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	CoordinateConstraintStack
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	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	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
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::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 < 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

Functions
static THREAD_LOCAL basic::Tracer	TR ("protocols.protein_interface_design.movers.AddChainBreak")
static THREAD_LOCAL basic::Tracer	TR ("protocols.protein_interface_design.movers.AddSidechainConstraintsToHotspots")
static THREAD_LOCAL basic::Tracer	TR_cst ("protocols.protein_interface_design.movers.AddSidechainConstraintsToHotspots_csts")
static THREAD_LOCAL basic::Tracer	TR ("protocols.protein_interface_design.BackrubDDMover")
static THREAD_LOCAL basic::Tracer	TR ("protocols.protein_interface_design.movers.BestHotspotCstMover")
static THREAD_LOCAL basic::Tracer	TR ("protocols.protein_interface_design.movers.BuildAlaPose")
static THREAD_LOCAL basic::Tracer	TR ("protocols.protein_interface_design.movers.DesignMinimizeHbonds")
static THREAD_LOCAL basic::Tracer	TR ("protocols.protein_interface_design.movers.DisulfideMover")
static THREAD_LOCAL basic::Tracer	TR ("protocols.protein_interface_design.movers.DockAndRetrieveSidechains")
static THREAD_LOCAL basic::Tracer	TR ("protocols.protein_interface_design.movers.DockWithHotspotMover")
static THREAD_LOCAL basic::Tracer	TR ("protocols.protein_interface_design.movers.FavorNativeResiduePreCycle")
static THREAD_LOCAL basic::Tracer	favor_nonnative_residue_tracer ("protocols.protein_interface_design.movers.FavorNonNativeResiduePreCycle")
static THREAD_LOCAL basic::Tracer	TR ("protocols.protein_interface_design.movers.HotspotDisjointedFoldTreeMover")
static THREAD_LOCAL basic::Tracer	TR ("protocols.protein_interface_design.movers.HotspotHasherMover")
static THREAD_LOCAL basic::Tracer	TR ("protocols.protein_interface_design.movers.LoopFinder")
static THREAD_LOCAL basic::Tracer	TR ("protocols.protein_interface_design.movers.LoopLengthChange")
static THREAD_LOCAL basic::Tracer	TR ("protocols.moves.LoopRemodelFromCommandLine")
static THREAD_LOCAL basic::Tracer	TR_report ("protocols.moves.LoopRemodelFromCommandLine.REPORT")
static THREAD_LOCAL basic::Tracer	TR ("protocols.protein_interface_design.movers.LoopOver")
static THREAD_LOCAL basic::Tracer	TR ("protocols.protein_interface_design.movers.LoopRemodel")
static THREAD_LOCAL 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 THREAD_LOCAL basic::Tracer	TR ("protocols.protein_interface_design.movers.PatchdockTransform")
static THREAD_LOCAL basic::Tracer	TR ("protocols.protein_interface_design.movers.PeptideStapleDesignMover")
static THREAD_LOCAL 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::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, Movers_map const &movers, basic::datacache::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::TagCOP tag, core::pose::Pose const &pose, core::Size const host_chain, basic::datacache::DataMap data)
	a utility function for parsing stubset information from a tag More...
static THREAD_LOCAL basic::Tracer	TR ("protocols.protein_interface_design.movers.PrepackMover")
static THREAD_LOCAL 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 THREAD_LOCAL basic::Tracer	TR ("protocols.protein_interface_design.movers.RandomMutation")
static THREAD_LOCAL basic::Tracer	TR ("protocols.protein_interface_design.movers.RepackMinimize")
static THREAD_LOCAL basic::Tracer	TR ("protocols.protein_interface_design.movers.SaveAndRetrieveSidechains")
static THREAD_LOCAL basic::Tracer	TR ("protocols.protein_interface_design.movers.SetAtomTree")
std::string	connect_from ("")
std::string	connect_to ("")
static THREAD_LOCAL basic::Tracer	TR ("protocols.protein_interface_design.movers.SetTemperatureFactor")
static THREAD_LOCAL basic::Tracer	tr ("protocols.protein_interface_design.movers.SetupHotspotConstraintsLoopsMover")
static THREAD_LOCAL basic::Tracer	TR ("protocols.protein_interface_design.movers.SetupHotspotConstraintsMover")
static THREAD_LOCAL basic::Tracer	TR ("protocols.protein_interface_design.movers.ShoveResidueMover")
static THREAD_LOCAL basic::Tracer	TR ("protocols.protein_interface_design.movers.SpinMover")
static THREAD_LOCAL basic::Tracer	TR ("protocols.protein_interface_design.movers.TaskAwareCsts")
static THREAD_LOCAL basic::Tracer	TR ("protocols.protein_interface_design.movers.TopologyBrokerMover")
static THREAD_LOCAL basic::Tracer	TR ("protocols.protein_interface_design.movers.TryRotamers")
static THREAD_LOCAL basic::Tracer	TR ("protocols.protein_interface_design.movers.VLB")

Variables
core::Size	anchor_num = 0

Typedef Documentation

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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().

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

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(), core::chemical::SHOVE_BB, 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().

static THREAD_LOCAL 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().

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

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().

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

References protocols::environment::find_mover(), 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().

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().

std::string protocols::protein_interface_design::movers::nearest_atom_for_constraint

(

core::conformation::Residue const

residue

)

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

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,
		core::pose::Pose const &	pose,
		core::Size const	host_chain,
		basic::datacache::DataMap	data
	)

a utility function for parsing stubset information from a tag

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(), 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
	)

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().

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().

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

static

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

static

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

static

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

static

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

static

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

static

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

static

Referenced by protocols::protein_interface_design::movers::TaskAwareCsts::apply(), protocols::protein_interface_design::movers::AddSidechainConstraintsToHotspots::apply(), protocols::protein_interface_design::movers::PatchdockTransform::apply(), protocols::protein_interface_design::movers::LoopLengthChange::apply(), protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover::apply(), protocols::protein_interface_design::movers::SetAtomTree::apply(), protocols::protein_interface_design::movers::RandomMutation::apply(), protocols::protein_interface_design::movers::SpinMover::apply(), protocols::protein_interface_design::movers::VLB::apply(), protocols::protein_interface_design::movers::PrepackMover::apply(), protocols::protein_interface_design::movers::HotspotHasherMover::apply(), protocols::protein_interface_design::movers::InterfaceRecapitulationMover::apply(), protocols::protein_interface_design::movers::LoopOver::apply(), protocols::protein_interface_design::movers::BestHotspotCstMover::apply(), protocols::protein_interface_design::movers::BackrubDDMover::apply(), protocols::protein_interface_design::movers::PlacementAuctionMover::apply(), protocols::protein_interface_design::movers::DockWithHotspotMover::apply(), protocols::protein_interface_design::movers::DesignMinimizeHbonds::apply(), protocols::protein_interface_design::movers::SaveAndRetrieveSidechains::apply(), protocols::protein_interface_design::movers::LoopFinder::apply(), protocols::protein_interface_design::movers::DisulfideMover::apply(), protocols::protein_interface_design::movers::LoopMoverFromCommandLine::apply(), protocols::protein_interface_design::movers::LoopRemodel::apply(), protocols::protein_interface_design::movers::TryRotamers::apply(), protocols::protein_interface_design::movers::PlaceStubMover::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::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::ShoveResidueMover::parse_my_tag(), protocols::protein_interface_design::movers::TaskAwareCsts::parse_my_tag(), protocols::protein_interface_design::movers::DockAndRetrieveSidechains::parse_my_tag(), protocols::protein_interface_design::movers::PatchdockTransform::parse_my_tag(), protocols::protein_interface_design::movers::LoopLengthChange::parse_my_tag(), protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover::parse_my_tag(), protocols::protein_interface_design::movers::TopologyBrokerMover::parse_my_tag(), protocols::protein_interface_design::movers::PrepackMover::parse_my_tag(), protocols::protein_interface_design::movers::SpinMover::parse_my_tag(), protocols::protein_interface_design::movers::BuildAlaPose::parse_my_tag(), protocols::protein_interface_design::movers::SetAtomTree::parse_my_tag(), protocols::protein_interface_design::movers::FavorNativeResiduePreCycle::parse_my_tag(), protocols::protein_interface_design::movers::VLB::parse_my_tag(), protocols::protein_interface_design::movers::HotspotHasherMover::parse_my_tag(), protocols::protein_interface_design::movers::PlaceOnLoop::parse_my_tag(), protocols::protein_interface_design::movers::LoopOver::parse_my_tag(), protocols::protein_interface_design::movers::BestHotspotCstMover::parse_my_tag(), protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::parse_my_tag(), protocols::protein_interface_design::movers::MapHotspot::parse_my_tag(), protocols::protein_interface_design::movers::SetupHotspotConstraintsMover::parse_my_tag(), protocols::protein_interface_design::movers::BackrubDDMover::parse_my_tag(), protocols::protein_interface_design::movers::DesignMinimizeHbonds::parse_my_tag(), protocols::protein_interface_design::movers::RepackMinimize::parse_my_tag(), protocols::protein_interface_design::movers::LoopFinder::parse_my_tag(), protocols::protein_interface_design::movers::DockWithHotspotMover::parse_my_tag(), protocols::protein_interface_design::movers::PlacementAuctionMover::parse_my_tag(), protocols::protein_interface_design::movers::DisulfideMover::parse_my_tag(), protocols::protein_interface_design::movers::LoopRemodel::parse_my_tag(), protocols::protein_interface_design::movers::TryRotamers::parse_my_tag(), protocols::protein_interface_design::movers::PlaceStubMover::parse_my_tag(), protocols::protein_interface_design::movers::LoopRemodel::pick_loop_frags(), 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().

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

static THREAD_LOCAL 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().

static THREAD_LOCAL 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().

static THREAD_LOCAL 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

)

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

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