an object which makes rigid-body transformation with translational and rotational perturbation More...

#include <Jump.hh>

Collaboration diagram for core::kinematics::Jump:

Public Types
typedef numeric::xyzVector< Real >	Vector

typedef numeric::xyzMatrix< Real >	Matrix

Public Member Functions
	Jump ()
	construction More...

	Jump (const RT &src_rt)
	constructor with only RT More...

	Jump (Stub const &stub1, Stub const &stub2)
	get RT from two stubs and ZERO rb_delta More...

	Jump (const Jump &src)
	copy constructor More...

Jump &	operator= (Jump const &src)
	copy operator More...

void	from_stubs (Stub const &stub1, Stub const &stub2)
	get a jump from two stubs More...

void	from_bond_cst (utility::vector1< Vector > &atoms, utility::vector1< Real > const &csts)
	get a jump from a bond cst definition More...

void	make_jump (Stub const &stub1, Stub &stub2) const
	make a jump from stub1 to stub2 More...

bool	ortho_check () const
	check RT's orthogonality More...

bool	nonzero_deltas () const
	check whether there is rb_delta not being transformed. More...

void	reset ()
	reset RT, rb_delta and rb_center More...

void	random_trans (const float dist_in)
	translate along a randomly chosen vector by dist_in More...

utility::vector1< Real >	gaussian_move (int const dir, float const trans_mag, float const rot_mag)
	Given the desired magnitude of the translation and rotation components, applies Gaussian perturbation to this jump. Return the move that was applied. More...

void	gaussian_move_single_rb (int const dir, float const mag, int rb)

void	rotation_by_matrix (Stub const &stub, Vector const &center, Matrix const &matrix)
	make a rotation "matrix" about the center "center" More...

void	rotation_by_axis (Stub const &stub, Vector const &axis, Vector const &center, float const alpha)
	make a rotation of alpha degrees around axix and center More...

void	translation_along_axis (Stub const &stub, Vector const &axis, float const dist)
	make a translation along axis by dist More...

void	identity_transform ()
	reset to identity matrix, 0 translation More...

void	reverse ()
	change the direction of a jump, e.g, upstream stub becomes downstream stub now. More...

Jump	reversed () const
	Return a new jump that is the inverse transformation. More...

Matrix const &	get_rotation () const
	get rotation matrix More...

Vector const &	get_translation () const
	get translation vector More...

void	set_rotation (Matrix const &R_in)
	set rotation matrix More...

void	set_translation (Vector const &t)
	set translation vector More...

void	fold_in_rb_deltas ()
	transform small changes in translation and rotation into jump More...

RT	rt () const
	return the RT modeled by this jump –> makes new Jump, calls fold_in_rb_delte and returns RT More...

utility::vector1< Real > const &	get_rb_delta (int const dir) const
	get rb_delta by direction More...

Real	get_rb_delta (int const rb_no, int const dir) const
	get rb_delta by direction and rb_number More...

void	set_rb_delta (int const rb_no, int const dir, Real const value)
	set rb_delta by direction and rb_number More...

void	set_rb_deltas (int const dir, utility::vector1< Real > const &)
	set rb_deltas by direction More...

Vector const &	get_rb_center (int const dir) const
	get rb_center by direction More...

void	set_rb_center (const int dir, Stub const &stub, Vector const &center)
	set rb_center by direction More...

Static Public Attributes
static const int	TRANS_X = 1

static const int	TRANS_Y = 2

static const int	TRANS_Z = 3

static const int	ROT_X = 4

static const int	ROT_Y = 5

static const int	ROT_Z = 6

Private Member Functions
int	rb_index (int const dir) const
	get the lookup index into rb_delta and rb_center from the direction dir. More...

Private Attributes
RT	rt_
	translation and rotation More...

utility::vector1 < utility::vector1< Real > >	rb_delta
	changes to translation and rotation More...

utility::vector1< Vector >	rb_center
	the center around which the rotation is performed More...

Friends
std::ostream &	operator<< (std::ostream &os, const Jump &jump)
	stream output operator More...

std::istream &	operator>> (std::istream &is, Jump &jump)
	stream input operator More...

Real	distance (Jump const &a_in, Jump const &b_in)
	RT root squared deviation. More...

Detailed Description

an object which makes rigid-body transformation with translational and rotational perturbation

See AtomTree overview and concepts for details.

Definition at line 43 of file Jump.hh.

Member Typedef Documentation

typedef numeric::xyzMatrix< Real > core::kinematics::Jump::Matrix

Definition at line 53 of file Jump.hh.

typedef numeric::xyzVector< Real > core::kinematics::Jump::Vector

Definition at line 52 of file Jump.hh.

Constructor & Destructor Documentation

core::kinematics::Jump::Jump ( )

inline

construction

Definition at line 57 of file Jump.hh.

core::kinematics::Jump::Jump ( const RT & src_rt)

inline

constructor with only RT

Definition at line 64 of file Jump.hh.

core::kinematics::Jump::Jump	(	Stub const &	stub1,
		Stub const &	stub2
	)

inline

get RT from two stubs and ZERO rb_delta

Definition at line 71 of file Jump.hh.

core::kinematics::Jump::Jump ( const Jump & src)

inline

copy constructor

Definition at line 78 of file Jump.hh.

Member Function Documentation

void core::kinematics::Jump::fold_in_rb_deltas ( )

transform small changes in translation and rotation into jump

Definition at line 76 of file Jump.cc.

References core::kinematics::RT::fold_in_rb_deltas(), rb_center, rb_delta, core::kinematics::RT::reverse(), rt_, and core::kinematics::ZERO.

Referenced by protocols::rigid::RigidBodyPerturbMover::apply(), core::kinematics::distance(), gaussian_move(), gaussian_move_single_rb(), core::kinematics::jump_distance(), random_trans(), core::optimization::symmetry::SymMinimizerMap::reset_jump_rb_deltas(), core::optimization::MinimizerMap::reset_jump_rb_deltas(), reverse(), reversed(), rotation_by_axis(), rotation_by_matrix(), rt(), set_rb_center(), set_rotation(), set_translation(), and translation_along_axis().

void core::kinematics::Jump::from_bond_cst	(	utility::vector1< Vector > &	atoms,
		utility::vector1< Real > const &	csts
	)

get a jump from a bond cst definition

this function translate a virtual bond type constraints into jump transformation. in atoms vector, A1, A2, A3, B1, B2, B3, and A1-B1 forms the virtual bond, like A3-A2-A1—B1-B2-B3 in csts vector, disAB, angleA and B, didedral A, AB and B. B1, B2 and B3 are moved given cst definition.

Definition at line 378 of file Jump.cc.

References distance, core::kinematics::RT::from_stubs(), core::kinematics::Stub::is_orthogonal(), rb_delta, rt_, core::kinematics::Stub::spherical(), and core::kinematics::ZERO.

Referenced by protocols::jumping::ResiduePairJump::build_cst_conformer_jumps().

void core::kinematics::Jump::from_stubs	(	Stub const &	stub1,
		Stub const &	stub2
	)

get a jump from two stubs

Note: : we dont reset rb_center!!!!!!!!!

Definition at line 361 of file Jump.cc.

References core::kinematics::RT::from_stubs(), rb_delta, rt_, and core::kinematics::ZERO.

Referenced by core::kinematics::tree::JumpAtom::update_internal_coords().

utility::vector1< Real > core::kinematics::Jump::gaussian_move	(	int const	dir,
		float const	trans_mag,
		float const	rot_mag
	)

Given the desired magnitude of the translation and rotation components, applies Gaussian perturbation to this jump. Return the move that was applied.

clear existing rb_delta first if any and then apply the gaussian move Return the move that was applied.

Definition at line 169 of file Jump.cc.

References fold_in_rb_deltas(), get_rb_delta(), core::kinematics::jump_RG(), and set_rb_delta().

Referenced by protocols::enzdes::PredesignPerturbMover::apply(), protocols::rigid::RigidBodyPerturbMover::apply(), and protocols::rigid::RigidBodyPerturbNoCenterMover::apply().

void core::kinematics::Jump::gaussian_move_single_rb	(	int const	dir,
		float const	mag,
		int	rb
	)

do a gaussian move along a certain rb direction

Definition at line 182 of file Jump.cc.

References fold_in_rb_deltas(), core::kinematics::jump_RG(), and set_rb_delta().

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

Jump::Vector const & core::kinematics::Jump::get_rb_center ( int const dir) const

inline

get rb_center by direction

Definition at line 324 of file Jump.hh.

References rb_center, and rb_index().

Referenced by core::kinematics::tree::JumpAtom::get_dof_axis_and_end_pos().

const utility::vector1< Real > & core::kinematics::Jump::get_rb_delta ( int const dir) const

inline

get rb_delta by direction

Definition at line 305 of file Jump.hh.

References rb_delta, and rb_index().

Referenced by core::kinematics::tree::JumpAtom::dof(), gaussian_move(), and core::kinematics::tree::JumpAtom::get_dof_axis_and_end_pos().

Real core::kinematics::Jump::get_rb_delta	(	int const	rb_no,
		int const	dir
	)		const

inline

get rb_delta by direction and rb_number

Definition at line 314 of file Jump.hh.

References rb_delta, and rb_index().

Jump::Matrix const & core::kinematics::Jump::get_rotation ( ) const

inline

get rotation matrix

inline definitions for Jump class

Definition at line 285 of file Jump.hh.

References core::kinematics::RT::get_rotation(), and rt_.

Referenced by protocols::electron_density::dockPoseIntoMap(), core::import_pose::atom_tree_diffs::dump_atom_tree_diff(), core::kinematics::jump_distance(), protocols::forge::remodel::RemodelLoopMover::repeat_generation(), and protocols::forge::remodel::RemodelLoopMover::repeat_generation_with_additional_residue().

Jump::Vector const & core::kinematics::Jump::get_translation ( ) const

inline

get translation vector

Definition at line 293 of file Jump.hh.

References core::kinematics::RT::get_translation(), and rt_.

Referenced by protocols::rigid::RigidBodyDofTransMover::apply(), core::import_pose::atom_tree_diffs::dump_atom_tree_diff(), core::kinematics::jump_distance(), protocols::rna::RNA_DeNovoProtocol::randomize_rigid_body_orientations(), protocols::forge::remodel::RemodelLoopMover::repeat_generation(), and protocols::forge::remodel::RemodelLoopMover::repeat_generation_with_additional_residue().

void core::kinematics::Jump::identity_transform ( )

reset to identity matrix, 0 translation

Definition at line 324 of file Jump.cc.

References core::kinematics::RT::identity_transform(), rb_center, rb_delta, rt_, and core::kinematics::ZERO.

void core::kinematics::Jump::make_jump	(	Stub const &	stub1,
		Stub &	stub2
	)		const

make a jump from stub1 to stub2

fold all the rb_delta first and then make the jump. make jump with stubs instead of FArrays

Definition at line 336 of file Jump.cc.

References core::kinematics::RT::fold_in_rb_deltas(), core::kinematics::RT::make_jump(), rb_center, rb_delta, core::kinematics::RT::reverse(), and rt_.

Referenced by protocols::motifs::Motif::place_atom_(), protocols::motifs::Motif::place_atoms_(), protocols::motifs::Motif::place_residue_(), and core::kinematics::tree::JumpAtom::update_xyz_coords().

bool core::kinematics::Jump::nonzero_deltas ( ) const

check whether there is rb_delta not being transformed.

Definition at line 129 of file Jump.cc.

References rb_delta.

Referenced by core::kinematics::operator<<(), and rt().

Jump& core::kinematics::Jump::operator= ( Jump const & src)

inline

copy operator

Definition at line 86 of file Jump.hh.

References rb_center, rb_delta, and rt_.

bool core::kinematics::Jump::ortho_check ( ) const

check RT's orthogonality

Definition at line 68 of file Jump.cc.

References core::kinematics::RT::ortho_check(), and rt_.

Referenced by core::conformation::Conformation::set_jump(), and core::conformation::Conformation::set_jump_now().

void core::kinematics::Jump::random_trans ( const float dist_in)

translate along a randomly chosen vector by dist_in

choose a random unit vector as the direction of translation, by selecting its spherical coordinates phi(0-180) and theta(0-360) then move dist_in along that direction

Definition at line 147 of file Jump.cc.

References fold_in_rb_deltas(), core::kinematics::jump_RG(), protocols::swa::phi(), rt_, and core::kinematics::RT::set_translation().

int core::kinematics::Jump::rb_index ( int const dir) const

inlineprivate

get the lookup index into rb_delta and rb_center from the direction dir.

dir should be 1 or -1

Definition at line 248 of file Jump.hh.

Referenced by get_rb_center(), get_rb_delta(), set_rb_delta(), and set_rb_deltas().

void core::kinematics::Jump::reset ( )

reset RT, rb_delta and rb_center

Definition at line 58 of file Jump.cc.

References rb_center, rb_delta, core::kinematics::RT::reset(), rt_, and core::kinematics::ZERO.

void core::kinematics::Jump::reverse ( )

change the direction of a jump, e.g, upstream stub becomes downstream stub now.

Definition at line 305 of file Jump.cc.

References fold_in_rb_deltas(), core::kinematics::RT::reverse(), and rt_.

Referenced by protocols::rigid::RigidBodyDofTransMover::apply(), protocols::rigid::RigidBodyDofPerturbMover::apply(), protocols::rna::RNA_JumpLibrary::read_jumps_from_file(), and reversed().

Jump core::kinematics::Jump::reversed ( ) const

Return a new jump that is the inverse transformation.

Definition at line 314 of file Jump.cc.

References fold_in_rb_deltas(), and reverse().

Referenced by protocols::motifs::Motif::Motif().

void core::kinematics::Jump::rotation_by_axis	(	Stub const &	stub,
		Vector const &	axis,
		Vector const &	center,
		float const	alpha
	)

make a rotation of alpha degrees around axix and center

stub should be the Stub of the upstream jump. this does a rotation by alpha degrees around the specified the axis and center, both of which are written in xyz frame

Parameters

alpha degrees

Definition at line 269 of file Jump.cc.

References fold_in_rb_deltas(), and rotation_by_matrix().

Referenced by protocols::protein_interface_design::movers::SpinMover::apply(), protocols::nonlocal::HelixRotate::apply(), protocols::rigid::WholeBodyRotationMover::apply(), protocols::rigid::RigidBodySpinMover::apply(), and protocols::rigid::RigidBodyDeterministicSpinMover::apply().

void core::kinematics::Jump::rotation_by_matrix	(	Stub const &	stub,
		Vector const &	center,
		Matrix const &	matrix
	)

make a rotation "matrix" about the center "center"

stub should be the Stub of the upstream jump. This routine has the effect (I think) of rotating the downstream stub by the rotation "matrix" about the center "center", both of which are written in xyz lab frame.

Definition at line 240 of file Jump.cc.

References fold_in_rb_deltas(), core::kinematics::RT::get_rotation(), core::kinematics::RT::get_translation(), core::kinematics::Stub::M, rt_, core::kinematics::RT::set_rotation(), core::kinematics::RT::set_translation(), and core::kinematics::Stub::v.

Referenced by protocols::rigid::RigidBodyRandomizeMover::apply(), protocols::ligand_docking::LigandDockProtocol::optimize_orientation3(), protocols::hotspot_hashing::StubGenerator::placeResidueOnPose(), and rotation_by_axis().

RT core::kinematics::Jump::rt ( ) const

return the RT modeled by this jump –> makes new Jump, calls fold_in_rb_delte and returns RT

Definition at line 501 of file Jump.cc.

References fold_in_rb_deltas(), nonzero_deltas(), and rt_.

Referenced by core::io::silent::BinaryRNASilentStruct::add_jump(), core::io::silent::BinaryProteinSilentStruct::add_jump(), and core::io::silent::ProteinSilentStruct_Template< T >::add_jump().

void core::kinematics::Jump::set_rb_center	(	const int	dir,
		Stub const &	stub,
		Vector const &	center
	)

set rb_center by direction

stub defines the local reference frame for the corresponding direction of the jump (forward == folding direction, backward = reverse) by which to transform center
center is an xyz position in the absolute (protein) reference frame
the column vectors of stub are unit vectors defined in the absolute reference frame( the frame in which center is defined)
so left-multiplying by stub.M.transposed() puts an absolute ref frame vector (like center) into the local jump reference frame
dir is the direction through the jump, 1 == forward == folding order, -1 == backward == reverse folding order
if dir == 1, the stub should be the stub for the downstream jump atom, (eg returned by "folder.downstream_jump_stub( jump_number )" or "downstream_jump_atom.get_stub()" ) and the center is the center of rotation for the downstream segment (ie the segment which is built later during folding). The center determines how the forward rb_deltas are interpreted, and is the center for rigid-body rotation during minimization.
if dir == -1, the stub should be the stub for the upstream jump atom, (eg returned by folder.upstream_jump_stub( jump_number ) ) and the center is the center of rotation for the upstream segment. The center determines how the reverse rb_deltas are interpreted, eg in perturbation moves when we modify the reverse rb-deltas directly, eg in the call "Jump::gaussian_move(-1,tmag,rmag)"

Definition at line 117 of file Jump.cc.

References fold_in_rb_deltas(), core::kinematics::Stub::M, rb_center, and core::kinematics::Stub::v.

Referenced by protocols::enzdes::PredesignPerturbMover::apply(), protocols::rigid::RigidBodyPerturbMover::apply(), protocols::rigid::RigidBodyRandomizeMover::apply(), protocols::rigid::RigidBodySpinMover::apply(), protocols::rigid::RigidBodyDeterministicSpinMover::apply(), and protocols::ligand_docking::LigandDockProtocol::optimize_orientation3().

void core::kinematics::Jump::set_rb_delta	(	int const	rb_no,
		int const	dir,
		Real const	value
	)

set rb_delta by direction and rb_number

Definition at line 196 of file Jump.cc.

References rb_delta, and rb_index().

Referenced by protocols::rigid::RigidBodyMotionMover::apply(), gaussian_move(), gaussian_move_single_rb(), and core::kinematics::tree::JumpAtom::set_dof().

void core::kinematics::Jump::set_rb_deltas	(	int const	dir,
		utility::vector1< Real > const &	rb_deltas
	)

set rb_deltas by direction

Definition at line 207 of file Jump.cc.

References rb_delta, and rb_index().

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

void core::kinematics::Jump::set_rotation ( Matrix const & R_in)

set rotation matrix

Definition at line 214 of file Jump.cc.

References fold_in_rb_deltas(), rt_, and core::kinematics::RT::set_rotation().

Referenced by protocols::electron_density::dockPoseIntoMap(), protocols::forge::remodel::RemodelLoopMover::repeat_generation(), and protocols::forge::remodel::RemodelLoopMover::repeat_generation_with_additional_residue().

void core::kinematics::Jump::set_translation ( Vector const & t)

set translation vector

Definition at line 225 of file Jump.cc.

References fold_in_rb_deltas(), rt_, and core::kinematics::RT::set_translation().

Referenced by protocols::rigid::RigidBodyDofTransMover::apply(), protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::get_base_atr_rep_score(), protocols::swa::rna::StepWiseRNA_ResidueSampler::get_base_atr_rep_score(), protocols::swa::StepWiseScreener::prepare_ghost_pose(), protocols::swa::protein::StepWiseProteinScreener::prepare_ghost_pose(), protocols::rna::RNA_DeNovoProtocol::randomize_rigid_body_orientations(), protocols::forge::remodel::RemodelLoopMover::repeat_generation(), and protocols::forge::remodel::RemodelLoopMover::repeat_generation_with_additional_residue().

void core::kinematics::Jump::translation_along_axis	(	Stub const &	stub,
		Vector const &	axis,
		float const	dist
	)

make a translation along axis by dist

stub should be the Stub of the upstream jump. this does a translation along the axis by dist. the axis is written in xyz frame

Definition at line 290 of file Jump.cc.

References fold_in_rb_deltas(), core::kinematics::RT::get_translation(), core::kinematics::Stub::M, rt_, and core::kinematics::RT::set_translation().

Referenced by protocols::nonlocal::SheetTranslate::apply(), protocols::rigid::WholeBodyTranslationMover::apply(), protocols::rigid::RigidBodyTransMover::apply(), core::scoring::DockingScoreFunction::operator()(), and protocols::hotspot_hashing::StubGenerator::placeResidueOnPose().

Friends And Related Function Documentation

Real distance	(	Jump const &	a_in,
		Jump const &	b_in
	)

friend

RT root squared deviation.

Definition at line 456 of file Jump.cc.

Referenced by from_bond_cst().

std::ostream& operator<<	(	std::ostream &	os,
		const Jump &	jump
	)

friend

stream output operator

Definition at line 424 of file Jump.cc.

std::istream& operator>>	(	std::istream &	is,
		Jump &	jump
	)

friend

stream input operator

Definition at line 409 of file Jump.cc.

Member Data Documentation

utility::vector1< Vector > core::kinematics::Jump::rb_center

private

the center around which the rotation is performed

3x2 table, for each of the two folding directions, the rotation center is written in the local frame of the downstream stub.

Definition at line 275 of file Jump.hh.

Referenced by fold_in_rb_deltas(), get_rb_center(), identity_transform(), make_jump(), core::kinematics::operator<<(), operator=(), core::kinematics::operator>>(), reset(), and set_rb_center().

utility::vector1< utility::vector1<Real> > core::kinematics::Jump::rb_delta

private

changes to translation and rotation

6x2 table, for each of the two folding directions, the first three are for translations along xyz, and the next three are for rotatation around xyz axes.

Definition at line 268 of file Jump.hh.

Referenced by fold_in_rb_deltas(), from_bond_cst(), from_stubs(), get_rb_delta(), identity_transform(), make_jump(), nonzero_deltas(), core::kinematics::operator<<(), operator=(), core::kinematics::operator>>(), reset(), set_rb_delta(), and set_rb_deltas().

const int core::kinematics::Jump::ROT_X = 4

static

Definition at line 48 of file Jump.hh.

const int core::kinematics::Jump::ROT_Y = 5

static

Definition at line 49 of file Jump.hh.

const int core::kinematics::Jump::ROT_Z = 6

static

Definition at line 50 of file Jump.hh.

RT core::kinematics::Jump::rt_

private

translation and rotation

Definition at line 262 of file Jump.hh.

Referenced by core::kinematics::distance(), fold_in_rb_deltas(), from_bond_cst(), from_stubs(), get_rotation(), get_translation(), identity_transform(), make_jump(), core::kinematics::operator<<(), operator=(), core::kinematics::operator>>(), ortho_check(), random_trans(), reset(), reverse(), rotation_by_matrix(), rt(), set_rotation(), set_translation(), and translation_along_axis().

const int core::kinematics::Jump::TRANS_X = 1

static

Definition at line 45 of file Jump.hh.

const int core::kinematics::Jump::TRANS_Y = 2

static

Definition at line 46 of file Jump.hh.

const int core::kinematics::Jump::TRANS_Z = 3

static

Definition at line 47 of file Jump.hh.

The documentation for this class was generated from the following files:

src/core/kinematics/Jump.hh
src/core/kinematics/Jump.cc

Public Types

Public Member Functions

Static Public Attributes

Private Member Functions

Private Attributes

Friends

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation