protocols::hotspot_hashing Namespace Reference

Namespaces
	movers

Classes
class	HotspotStub
class	HotspotStubSet
class	VectorPair
class	SearchPattern
class	ConstPattern
class	TestPattern
class	LSMSearchPattern
class	RotationSearchPattern
class	SphericalRotationSearchPattern
class	CartesianSearchPattern
class	PartitionedSearchPattern
class	ComposeSearchPatterns
class	SearchPatternTransform
class	SearchPatternExpansion
class	SearchPatternRotSetOp
class	AddSearchPatternRotSetOp
class	SICPatternAtTransform
class	StubGenerator
class	SurfaceSearchPattern

Typedefs
typedef utility::pointer::shared_ptr< HotspotStub >	HotspotStubOP
typedef utility::pointer::shared_ptr< HotspotStub const >	HotspotStubCOP
typedef utility::pointer::shared_ptr< HotspotStubSet >	HotspotStubSetOP
typedef utility::pointer::shared_ptr< HotspotStubSet const >	HotspotStubSetCOP
typedef utility::pointer::shared_ptr< SearchPattern >	SearchPatternOP
typedef utility::pointer::shared_ptr< SearchPattern const >	SearchPatternCOP
typedef numeric::xyzMatrix< core::Real >	Matrix
typedef numeric::xyzVector< core::Real >	Vector
typedef utility::pointer::shared_ptr< SearchPatternRotSetOp >	SearchPatternRotSetOpOP
typedef utility::pointer::shared_ptr< SearchPatternRotSetOp const >	SearchPatternRotSetOpCOP
typedef utility::pointer::shared_ptr< AddSearchPatternRotSetOp >	AddSearchPatternRotSetOpOP
typedef utility::pointer::shared_ptr< AddSearchPatternRotSetOp const >	AddSearchPatternRotSetOpCOP

Enumerations
enum	StubStatus { reject =1 , accept , unchecked }

Functions
static basic::Tracer	TR ("protocols.hotspot_hashing")
core::scoring::constraints::ConstraintCOPs	remove_hotspot_constraints_from_pose (core::pose::Pose &)
	utility function for deleting all backbone stub constraints from a pose. Returns the removed constraints (ambiguous). More...
core::Real	residue_sc_rmsd_no_super (core::conformation::ResidueCOP res1, core::conformation::ResidueCOP res2, bool const fxnal_group_only=false)
	utility function to calculate per-residue sidechain rmsd without superposition More...
core::Real	stub_tgt_angle (core::pose::Pose const &pose, core::conformation::ResidueCOP stub, core::Size const target_res)
	utility function to make sure stub's Cbeta is not pointed away from the target. Returns true if stub is pointed generally towards target's center of mass. Returns false otherwise. algorithm: get vector between CA and target center of mass, then CA-CB vector. Check alignment between the two. doesn't take into account hotspots at the end of the pose so might be a little off in CoM. But probably pretty OK More...
std::ostream &	operator<< (std::ostream &stream, const Vector &vector)
std::istream &	operator>> (std::istream &stream, Vector &v)
std::ostream &	stub_to_points (std::ostream &stream, const core::kinematics::Stub &stub)
std::istream &	stub_from_points (std::istream &stream, core::kinematics::Stub &stub)
std::ostream &	operator<< (std::ostream &stream, const VectorPair &pair)
std::istream &	operator>> (std::istream &stream, VectorPair &pair)
static basic::Tracer	TR ("protocols.hotspot_hashing.SearchPatternRotSetOp")
static basic::Tracer	TR ("protocols.hotspot_hashing.SICSearchPattern")
static basic::Tracer	tr ("protocols.hotspot_hashing.StubGenerator")
static basic::Tracer	TR ("protocols.hotspot_hashing.SurfaceSearchPattern")

Typedef Documentation

AddSearchPatternRotSetOpCOP

typedef utility::pointer::shared_ptr< AddSearchPatternRotSetOp const > protocols::hotspot_hashing::AddSearchPatternRotSetOpCOP

AddSearchPatternRotSetOpOP

typedef utility::pointer::shared_ptr< AddSearchPatternRotSetOp > protocols::hotspot_hashing::AddSearchPatternRotSetOpOP

HotspotStubCOP

typedef utility::pointer::shared_ptr< HotspotStub const > protocols::hotspot_hashing::HotspotStubCOP

HotspotStubOP

typedef utility::pointer::shared_ptr< HotspotStub > protocols::hotspot_hashing::HotspotStubOP

HotspotStubSetCOP

typedef utility::pointer::shared_ptr< HotspotStubSet const > protocols::hotspot_hashing::HotspotStubSetCOP

HotspotStubSetOP

typedef utility::pointer::shared_ptr< HotspotStubSet > protocols::hotspot_hashing::HotspotStubSetOP

Matrix

typedef numeric::xyzMatrix< core::Real > protocols::hotspot_hashing::Matrix

SearchPatternCOP

typedef utility::pointer::shared_ptr<SearchPattern const> protocols::hotspot_hashing::SearchPatternCOP

SearchPatternOP

typedef utility::pointer::shared_ptr<SearchPattern> protocols::hotspot_hashing::SearchPatternOP

SearchPatternRotSetOpCOP

typedef utility::pointer::shared_ptr< SearchPatternRotSetOp const > protocols::hotspot_hashing::SearchPatternRotSetOpCOP

SearchPatternRotSetOpOP

typedef utility::pointer::shared_ptr< SearchPatternRotSetOp > protocols::hotspot_hashing::SearchPatternRotSetOpOP

Vector

typedef numeric::xyzVector< core::Real > protocols::hotspot_hashing::Vector

Enumeration Type Documentation

StubStatus

enum protocols::hotspot_hashing::StubStatus

Enumerator
reject
accept
unchecked

Function Documentation

operator<<() [1/2]

std::ostream& protocols::hotspot_hashing::operator<< ( std::ostream &  stream, const Vector &  vector  )

inline

operator<<() [2/2]

std::ostream& protocols::hotspot_hashing::operator<< ( std::ostream &  stream, const VectorPair &  pair  )

inline

References core::scoring::pair.

operator>>() [1/2]

std::istream& protocols::hotspot_hashing::operator>> ( std::istream &  stream, Vector &  v  )

inline

operator>>() [2/2]

std::istream& protocols::hotspot_hashing::operator>> ( std::istream &  stream, VectorPair &  pair  )

inline

References core::scoring::pair.

remove_hotspot_constraints_from_pose()

core::scoring::constraints::ConstraintCOPs protocols::hotspot_hashing::remove_hotspot_constraints_from_pose

(

core::pose::Pose &

pose

)

utility function for deleting all backbone stub constraints from a pose. Returns the removed constraints (ambiguous).

Searches for all ambiguous constraints that have a backbone stub active constraint. and removes them from the pose. Returns a vector of the removed constraints.

References core::pose::Pose::constraint_set(), protocols::hotspot_hashing::HotspotStubSet::end(), and core::pose::Pose::remove_constraints().

Referenced by protocols::protein_interface_design::movers::DockWithHotspotMover::apply(), protocols::protein_interface_design::movers::PlacementMinimizationMover::apply(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::apply(), protocols::protein_interface_design::movers::PlaceStubMover::apply(), protocols::protein_interface_design::filters::StubScoreFilter::compute(), protocols::protein_interface_design::movers::PlaceOnLoop::loop_length(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::minimize_all(), protocols::protein_interface_design::movers::PlacementMinimizationMover::refresh_bbstub_constraints(), and protocols::protein_interface_design::movers::PlaceStubMover::StubMinimize().

residue_sc_rmsd_no_super()

core::Real protocols::hotspot_hashing::residue_sc_rmsd_no_super	(	core::conformation::ResidueCOP	res1,
		core::conformation::ResidueCOP	res2,
		bool const	fxnal_group_only
	)

utility function to calculate per-residue sidechain rmsd without superposition

Iterates over all non-hydrogen sidechain atoms of two residues and returns their rmsd without superposition.

References core::scoring::residue_sc_rmsd_no_super().

Referenced by protocols::hotspot_hashing::HotspotStubSet::cluster(), and protocols::hotspot_hashing::HotspotStubSet::colonyE().

stub_from_points()

std::istream& protocols::hotspot_hashing::stub_from_points ( std::istream &  stream, core::kinematics::Stub &  stub  )

inline

References core::pose::motif::a(), protocols::match::upstream::b, and core::kinematics::Stub::from_four_points().

stub_tgt_angle()

core::Real protocols::hotspot_hashing::stub_tgt_angle	(	core::pose::Pose const &	pose,
		core::conformation::ResidueCOP	stub,
		core::Size const	target_res
	)

utility function to make sure stub's Cbeta is not pointed away from the target. Returns true if stub is pointed generally towards target's center of mass. Returns false otherwise. algorithm: get vector between CA and target center of mass, then CA-CB vector. Check alignment between the two. doesn't take into account hotspots at the end of the pose so might be a little off in CoM. But probably pretty OK

utility function to make sure stub's Cbeta is not pointed away from the target.

References core::conformation::Residue::atom_index(), core::pose::Pose::residue(), core::pose::residue_center_of_mass(), core::pose::Pose::size(), TR(), and core::conformation::Residue::xyz().

Referenced by protocols::hotspot_hashing::HotspotStubSet::fill().

stub_to_points()

std::ostream& protocols::hotspot_hashing::stub_to_points ( std::ostream &  stream, const core::kinematics::Stub &  stub  )

inline

References core::pose::motif::a(), protocols::match::upstream::b, and core::kinematics::Stub::local2global().

Referenced by protocols::hotspot_hashing::movers::PlaceProbeMover::execute_one_search(), and protocols::hotspot_hashing::SearchPatternRotSetOp::get_rigid_body_confs().

TR() [1/4]

static basic::Tracer protocols::hotspot_hashing::TR ( "protocols.hotspot_hashing"  )

static

Referenced by protocols::hotspot_hashing::HotspotStubSet::add_hotspot_constraints_to_pose(), protocols::hotspot_hashing::HotspotStubSet::add_hotspot_constraints_to_wholepose(), protocols::hotspot_hashing::HotspotStubSet::cluster(), protocols::hotspot_hashing::HotspotStubSet::colonyE(), protocols::hotspot_hashing::HotspotStubSet::create_hotspot_after_pose(), protocols::hotspot_hashing::HotspotStubSet::evaluate_stub_self_energy_(), protocols::hotspot_hashing::HotspotStubSet::fill(), protocols::hotspot_hashing::SearchPatternRotSetOp::get_rigid_body_confs(), protocols::hotspot_hashing::SearchPatternRotSetOp::increase_packer_residue_radius(), protocols::hotspot_hashing::HotspotStubSet::pair_with_scaffold(), protocols::hotspot_hashing::HotspotStubSet::read_data(), protocols::hotspot_hashing::HotspotStubSet::remove_random_stubs_from_set(), protocols::hotspot_hashing::HotspotStubSet::remove_stub(), protocols::hotspot_hashing::HotspotStubSet::rescore(), protocols::hotspot_hashing::HotspotStubSet::retrieve(), protocols::hotspot_hashing::SICPatternAtTransform::Searchpoints(), protocols::hotspot_hashing::HotspotStubSet::setup_hotspot_foldtree_(), protocols::hotspot_hashing::SICPatternAtTransform::SICPatternAtTransform(), stub_tgt_angle(), protocols::hotspot_hashing::HotspotStubSet::subset(), protocols::hotspot_hashing::SurfaceSearchPattern::SurfaceSearchPattern(), and protocols::hotspot_hashing::HotspotStubSet::write_all().

TR() [2/4]

static basic::Tracer protocols::hotspot_hashing::TR ( "protocols.hotspot_hashing.SearchPatternRotSetOp"  )

static

TR() [3/4]

static basic::Tracer protocols::hotspot_hashing::TR ( "protocols.hotspot_hashing.SICSearchPattern"  )

static

tr()

static basic::Tracer protocols::hotspot_hashing::tr ( "protocols.hotspot_hashing.StubGenerator"  )

static

Referenced by protocols::hotspot_hashing::StubGenerator::placeResidueAtTransform(), and protocols::hotspot_hashing::StubGenerator::placeResidueOnPose().

TR() [4/4]

static basic::Tracer protocols::hotspot_hashing::TR ( "protocols.hotspot_hashing.SurfaceSearchPattern"  )

static