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protocols::rigid Namespace Reference

Classes

class  MovePoseToMembraneCenterMover
 move pose into a membrane More...
 
class  MembraneCenterPerturbationMover
 perturb the pose along membrane normal More...
 
class  MembraneNormalPerturbationMover
 rotation pose around membrane center, perturb the membrane normal vector relative to the pose More...
 
class  WholeBodyTranslationMover
 translate the whole pose More...
 
class  WholeBodyRotationMover
 rotate the whole pose More...
 
class  RigidBodyMotionMover
 
class  RigidBodyMover
 Rigid-body random translate/rotate around centroid of downstream side of a jump. More...
 
class  RigidBodyPerturbMover
 
class  RigidBodyPerturbNoCenterMover
 does a perturbation defined by the rotational and translational magnitudes without setting up the center Can be defined through a move map or with rb_jump Defining through a movemap with multiple jumps leads to a random jump being chosen at apply time, NOT at construction time! This is done to simplify docking with more than one active jump. More...
 
class  RigidBodyRandomizeMover
 
class  RigidBodySpinMover
 
class  RigidBodyDeterministicSpinMover
 
class  RigidBodyTransMover
 
class  UniformSphereTransMover
 Rigid-body move that evenly samples the space within a sphere. More...
 
class  RigidBodyDofRandomizeMover
 
class  RigidBodyDofSeqRandomizeMover
 
class  RigidBodyDofTransMover
 
class  RigidBodyDofSeqTransMover
 
class  RigidBodyDofRandomTransMover
 
class  RigidBodyDofPerturbMover
 does a perturbation defined by the rotational and translational magnitudes Allowed dofs are specified by a map Can be defined through a move map or with rb_jump. A single jump is selected More...
 
class  RigidBodyDofSeqPerturbMover
 does a perturbation defined by the rotational and translational magnitudes Allowed dofs are specified by a map Can be defined through a move map or with rb_jump. All jumps are selected in random order More...
 
class  RigidBodyPerturbNoCenterMoverCreator
 
class  RollMover
 
class  RollMoverCreator
 
class  RotateJumpAxisMover
 

Typedefs

typedef
utility::pointer::owning_ptr
< RigidBodyMotionMover > 		RigidBodyMotionMoverOP
 
typedef
utility::pointer::owning_ptr
< RigidBodyMotionMover const > 		RigidBodyMotionMoverCOP
 
typedef
utility::pointer::owning_ptr
< RigidBodyMover > 		RigidBodyMoverOP
 
typedef
utility::pointer::owning_ptr
< RigidBodyMover const > 		RigidBodyMoverCOP
 
typedef
utility::pointer::owning_ptr
< RigidBodyPerturbMover > 		RigidBodyPerturbMoverOP
 
typedef
utility::pointer::owning_ptr
< RigidBodyPerturbMover const > 		RigidBodyPerturbMoverCOP
 
typedef
utility::pointer::owning_ptr
< RigidBodyPerturbNoCenterMover > 		RigidBodyPerturbNoCenterMoverOP
 
typedef
utility::pointer::owning_ptr
< RigidBodyPerturbNoCenterMover
const > 		RigidBodyPerturbNoCenterMoverCOP
 
typedef
utility::pointer::owning_ptr
< RigidBodyRandomizeMover > 		RigidBodyRandomizeMoverOP
 
typedef
utility::pointer::owning_ptr
< RigidBodyRandomizeMover
const > 		RigidBodyRandomizeMoverCOP
 
typedef
utility::pointer::owning_ptr
< RigidBodySpinMover > 		RigidBodySpinMoverOP
 
typedef
utility::pointer::owning_ptr
< RigidBodySpinMover const > 		RigidBodySpinMoverCOP
 
typedef
utility::pointer::owning_ptr
< RigidBodyTransMover > 		RigidBodyTransMoverOP
 
typedef
utility::pointer::owning_ptr
< RigidBodyTransMover const > 		RigidBodyTransMoverCOP
 
typedef
utility::pointer::owning_ptr
< UniformSphereTransMover > 		UniformSphereTransMoverOP
 
typedef
utility::pointer::owning_ptr
< UniformSphereTransMover
const > 		UniformSphereTransMoverCOP
 
typedef
utility::pointer::owning_ptr
< RigidBodyDofRandomizeMover > 		RigidBodyDofRandomizeMoverOP
 
typedef
utility::pointer::owning_ptr
< RigidBodyDofRandomizeMover
const > 		RigidBodyDofRandomizeMoverCOP
 
typedef
utility::pointer::owning_ptr
< RigidBodyDofSeqRandomizeMover > 		RigidBodyDofSeqRandomizeMoverOP
 
typedef
utility::pointer::owning_ptr
< RigidBodyDofSeqRandomizeMover
const > 		RigidBodyDofSeqRandomizeMoverCOP
 
typedef
utility::pointer::owning_ptr
< RigidBodyDofTransMover > 		RigidBodyDofTransMoverOP
 
typedef
utility::pointer::owning_ptr
< RigidBodyDofTransMover const > 		RigidBodyDofTransMoverCOP
 
typedef
utility::pointer::owning_ptr
< RigidBodyDofSeqTransMover > 		RigidBodyDofSeqTransMoverOP
 
typedef
utility::pointer::owning_ptr
< RigidBodyDofSeqTransMover
const > 		RigidBodyDofSeqTransMoverCOP
 
typedef
utility::pointer::owning_ptr
< RigidBodyDofRandomTransMover > 		RigidBodyDofRandomTransMoverOP
 
typedef
utility::pointer::owning_ptr
< RigidBodyDofRandomTransMover
const > 		RigidBodyDofRandomTransMoverCOP
 
typedef
utility::pointer::owning_ptr
< RigidBodyDofPerturbMover > 		RigidBodyDofPerturbMoverOP
 
typedef
utility::pointer::owning_ptr
< RigidBodyDofPerturbMover
const > 		RigidBodyDofPerturbMoverCOP
 
typedef
utility::pointer::owning_ptr
< RigidBodyDofSeqPerturbMover > 		RigidBodyDofSeqPerturbMoverOP
 
typedef
utility::pointer::owning_ptr
< RigidBodyDofSeqPerturbMover
const > 		RigidBodyDofSeqPerturbMoverCOP
 
typedef
utility::pointer::owning_ptr
< RollMover > 		RollMoverOP
 
typedef
utility::pointer::owning_ptr
< RollMover const > 		RollMoverCOP
 
typedef
utility::pointer::owning_ptr
< RotateJumpAxisMover > 		RotateJumpAxisMoverOP
 
typedef
utility::pointer::owning_ptr
< RotateJumpAxisMover const > 		RotateJumpAxisMoverCOP
 

Enumerations

enum  Partner { partner_upstream = 1, partner_downstream }
 Partner, which partner gets moved. More...
 
enum  Direction { c2n =-1, random =0, n2c =1 }
 Direction, which direction. More...
 

Functions

static
numeric::random::RandomGenerator 		RG (67729)
 
static basic::Tracer TR ("protocols.moves.PoseMembraneRigidBodyMover")
 
int gaussian_jump_move (pose::Pose &pose, kinematics::MoveMap const &mm, Real const translation_magnitude, Real const rotation_magnitude, int const dir)
 
void gaussian_jump_move (pose::Pose &pose, int const jump_number, Real const translation_magnitude, Real const rotation_magnitude, int dir)
 
static basic::Tracer TR ("protocols.moves.RigidBodyMotionMover")
 
double angle_between (const numeric::xyzVector< double > &a, const numeric::xyzVector< double > &b)
 
static basic::Tracer TR ("protocols.moves.RigidBodyMover")
 
static basic::Tracer TRBM ("protocols.moves.RigidBodyMover")
 
static
numeric::random::RandomGenerator 		RG (43225)
 
const Real max_allowed_rot_mag (60.0)
 
std::ostream & operator<< (std::ostream &os, RigidBodyPerturbMover const &mover)
 
std::ostream & operator<< (std::ostream &os, RigidBodyRandomizeMover const &randommover)
 
std::ostream & operator<< (std::ostream &os, RigidBodySpinMover const &spinmover)
 
std::ostream & operator<< (std::ostream &os, RigidBodyDeterministicSpinMover const &spinmover)
 
std::ostream & operator<< (std::ostream &os, RigidBodyTransMover const &mover)
 

Typedef Documentation

typedef utility::pointer::owning_ptr< RigidBodyDofPerturbMover const > protocols::rigid::RigidBodyDofPerturbMoverCOP

Definition at line 74 of file RigidBodyMover.fwd.hh.

typedef utility::pointer::owning_ptr< RigidBodyDofPerturbMover > protocols::rigid::RigidBodyDofPerturbMoverOP

Definition at line 72 of file RigidBodyMover.fwd.hh.

typedef utility::pointer::owning_ptr< RigidBodyDofRandomizeMover const > protocols::rigid::RigidBodyDofRandomizeMoverCOP

Definition at line 54 of file RigidBodyMover.fwd.hh.

typedef utility::pointer::owning_ptr< RigidBodyDofRandomizeMover > protocols::rigid::RigidBodyDofRandomizeMoverOP

Definition at line 52 of file RigidBodyMover.fwd.hh.

typedef utility::pointer::owning_ptr< RigidBodyDofRandomTransMover const > protocols::rigid::RigidBodyDofRandomTransMoverCOP

Definition at line 70 of file RigidBodyMover.fwd.hh.

typedef utility::pointer::owning_ptr< RigidBodyDofRandomTransMover > protocols::rigid::RigidBodyDofRandomTransMoverOP

Definition at line 68 of file RigidBodyMover.fwd.hh.

typedef utility::pointer::owning_ptr< RigidBodyDofSeqPerturbMover const > protocols::rigid::RigidBodyDofSeqPerturbMoverCOP

Definition at line 78 of file RigidBodyMover.fwd.hh.

typedef utility::pointer::owning_ptr< RigidBodyDofSeqPerturbMover > protocols::rigid::RigidBodyDofSeqPerturbMoverOP

Definition at line 76 of file RigidBodyMover.fwd.hh.

typedef utility::pointer::owning_ptr< RigidBodyDofSeqRandomizeMover const > protocols::rigid::RigidBodyDofSeqRandomizeMoverCOP

Definition at line 58 of file RigidBodyMover.fwd.hh.

typedef utility::pointer::owning_ptr< RigidBodyDofSeqRandomizeMover > protocols::rigid::RigidBodyDofSeqRandomizeMoverOP

Definition at line 56 of file RigidBodyMover.fwd.hh.

typedef utility::pointer::owning_ptr< RigidBodyDofSeqTransMover const > protocols::rigid::RigidBodyDofSeqTransMoverCOP

Definition at line 66 of file RigidBodyMover.fwd.hh.

typedef utility::pointer::owning_ptr< RigidBodyDofSeqTransMover > protocols::rigid::RigidBodyDofSeqTransMoverOP

Definition at line 64 of file RigidBodyMover.fwd.hh.

typedef utility::pointer::owning_ptr< RigidBodyDofTransMover const > protocols::rigid::RigidBodyDofTransMoverCOP

Definition at line 62 of file RigidBodyMover.fwd.hh.

typedef utility::pointer::owning_ptr< RigidBodyDofTransMover > protocols::rigid::RigidBodyDofTransMoverOP

Definition at line 60 of file RigidBodyMover.fwd.hh.

typedef utility::pointer::owning_ptr<RigidBodyMotionMover const> protocols::rigid::RigidBodyMotionMoverCOP

Definition at line 23 of file RigidBodyMotionMover.fwd.hh.

typedef utility::pointer::owning_ptr<RigidBodyMotionMover> protocols::rigid::RigidBodyMotionMoverOP

Definition at line 21 of file RigidBodyMotionMover.fwd.hh.

typedef utility::pointer::owning_ptr< RigidBodyMover const > protocols::rigid::RigidBodyMoverCOP

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

typedef utility::pointer::owning_ptr< RigidBodyMover > protocols::rigid::RigidBodyMoverOP

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

typedef utility::pointer::owning_ptr< RigidBodyPerturbMover const > protocols::rigid::RigidBodyPerturbMoverCOP

Definition at line 30 of file RigidBodyMover.fwd.hh.

typedef utility::pointer::owning_ptr< RigidBodyPerturbMover > protocols::rigid::RigidBodyPerturbMoverOP

Definition at line 28 of file RigidBodyMover.fwd.hh.

typedef utility::pointer::owning_ptr< RigidBodyPerturbNoCenterMover const > protocols::rigid::RigidBodyPerturbNoCenterMoverCOP

Definition at line 34 of file RigidBodyMover.fwd.hh.

typedef utility::pointer::owning_ptr< RigidBodyPerturbNoCenterMover > protocols::rigid::RigidBodyPerturbNoCenterMoverOP

Definition at line 32 of file RigidBodyMover.fwd.hh.

typedef utility::pointer::owning_ptr< RigidBodyRandomizeMover const > protocols::rigid::RigidBodyRandomizeMoverCOP

Definition at line 38 of file RigidBodyMover.fwd.hh.

typedef utility::pointer::owning_ptr< RigidBodyRandomizeMover > protocols::rigid::RigidBodyRandomizeMoverOP

Definition at line 36 of file RigidBodyMover.fwd.hh.

typedef utility::pointer::owning_ptr< RigidBodySpinMover const > protocols::rigid::RigidBodySpinMoverCOP

Definition at line 42 of file RigidBodyMover.fwd.hh.

typedef utility::pointer::owning_ptr< RigidBodySpinMover > protocols::rigid::RigidBodySpinMoverOP

Definition at line 40 of file RigidBodyMover.fwd.hh.

typedef utility::pointer::owning_ptr< RigidBodyTransMover const > protocols::rigid::RigidBodyTransMoverCOP

Definition at line 46 of file RigidBodyMover.fwd.hh.

typedef utility::pointer::owning_ptr< RigidBodyTransMover > protocols::rigid::RigidBodyTransMoverOP

Definition at line 44 of file RigidBodyMover.fwd.hh.

typedef utility::pointer::owning_ptr< RollMover const > protocols::rigid::RollMoverCOP

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

typedef utility::pointer::owning_ptr< RollMover > protocols::rigid::RollMoverOP

Definition at line 22 of file RollMover.fwd.hh.

typedef utility::pointer::owning_ptr< RotateJumpAxisMover const > protocols::rigid::RotateJumpAxisMoverCOP

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

typedef utility::pointer::owning_ptr< RotateJumpAxisMover > protocols::rigid::RotateJumpAxisMoverOP

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

typedef utility::pointer::owning_ptr< UniformSphereTransMover const > protocols::rigid::UniformSphereTransMoverCOP

Definition at line 50 of file RigidBodyMover.fwd.hh.

typedef utility::pointer::owning_ptr< UniformSphereTransMover > protocols::rigid::UniformSphereTransMoverOP

Definition at line 48 of file RigidBodyMover.fwd.hh.

Enumeration Type Documentation

enum protocols::rigid::Direction

Direction, which direction.

Enumerator
c2n 
random 
n2c 

Definition at line 63 of file RigidBodyMover.hh.

enum protocols::rigid::Partner

Partner, which partner gets moved.

Enumerator
partner_upstream 
partner_downstream 

Definition at line 57 of file RigidBodyMover.hh.

Function Documentation

double protocols::rigid::angle_between ( const numeric::xyzVector< double > &  a,
const numeric::xyzVector< double > &  b 
)

Definition at line 54 of file RigidBodyMotionMover.cc.

Referenced by protocols::rigid::RigidBodyMotionMover::compute_bias().

int protocols::rigid::gaussian_jump_move ( pose::Pose &  pose,
kinematics::MoveMap const &  mm,
Real const  translation_magnitude,
Real const  rotation_magnitude,
int const  dir 
)

Definition at line 45 of file rigid_body_moves.cc.

References core::kinematics::MoveMap::get_jump(), core::pose::Pose::num_jump(), and core::pack::interaction_graph::T().

void protocols::rigid::gaussian_jump_move ( pose::Pose &  pose,
int const  jump_number,
Real const  translation_magnitude,
Real const  rotation_magnitude,
int  dir 
)

Definition at line 70 of file rigid_body_moves.cc.

References core::pose::Pose::jump(), and core::pose::Pose::set_jump().

const Real protocols::rigid::max_allowed_rot_mag ( 60.  0)

Referenced by protocols::rigid::RigidBodyPerturbMover::apply().

std::ostream& protocols::rigid::operator<< ( std::ostream &  os,
RigidBodyPerturbMover const &  mover 
)

Definition at line 285 of file RigidBodyMover.cc.

References protocols::rigid::RigidBodyPerturbMover::get_rot_mag(), protocols::rigid::RigidBodyPerturbMover::get_trans_mag(), protocols::moves::operator<<(), and protocols::rigid::RigidBodyMover::rb_jump().

std::ostream& protocols::rigid::operator<< ( std::ostream &  os,
RigidBodyRandomizeMover const &  randommover 
)

Definition at line 506 of file RigidBodyMover.cc.

References protocols::rigid::RigidBodyRandomizeMover::get_phi(), protocols::rigid::RigidBodyRandomizeMover::get_psi(), protocols::moves::operator<<(), and protocols::rigid::RigidBodyMover::rb_jump().

std::ostream& protocols::rigid::operator<< ( std::ostream &  os,
RigidBodySpinMover const &  spinmover 
)

Definition at line 588 of file RigidBodyMover.cc.

References protocols::moves::operator<<(), and protocols::rigid::RigidBodyMover::rb_jump().

std::ostream& protocols::rigid::operator<< ( std::ostream &  os,
RigidBodyDeterministicSpinMover const &  spinmover 
)

Definition at line 664 of file RigidBodyMover.cc.

References protocols::moves::operator<<(), and protocols::rigid::RigidBodyMover::rb_jump().

std::ostream& protocols::rigid::operator<< ( std::ostream &  os,
RigidBodyTransMover const &  mover 
)

Definition at line 714 of file RigidBodyMover.cc.

References protocols::moves::operator<<(), and protocols::rigid::RigidBodyMover::rb_jump().

static numeric::random::RandomGenerator protocols::rigid::RG ( 67729  )
static

Referenced by protocols::rigid::RigidBodySpinMover::apply(), protocols::rigid::RigidBodyDofRandomizeMover::apply(), protocols::rigid::RotateJumpAxisMover::calc_angle(), and protocols::rigid::UniformSphereTransMover::reset_trans_axis().

static numeric::random::RandomGenerator protocols::rigid::RG ( 43225  )
static
static basic::Tracer protocols::rigid::TR ( "protocols.moves.RigidBodyMotionMover"  )
static
static basic::Tracer protocols::rigid::TR ( "protocols.moves.RigidBodyMover"  )
static
static basic::Tracer protocols::rigid::TR ( "protocols.moves.PoseMembraneRigidBodyMover"  )
static

Referenced by protocols::rigid::RigidBodyMotionMover::apply(), protocols::rigid::RotateJumpAxisMover::apply(), protocols::rigid::RigidBodyPerturbMover::apply(), and protocols::rigid::RigidBodyPerturbNoCenterMover::apply().

static basic::Tracer protocols::rigid::TRBM ( "protocols.moves.RigidBodyMover"  )
static

Referenced by protocols::rigid::RigidBodyRandomizeMover::apply(), protocols::rigid::RigidBodySpinMover::apply(), protocols::rigid::RigidBodyDeterministicSpinMover::apply(), protocols::rigid::RigidBodyTransMover::apply(), protocols::rigid::RigidBodyDofRandomizeMover::apply(), protocols::rigid::RigidBodyDofTransMover::apply(), protocols::rigid::RigidBodyPerturbMover::RigidBodyPerturbMover(), and protocols::rigid::RigidBodyPerturbNoCenterMover::RigidBodyPerturbNoCenterMover().

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