.protein_interface_design.movers.PlaceOnLoop"  )
static

◆ TR() [22/36]

static basic::Tracer protocols::protein_interface_design::movers::TR ( "protocols.protein_interface_design.movers.PrepackMover"  )
static

◆ TR() [23/36]

static basic::Tracer protocols::protein_interface_design::movers::TR ( "protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover"  ,
t_info   
)
static

◆ TR() [24/36]

static basic::Tracer protocols::protein_interface_design::movers::TR ( "protocols.protein_interface_design.movers.RandomMutation"  )
static

◆ TR() [25/36]

static basic::Tracer protocols::protein_interface_design::movers::TR ( "protocols.protein_interface_design.movers.RepackMinimize"  )
static

◆ TR() [26/36]

static basic::Tracer protocols::protein_interface_design::movers::TR ( "protocols.protein_interface_design.movers.SaveAndRetrieveSidechains"  )
static

◆ TR() [27/36]

static basic::Tracer protocols::protein_interface_design::movers::TR ( "protocols.protein_interface_design.movers.SecretionOptimizationMover"  )
static

◆ TR() [28/36]

static basic::Tracer protocols::protein_interface_design::movers::TR ( "protocols.protein_interface_design.movers.SetAtomTree"  )
static

◆ TR() [29/36]

static basic::Tracer protocols::protein_interface_design::movers::TR ( "protocols.protein_interface_design.movers.SetTemperatureFactor"  )
static

◆ tr()

static basic::Tracer protocols::protein_interface_design::movers::tr ( "protocols.protein_interface_design.movers.SetupHotspotConstraintsLoopsMover"  )
static

Referenced by protocols::protein_interface_design::movers::SetupHotspotConstraintsLoopsMover::apply(), protocols::protein_interface_design::movers::SetupHotspotConstraintsLoopsMover::generate_csts(), and protocols::protein_interface_design::movers::SetupHotspotConstraintsLoopsMover::parse_my_tag().

◆ TR() [30/36]

static basic::Tracer protocols::protein_interface_design::movers::TR ( "protocols.protein_interface_design.movers.SetupHotspotConstraintsMover"  )
static

◆ TR() [31/36]

static basic::Tracer protocols::protein_interface_design::movers::TR ( "protocols.protein_interface_design.movers.ShoveResidueMover"  )
static

◆ TR() [32/36]

static basic::Tracer protocols::protein_interface_design::movers::TR ( "protocols.protein_interface_design.movers.SpinMover"  )
static

◆ TR() [33/36]

static basic::Tracer protocols::protein_interface_design::movers::TR ( "protocols.protein_interface_design.movers.TaskAwareCsts"  )
static

◆ TR() [34/36]

static basic::Tracer protocols::protein_interface_design::movers::TR ( "protocols.protein_interface_design.movers.TopologyBrokerMover"  )
static

◆ TR() [35/36]

static basic::Tracer protocols::protein_interface_design::movers::TR ( "protocols.protein_interface_design.movers.TryRotamers"  )
static

◆ TR() [36/36]

static basic::Tracer protocols::protein_interface_design::movers::TR ( "protocols.protein_interface_design.movers.VLB"  )
static

◆ TR_cst()

static basic::Tracer protocols::protein_interface_design::movers::TR_cst ( "protocols.protein_interface_design.movers.AddSidechainConstraintsToHotspots_csts"  )
static

Referenced by protocols::protein_interface_design::movers::AddSidechainConstraintsToHotspots::apply().

◆ TR_report()

static basic::Tracer protocols::protein_interface_design::movers::TR_report ( "protocols.moves.LoopRemodelFromCommandLine.REPORT"  )
static

◆ unfold_complex()

void protocols::protein_interface_design::movers::unfold_complex ( core::pose::PoseOP  pose)

References core::sequence::end.

Referenced by protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::add_states().

Variable Documentation

◆ anchor_num

core::Size protocols::protein_interface_design::movers::anchor_num = 0

Referenced by protocols::protein_interface_design::movers::SetAtomTree::apply(), and protocols::protein_interface_design::movers::SetAtomTree::create_atom_tree().

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