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
	This Mover does a perturbation defined by the rotational and translational magnitudes. More...
class	RigidBodyPerturbRandomJumpMover
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
	A Mover that spins about a random axis. More...
class	RigidBodyDeterministicSpinMover
class	RigidBodyTiltMover
	A Mover that tilts around the spin axis. More...
class	RigidBodyTransMover
	This Mover translate down an axis. More...
class	UniformSphereTransMover
	Rigid-body move that evenly samples the space within a sphere. More...
class	RigidBodyDofRandomizeMover
	A Mover that initializes all DOFs in the system randomly. It starts with rotation angles only. More...
class	RigidBodyDofSeqRandomizeMover
	A Mover that initializes all DOFs in the system randomly. It starts with rotation angles only. 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	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	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	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	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	RigidBodyTransMoverCreator
class	RigidBodyPerturbNoCenterMoverCreator
class	RigidBodyTiltMoverCreator
class	RollMover
class	RollMoverCreator
class	RotateJumpAxisMover
class	UniformRigidBodyCM
class	UniformRigidBodyCMCreator
class	UniformRigidBodyMover
class	UniformRigidBodyMoverCreator

Typedefs
typedef utility::pointer::shared_ptr< RigidBodyMotionMover >	RigidBodyMotionMoverOP
typedef utility::pointer::shared_ptr< RigidBodyMotionMover const >	RigidBodyMotionMoverCOP
typedef utility::pointer::shared_ptr< RigidBodyMover >	RigidBodyMoverOP
typedef utility::pointer::shared_ptr< RigidBodyMover const >	RigidBodyMoverCOP
typedef utility::pointer::shared_ptr< RigidBodyPerturbMover >	RigidBodyPerturbMoverOP
typedef utility::pointer::shared_ptr< RigidBodyPerturbMover const >	RigidBodyPerturbMoverCOP
typedef utility::pointer::shared_ptr< RigidBodyPerturbRandomJumpMover >	RigidBodyPerturbRandomJumpMoverOP
typedef utility::pointer::shared_ptr< RigidBodyPerturbRandomJumpMover const >	RigidBodyPerturbRandomJumpMoverCOP
typedef utility::pointer::shared_ptr< RigidBodyPerturbNoCenterMover >	RigidBodyPerturbNoCenterMoverOP
typedef utility::pointer::shared_ptr< RigidBodyPerturbNoCenterMover const >	RigidBodyPerturbNoCenterMoverCOP
typedef utility::pointer::shared_ptr< RigidBodyRandomizeMover >	RigidBodyRandomizeMoverOP
typedef utility::pointer::shared_ptr< RigidBodyRandomizeMover const >	RigidBodyRandomizeMoverCOP
typedef utility::pointer::shared_ptr< RigidBodySpinMover >	RigidBodySpinMoverOP
typedef utility::pointer::shared_ptr< RigidBodySpinMover const >	RigidBodySpinMoverCOP
typedef utility::pointer::shared_ptr< RigidBodySpinMover >	RigidBodyDeterministicSpinMoverOP
typedef utility::pointer::shared_ptr< RigidBodySpinMover const >	RigidBodyDeterministicSpinMoverCOP
typedef utility::pointer::shared_ptr< RigidBodyTiltMover >	RigidBodyTiltMoverOP
typedef utility::pointer::shared_ptr< RigidBodyTiltMover const >	RigidBodyTiltMoverCOP
typedef utility::pointer::shared_ptr< RigidBodyTransMover >	RigidBodyTransMoverOP
typedef utility::pointer::shared_ptr< RigidBodyTransMover const >	RigidBodyTransMoverCOP
typedef utility::pointer::shared_ptr< UniformSphereTransMover >	UniformSphereTransMoverOP
typedef utility::pointer::shared_ptr< UniformSphereTransMover const >	UniformSphereTransMoverCOP
typedef utility::pointer::shared_ptr< RigidBodyDofRandomizeMover >	RigidBodyDofRandomizeMoverOP
typedef utility::pointer::shared_ptr< RigidBodyDofRandomizeMover const >	RigidBodyDofRandomizeMoverCOP
typedef utility::pointer::shared_ptr< RigidBodyDofSeqRandomizeMover >	RigidBodyDofSeqRandomizeMoverOP
typedef utility::pointer::shared_ptr< RigidBodyDofSeqRandomizeMover const >	RigidBodyDofSeqRandomizeMoverCOP
typedef utility::pointer::shared_ptr< RigidBodyDofTransMover >	RigidBodyDofTransMoverOP
typedef utility::pointer::shared_ptr< RigidBodyDofTransMover const >	RigidBodyDofTransMoverCOP
typedef utility::pointer::shared_ptr< RigidBodyDofSeqTransMover >	RigidBodyDofSeqTransMoverOP
typedef utility::pointer::shared_ptr< RigidBodyDofSeqTransMover const >	RigidBodyDofSeqTransMoverCOP
typedef utility::pointer::shared_ptr< RigidBodyDofRandomTransMover >	RigidBodyDofRandomTransMoverOP
typedef utility::pointer::shared_ptr< RigidBodyDofRandomTransMover const >	RigidBodyDofRandomTransMoverCOP
typedef utility::pointer::shared_ptr< RigidBodyDofPerturbMover >	RigidBodyDofPerturbMoverOP
typedef utility::pointer::shared_ptr< RigidBodyDofPerturbMover const >	RigidBodyDofPerturbMoverCOP
typedef utility::pointer::shared_ptr< RigidBodyDofSeqPerturbMover >	RigidBodyDofSeqPerturbMoverOP
typedef utility::pointer::shared_ptr< RigidBodyDofSeqPerturbMover const >	RigidBodyDofSeqPerturbMoverCOP
typedef utility::pointer::shared_ptr< RollMover >	RollMoverOP
typedef utility::pointer::shared_ptr< RollMover const >	RollMoverCOP
typedef utility::pointer::shared_ptr< RotateJumpAxisMover >	RotateJumpAxisMoverOP
typedef utility::pointer::shared_ptr< RotateJumpAxisMover const >	RotateJumpAxisMoverCOP
typedef utility::pointer::shared_ptr< UniformRigidBodyCM >	UniformRigidBodyCMOP
typedef utility::pointer::shared_ptr< UniformRigidBodyCM const >	UniformRigidBodyCMCOP
typedef utility::pointer::shared_ptr< UniformRigidBodyMover >	UniformRigidBodyMoverOP
typedef utility::pointer::shared_ptr< UniformRigidBodyMover const >	UniformRigidBodyMoverCOP

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 basic::Tracer	TR ("protocols.moves.PoseMembraneRigidBodyMover")
static basic::Tracer	TR ("protocols.rigid.rigid_body")
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")
core::Real	angle_between (const numeric::xyzVector< core::Real > &a, const numeric::xyzVector< core::Real > &b)
static basic::Tracer	TR ("protocols.rigid.RigidBodyMover")
static basic::Tracer	TRBM ("protocols.moves.RigidBodyMover")
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)
static basic::Tracer	tr ("protocols.rigid.UniformRigidBodyCM", basic::t_info)
static basic::Tracer	tr ("protocols.rigid.UniformRigidBodyMover", basic::t_info)

Variables
std::string const	DOCKJUMP_TAG = "_dockjump"
int const	NO_JUMP = 0

Typedef Documentation

RigidBodyDeterministicSpinMoverCOP

typedef utility::pointer::shared_ptr< RigidBodySpinMover const > protocols::rigid::RigidBodyDeterministicSpinMoverCOP

RigidBodyDeterministicSpinMoverOP

typedef utility::pointer::shared_ptr< RigidBodySpinMover > protocols::rigid::RigidBodyDeterministicSpinMoverOP

RigidBodyDofPerturbMoverCOP

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

RigidBodyDofPerturbMoverOP

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

RigidBodyDofRandomizeMoverCOP

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

RigidBodyDofRandomizeMoverOP

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

RigidBodyDofRandomTransMoverCOP

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

RigidBodyDofRandomTransMoverOP

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

RigidBodyDofSeqPerturbMoverCOP

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

RigidBodyDofSeqPerturbMoverOP

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

RigidBodyDofSeqRandomizeMoverCOP

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

RigidBodyDofSeqRandomizeMoverOP

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

RigidBodyDofSeqTransMoverCOP

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

RigidBodyDofSeqTransMoverOP

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

RigidBodyDofTransMoverCOP

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

RigidBodyDofTransMoverOP

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

RigidBodyMotionMoverCOP

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

RigidBodyMotionMoverOP

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

RigidBodyMoverCOP

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

RigidBodyMoverOP

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

RigidBodyPerturbMoverCOP

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

RigidBodyPerturbMoverOP

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

RigidBodyPerturbNoCenterMoverCOP

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

RigidBodyPerturbNoCenterMoverOP

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

RigidBodyPerturbRandomJumpMoverCOP

typedef utility::pointer::shared_ptr< RigidBodyPerturbRandomJumpMover const > protocols::rigid::RigidBodyPerturbRandomJumpMoverCOP

RigidBodyPerturbRandomJumpMoverOP

typedef utility::pointer::shared_ptr< RigidBodyPerturbRandomJumpMover > protocols::rigid::RigidBodyPerturbRandomJumpMoverOP

RigidBodyRandomizeMoverCOP

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

RigidBodyRandomizeMoverOP

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

RigidBodySpinMoverCOP

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

RigidBodySpinMoverOP

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

RigidBodyTiltMoverCOP

typedef utility::pointer::shared_ptr< RigidBodyTiltMover const > protocols::rigid::RigidBodyTiltMoverCOP

RigidBodyTiltMoverOP

typedef utility::pointer::shared_ptr< RigidBodyTiltMover > protocols::rigid::RigidBodyTiltMoverOP

RigidBodyTransMoverCOP

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

RigidBodyTransMoverOP

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

RollMoverCOP

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

RollMoverOP

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

RotateJumpAxisMoverCOP

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

RotateJumpAxisMoverOP

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

UniformRigidBodyCMCOP

typedef utility::pointer::shared_ptr< UniformRigidBodyCM const > protocols::rigid::UniformRigidBodyCMCOP

UniformRigidBodyCMOP

typedef utility::pointer::shared_ptr< UniformRigidBodyCM > protocols::rigid::UniformRigidBodyCMOP

UniformRigidBodyMoverCOP

typedef utility::pointer::shared_ptr< UniformRigidBodyMover const > protocols::rigid::UniformRigidBodyMoverCOP

UniformRigidBodyMoverOP

typedef utility::pointer::shared_ptr< UniformRigidBodyMover > protocols::rigid::UniformRigidBodyMoverOP

UniformSphereTransMoverCOP

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

UniformSphereTransMoverOP

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

Enumeration Type Documentation

Direction

enum protocols::rigid::Direction

Direction, which direction.

Enumerator
c2n
random
n2c

Partner

enum protocols::rigid::Partner

Partner, which partner gets moved.

Enumerator
partner_upstream
partner_downstream

Function Documentation

angle_between()

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

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

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

gaussian_jump_move() [1/2]

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::kinematics::Jump::gaussian_move(), core::pose::Pose::jump(), and core::pose::Pose::set_jump().

gaussian_jump_move() [2/2]

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(), core::scoring::rg, and TR().

max_allowed_rot_mag()

const Real protocols::rigid::max_allowed_rot_mag

(

60.

0

)

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

operator<<() [1/2]

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

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

operator<<() [2/2]

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

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

TR() [1/4]

static basic::Tracer protocols::rigid::TR ( "protocols.moves.PoseMembraneRigidBodyMover"  )

static

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

TR() [2/4]

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

static

TR() [3/4]

static basic::Tracer protocols::rigid::TR ( "protocols.rigid.rigid_body"  )

static

TR() [4/4]

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

static

tr() [1/2]

static basic::Tracer protocols::rigid::tr ( "protocols.rigid.UniformRigidBodyCM"  , basic::t_info    )

static

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

tr() [2/2]

static basic::Tracer protocols::rigid::tr ( "protocols.rigid.UniformRigidBodyMover"  , basic::t_info    )

static

TRBM()

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::RigidBodyTiltMover::apply(), protocols::rigid::RigidBodyTransMover::apply(), protocols::rigid::RigidBodyDofRandomizeMover::apply(), protocols::rigid::RigidBodyDofTransMover::apply(), protocols::rigid::RigidBodyDofSeqTransMover::apply(), protocols::rigid::RigidBodyDofRandomTransMover::apply(), protocols::rigid::RigidBodyDofSeqPerturbMover::apply(), protocols::rigid::RigidBodyTiltMover::find_tilt_center(), protocols::rigid::RigidBodyTiltMover::parse_my_tag(), protocols::rigid::RigidBodyDofPerturbMover::RigidBodyDofPerturbMover(), protocols::rigid::RigidBodyDofRandomTransMover::RigidBodyDofRandomTransMover(), protocols::rigid::RigidBodyDofSeqPerturbMover::RigidBodyDofSeqPerturbMover(), protocols::rigid::RigidBodyDofSeqTransMover::RigidBodyDofSeqTransMover(), protocols::rigid::RigidBodyDofTransMover::RigidBodyDofTransMover(), protocols::rigid::RigidBodyPerturbMover::RigidBodyPerturbMover(), protocols::rigid::RigidBodyPerturbNoCenterMover::RigidBodyPerturbNoCenterMover(), and protocols::rigid::RigidBodyTiltMover::tilt().

Variable Documentation

DOCKJUMP_TAG

std::string const protocols::rigid::DOCKJUMP_TAG = "_dockjump"

Referenced by protocols::rigid::UniformRigidBodyCM::passport_updated(), and protocols::rigid::UniformRigidBodyCM::yield_claims().

NO_JUMP

int const protocols::rigid::NO_JUMP = 0

Referenced by protocols::rigid::UniformRigidBodyMover::apply(), protocols::rigid::UniformRigidBodyMover::complex_type_gen(), and protocols::rigid::UniformRigidBodyMover::parse_my_tag().