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	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	NullDesignMover
	does absolutely nothing. useful as if you want to havea final filter without making a move. this can now be assimilated with NullMover More...

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	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	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	BBDofs

class	ResidueBBDofs
	container for BBDofs, providing a convenient operator [], size, other methods and iterators that allow splice to treat ResidueBBDofs as a simple vector (even though it contains other elements as well) More...

class	Splice
	designs alanine residues in place of the residue identities at the interface. Retains interface glycines and prolines. More...

class	SpliceCreator

class	SpliceSegment
	utility class and functions for dealing with sequence profiles for varying segments in Splice More...

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	TryRotamers

class	TryRotamersCreator

class	VLB
	user interface for YAB's Variable Length Build. More...

class	VLBCreator

Typedefs
typedef core::Real	Real

typedef core::pose::Pose	Pose

typedef utility::pointer::owning_ptr < BuildAlaPose >	BuildAlaPoseOP

typedef utility::pointer::owning_ptr < BuildAlaPose const >	BuildAlaPoseCOP

typedef utility::pointer::owning_ptr < LoopLengthChange >	LoopLengthChangeOP

typedef utility::pointer::owning_ptr < LoopLengthChange const >	LoopLengthChangeCOP

typedef utility::pointer::owning_ptr < LoopMoverFromCommandLine >	LoopMoverFromCommandLineOP

typedef utility::pointer::owning_ptr < LoopMoverFromCommandLine const >	LoopMoverFromCommandLineCOP

typedef utility::pointer::owning_ptr < LoopRemodel >	LoopRemodelOP

typedef utility::pointer::owning_ptr < LoopRemodel const >	LoopRemodelCOP

typedef utility::pointer::owning_ptr < PlacementAuctionMover >	PlacementAuctionMoverOP

typedef utility::pointer::owning_ptr < PlacementAuctionMover const >	PlacementAuctionMoverCOP

typedef utility::pointer::owning_ptr < PlacementMinimizationMover >	PlacementMinimizationMoverOP

typedef utility::pointer::owning_ptr < PlacementMinimizationMover const >	PlacementMinimizationMoverCOP

typedef utility::pointer::owning_ptr < PlaceOnLoop >	PlaceOnLoopOP

typedef utility::pointer::owning_ptr < PlaceOnLoop const >	PlaceOnLoopCOP

typedef utility::pointer::owning_ptr < PlaceStubMover >	PlaceStubMoverOP

typedef utility::pointer::owning_ptr < PlaceStubMover const >	PlaceStubMoverCOP

typedef utility::pointer::owning_ptr < RandomMutation >	RandomMutationOP

typedef utility::pointer::owning_ptr < RandomMutation const >	RandomMutationCOP

typedef utility::pointer::owning_ptr < SaveAndRetrieveSidechains >	SaveAndRetrieveSidechainsOP

typedef utility::pointer::owning_ptr < SaveAndRetrieveSidechains const >	SaveAndRetrieveSidechainsCOP

typedef utility::pointer::owning_ptr < SetTemperatureFactor >	SetTemperatureFactorOP

typedef utility::pointer::owning_ptr < SetTemperatureFactor const >	SetTemperatureFactorCOP

typedef utility::pointer::owning_ptr < SetupHotspotConstraintsLoopsMover >	SetupHotspotConstraintsLoopsMoverOP

typedef utility::pointer::owning_ptr < SetupHotspotConstraintsLoopsMover const >	SetupHotspotConstraintsLoopsMoverCOP

typedef utility::pointer::owning_ptr < SetupHotspotConstraintsMover >	SetupHotspotConstraintsMoverOP

typedef utility::pointer::owning_ptr < SetupHotspotConstraintsMover const >	SetupHotspotConstraintsMoverCOP

typedef utility::pointer::owning_ptr < Splice >	SpliceOP

typedef utility::pointer::owning_ptr < Splice const >	SpliceCOP

typedef utility::pointer::owning_ptr < SpliceSegment >	SpliceSegmentOP

typedef utility::pointer::owning_ptr < SpliceSegment const >	SpliceSegmentCOP

typedef utility::pointer::owning_ptr < SubroutineMover >	SubroutineMoverOP

typedef utility::pointer::owning_ptr < SubroutineMover const >	SubroutineMoverCOP

typedef utility::pointer::owning_ptr < TaskAwareCsts >	TaskAwareCstsOP

typedef utility::pointer::owning_ptr < TaskAwareCsts const >	TaskAwareCstsCOP

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")

static numeric::random::RandomGenerator	RG (1581948)

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.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")

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)

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

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

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::constraints::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::constraints::HarmonicFuncOP &coord_cst_func)

void	generate_taskfactory_and_add_task_awareness (utility::tag::TagPtr const tag, Movers_map const &movers, DataMap &data, core::pack::task::TaskFactoryOP &task_factory)

core::scoring::ScoreFunctionOP	make_stub_scorefxn ()

utility::vector1< std::pair < protocols::hotspot_hashing::HotspotStubSetOP, std::pair < protocols::hotspot_hashing::HotspotStubOP, core::Size > > >	parse_stub_sets (utility::tag::TagPtr const tag, core::pose::Pose const &pose, core::Size const host_chain, protocols::moves::DataMap data)
	a utility function for parsing stubset information from a tag 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)

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

static numeric::random::RandomGenerator	RG (2111918)

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.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")

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

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

static numeric::random::RandomGenerator	RG (12454)

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

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

static basic::Tracer	TR_ccd ("protocols.protein_interface_design.movers.Splice_ccd")

static numeric::random::RandomGenerator	RG (78289)

void	copy_stretch (core::pose::Pose &target, core::pose::Pose const &source, core::Size const from_res, core::Size const to_res)
	copy a stretch of aligned phi-psi dofs from source to target. No repacking no nothing. The core function, copy_segment, copies residues from the source to the target without aligning the residues, thereby delivering all of their dofs More...

utility::vector1< core::Size >	find_residues_on_chain1_outside_interface (core::pose::Pose const &pose)

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

SequenceProfileOP	concatenate_profiles (utility::vector1< SequenceProfileOP > const profiles)
	generate one long sequence profile out of several sequence-profile segments. More...

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

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

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

Variables
core::Size	anchor_num = 0

Typedef Documentation

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Definition at line 96 of file BackrubDDMover.cc.

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

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

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

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

typedef core::Real protocols::protein_interface_design::movers::Real

Definition at line 95 of file BackrubDDMover.cc.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

typedef utility::pointer::owning_ptr< Splice const > protocols::protein_interface_design::movers::SpliceCOP

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

typedef utility::pointer::owning_ptr< Splice > protocols::protein_interface_design::movers::SpliceOP

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

typedef utility::pointer::owning_ptr< SpliceSegment const > protocols::protein_interface_design::movers::SpliceSegmentCOP

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

typedef utility::pointer::owning_ptr< SpliceSegment > protocols::protein_interface_design::movers::SpliceSegmentOP

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

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

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

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

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

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

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

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

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

Function Documentation

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::constraints::HarmonicFuncOP	coord_cst_func,
		core::id::AtomID const	anchor_atom
	)

Definition at line 120 of file PlaceUtils.cc.

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

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::constraints::HarmonicFuncOP &	coord_cst_func
	)

Definition at line 274 of file PlaceUtils.cc.

References core::conformation::Residue::aa(), core::chemical::aa_gly, core::scoring::constraints::add_coordinate_constraints(), 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().

core::sequence::SequenceProfileOP protocols::protein_interface_design::movers::concatenate_profiles ( utility::vector1< SequenceProfileOP > const profiles)

generate one long sequence profile out of several sequence-profile segments.

Definition at line 76 of file SpliceSegment.cc.

Referenced by protocols::protein_interface_design::movers::Splice::generate_sequence_profile().

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().

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().

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

Definition at line 138 of file MapHotspot.cc.

References 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_now(), core::pose::Pose::total_residue(), core::conformation::Conformation::update_polymeric_connection(), and core::pose::Pose::update_residue_neighbors().

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

void protocols::protein_interface_design::movers::copy_stretch	(	core::pose::Pose &	target,
		core::pose::Pose const &	source,
		core::Size const	from_res,
		core::Size const	to_res
	)

copy a stretch of aligned phi-psi dofs from source to target. No repacking no nothing. The core function, copy_segment, copies residues from the source to the target without aligning the residues, thereby delivering all of their dofs

Definition at line 151 of file Splice.cc.

References core::pose::Pose::copy_segment(), protocols::rosetta_scripts::find_nearest_res(), core::pose::Pose::fold_tree(), and protocols::protein_interface_design::movers::LoopLengthChange::loop_start().

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

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

static

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

Definition at line 223 of file PlaceUtils.cc.

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().

utility::vector1< core::Size > protocols::protein_interface_design::movers::find_residues_on_chain1_outside_interface ( core::pose::Pose const & pose)

Definition at line 1122 of file Splice.cc.

References protocols::rosetta_scripts::residue_packer_states().

Referenced by protocols::protein_interface_design::movers::Splice::add_sequence_constraints().

void protocols::protein_interface_design::movers::generate_taskfactory_and_add_task_awareness	(	utility::tag::TagPtr const	tag,
		Movers_map const &	movers,
		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.

Definition at line 297 of file PlaceUtils.cc.

References protocols::moves::DataMap::add(), protocols::moves::DataMap::get(), protocols::moves::DataMap::has(), and core::scoring::TR().

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

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

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

Definition at line 325 of file PlaceUtils.cc.

References core::scoring::backbone_stub_constraint, core::scoring::coordinate_constraint, core::scoring::fa_dun, core::scoring::fa_rep, and core::scoring::ScoreFunction::reset().

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().

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

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::TagPtr const	tag,
		core::pose::Pose const &	pose,
		core::Size const	host_chain,
		protocols::moves::DataMap	data
	)

a utility function for parsing stubset information from a tag

Definition at line 338 of file PlaceUtils.cc.

References core::chemical::aa_ala, core::chemical::aa_gly, core::chemical::aa_pro, core::pack::task::TaskFactory::create_packer_task(), core::scoring::ScoreFunctionFactory::create_score_function(), protocols::moves::DataMap::get(), protocols::moves::DataMap::has(), core::conformation::Residue::is_protein(), core::chemical::num_canonical_aas, core::pack::pack_rotamers(), core::pack::task::parse_resfile(), core::pose::Pose::residue(), core::scoring::SCORE12_PATCH, core::scoring::STANDARD_WTS, core::pose::Pose::total_residue(), and core::scoring::TR().

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

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

Definition at line 148 of file ProteinInterfaceMultiStateDesignMover.cc.

References protocols::swa::translate().

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

static numeric::random::RandomGenerator protocols::protein_interface_design::movers::RG ( 12454 )

static

static numeric::random::RandomGenerator protocols::protein_interface_design::movers::RG ( 2111918 )

static

static numeric::random::RandomGenerator protocols::protein_interface_design::movers::RG ( 78289 )

static

static numeric::random::RandomGenerator protocols::protein_interface_design::movers::RG ( 1581948 )

static

Referenced by protocols::protein_interface_design::movers::SpinMover::apply(), protocols::protein_interface_design::movers::PlaceStubMover::apply(), protocols::protein_interface_design::movers::Splice::find_dbase_entry(), and protocols::protein_interface_design::movers::PlaceOnLoop::loop_length().

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

Definition at line 88 of file PlaceUtils.cc.

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

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

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

static basic::Tracer protocols::protein_interface_design::movers::TR_ccd ( "protocols.protein_interface_design.movers.Splice_ccd" )

static

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

static

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

static

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

Definition at line 156 of file ProteinInterfaceMultiStateDesignMover.cc.

References core::sequence::end.

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

Variable Documentation

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

Definition at line 68 of file SetAtomTree.cc.

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

Classes

Typedefs

Functions

Variables

Typedef Documentation

Function Documentation

Variable Documentation