protocols::rigid Namespace Reference

Classes
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	MovePoseToMembraneCenterMover
	move pose into a membrane More...
class	RigidBodyDeterministicSpinMover
class	RigidBodyDofPerturbMover
	This Mover 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	RigidBodyDofRandomizeMover
	A Mover that initializes all DOFs in the system randomly. It starts with rotation angles only. More...
class	RigidBodyDofRandomTransMover
	A Mover that translates down an axis determined by the available DOFs. Translations are made along all allowed directions (x,y or z) for a randomly selected jump. More...
class	RigidBodyDofSeqPerturbMover
	This Mover 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	RigidBodyDofSeqRandomizeMover
	A Mover that initializes all DOFs in the system randomly. It starts with rotation angles only. More...
class	RigidBodyDofSeqTransMover
	A Mover that translates down an axis determined by the available DOFs. Translations are made along all allowed directions (x,y or z) for a selected jump. Jumps are visited in random order. More...
class	RigidBodyDofTransMover
	A Mover that translates down an axis determined by the available DOFs. Translations are made along all allowed directions (x,y or z) for a selected jump. More...
class	RigidBodyMotionMover
class	RigidBodyMover
	Rigid-body random translate/rotate around centroid of downstream side of a jump. More...
class	RigidBodyPerturbMover
	This Mover does a perturbation defined by the rotational and translational magnitudes. More...
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	RigidBodyPerturbNoCenterMoverCreator
class	RigidBodyRandomizeMover
class	RigidBodySpinMover
	A Mover that spins about a random axis. More...
class	RigidBodyTransMover
	This Mover translate down an axis. More...
class	RigidBodyTransMoverCreator
class	RollMover
class	RollMoverCreator
class	RotateJumpAxisMover
class	UniformSphereTransMover
	Rigid-body move that evenly samples the space within a sphere. More...
class	WholeBodyRotationMover
	rotate the whole pose More...
class	WholeBodyTranslationMover
	translate the whole pose More...

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
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)
double	angle_between (const numeric::xyzVector< double > &a, const numeric::xyzVector< double > &b)
std::ostream &	operator<< (std::ostream &os, RigidBodyPerturbMover const &mover)
std::ostream &	operator<< (std::ostream &os, RigidBodyRandomizeMover const &randommover)

Variables
static numeric::random::RandomGenerator	RG (67729)
static basic::Tracer	TR ("protocols.moves.PoseMembraneRigidBodyMover")
static numeric::random::RandomGenerator	RG (6245211)
static basic::Tracer	TR ("protocols.moves.RigidBodyMotionMover")
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)

Typedef Documentation

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Enumeration Type Documentation

enum protocols::rigid::Direction

Direction, which direction.

Enumerator
c2n
random
n2c

enum protocols::rigid::Partner

Partner, which partner gets moved.

Enumerator
partner_upstream
partner_downstream

Function Documentation

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

References numeric::xyzVector< class >::dot(), numeric::xyzVector< class >::length(), and radians().

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
	)

References core::kinematics::MoveMap::get_jump(), core::pose::Pose::num_jump(), numeric::random::RandomGenerator::random_element(), and RG.

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

References core::pose::Pose::jump(), runtime_assert, core::pose::Pose::set_jump(), and numeric::random::uniform().

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

References protocols::rigid::RigidBodyPerturbMover::show().

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

References protocols::rigid::RigidBodyRandomizeMover::show().

Variable Documentation

const Real protocols::rigid::max_allowed_rot_mag(60.0)

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

numeric::random::RandomGenerator protocols::rigid::RG(6245211)

static

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

static

Referenced by protocols::rigid::RigidBodyPerturbMover::apply(), protocols::rigid::RigidBodyPerturbNoCenterMover::apply(), protocols::rigid::RigidBodySpinMover::apply(), protocols::rigid::RigidBodyDofRandomizeMover::apply(), protocols::rigid::RotateJumpAxisMover::calc_angle(), gaussian_jump_move(), protocols::rigid::UniformSphereTransMover::reset_trans_axis(), protocols::rigid::RigidBodyDofPerturbMover::RigidBodyDofPerturbMover(), and protocols::rigid::RigidBodyDofTransMover::RigidBodyDofTransMover().

numeric::random::RandomGenerator protocols::rigid::RG(43225)

static

basic::Tracer protocols::rigid::TR("protocols.moves.RigidBodyMotionMover")

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().

basic::Tracer protocols::rigid::TR("protocols.moves.RigidBodyMover")

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().