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protocols::hotspot_hashing Namespace Reference

Namespaces

 movers
 

Classes

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

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

typedef utility::pointer::shared_ptr< HotspotStub const > protocols::hotspot_hashing::HotspotStubCOP
typedef utility::pointer::shared_ptr< HotspotStub > protocols::hotspot_hashing::HotspotStubOP
typedef utility::pointer::shared_ptr< HotspotStubSet const > protocols::hotspot_hashing::HotspotStubSetCOP
typedef utility::pointer::shared_ptr< HotspotStubSet > protocols::hotspot_hashing::HotspotStubSetOP
typedef numeric::xyzMatrix< core::Real > protocols::hotspot_hashing::Matrix
typedef utility::pointer::shared_ptr<SearchPattern const> protocols::hotspot_hashing::SearchPatternCOP
typedef utility::pointer::shared_ptr<SearchPattern> protocols::hotspot_hashing::SearchPatternOP
typedef utility::pointer::shared_ptr< SearchPatternRotSetOp const > protocols::hotspot_hashing::SearchPatternRotSetOpCOP
typedef numeric::xyzVector< core::Real > protocols::hotspot_hashing::Vector

Enumeration Type Documentation

Enumerator
reject 
accept 
unchecked 

Function Documentation

std::ostream& protocols::hotspot_hashing::operator<< ( std::ostream &  stream,
const Vector vector 
)
inline
std::ostream& protocols::hotspot_hashing::operator<< ( std::ostream &  stream,
const VectorPair &  pair 
)
inline
std::istream& protocols::hotspot_hashing::operator>> ( std::istream &  stream,
Vector v 
)
inline
std::istream& protocols::hotspot_hashing::operator>> ( std::istream &  stream,
VectorPair &  pair 
)
inline
core::scoring::constraints::ConstraintCOPs protocols::hotspot_hashing::remove_hotspot_constraints_from_pose ( core::pose::Pose pose)
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().

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

std::ostream& protocols::hotspot_hashing::stub_to_points ( std::ostream &  stream,
const core::kinematics::Stub stub 
)
inline
static basic::Tracer protocols::hotspot_hashing::TR ( "protocols.hotspot_hashing.SurfaceSearchPattern"  )
static
static basic::Tracer protocols::hotspot_hashing::TR ( "protocols.hotspot_hashing.SearchPatternRotSetOp"  )
static
static basic::Tracer protocols::hotspot_hashing::tr ( "protocols.hotspot_hashing.StubGenerator"  )
static
static basic::Tracer protocols::hotspot_hashing::TR ( "protocols.hotspot_hashing.SICSearchPattern"  )
static
static basic::Tracer protocols::hotspot_hashing::TR ( "protocols.hotspot_hashing"  )
static