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

#include <Jump.hh>

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 &)=default
	copy constructor More...

Jump &	operator= (Jump const &)=default
	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...

bool	get_invert_upstream () const

bool	get_invert_downstream () const

void	set_invert (bool upstream, bool downstream)

bool	operator== (Jump const &) const

bool	operator!= (Jump const &other) const

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

static Matrix	mirror_z_transform = numeric::xyzMatrix< core::Real >::rows( 1.,0.,0., 0.,1.,0., 0.,0.,-1. )

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...

bool	invert_upstream_
	are the upstream or downstream residues an inverted coordinate system (Z <- -X cross Y) More...

bool	invert_downstream_

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.

Member Typedef Documentation

◆ Matrix

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

◆ Vector

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

Constructor & Destructor Documentation

◆ Jump() [1/4]

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

inline

construction

◆ Jump() [2/4]

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

inline

constructor with only RT

◆ Jump() [3/4]

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

inline

get RT from two stubs and ZERO rb_delta

◆ Jump() [4/4]

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

default

copy constructor

Member Function Documentation

◆ fold_in_rb_deltas()

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

transform small changes in translation and rotation into jump

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

◆ from_bond_cst()

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.

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().

◆ from_stubs()

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

get a jump from two stubs

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

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

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

◆ gaussian_move()

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.

References fold_in_rb_deltas(), get_rb_delta(), core::scoring::rg, and set_rb_delta().

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

◆ gaussian_move_single_rb()

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

References fold_in_rb_deltas(), core::scoring::rg, and set_rb_delta().

Referenced by protocols::rigid::RigidBodyDofPerturbMover::apply(), and protocols::cryst::DockLatticeMover::perturb_rb().

◆ get_invert_downstream()

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

inline

References invert_downstream_.

Referenced by core::kinematics::tree::JumpAtom::get_dof_axis_and_end_pos(), core::kinematics::tree::JumpAtom::get_inversion(), and core::kinematics::tree::JumpAtom::update_internal_coords().

◆ get_invert_upstream()

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

inline

References invert_upstream_.

Referenced by core::kinematics::tree::JumpAtom::get_dof_axis_and_end_pos(), core::kinematics::tree::JumpAtom::get_inversion(), core::kinematics::tree::JumpAtom::update_internal_coords(), core::kinematics::tree::JumpAtom::update_stub(), and core::kinematics::tree::JumpAtom::update_xyz_coords().

◆ get_rb_center()

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

inline

get rb_center by direction

References rb_center, and rb_index().

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

◆ get_rb_delta() [1/2]

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

inline

get rb_delta by direction

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().

◆ get_rb_delta() [2/2]

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

inline

get rb_delta by direction and rb_number

References rb_delta, and rb_index().

◆ get_rotation()

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

inline

get rotation matrix

inline definitions for Jump class

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

Referenced by protocols::multistage_rosetta_scripts::cluster::metrics::JumpMetric::analyze(), protocols::rigid::UniformRigidBodyMover::apply(), protocols::rigid::RigidBodyDofRandomizeMover::apply(), protocols::matdes::SymDofMover::apply(), core::kinematics::inverse::calculate_new_jump(), protocols::matdes::GetRBDOFValues::compute(), core::import_pose::atom_tree_diffs::dump_atom_tree_diff(), core::scoring::loop_graph::evaluator::SixDTransRotPotential::evaluate(), core::scoring::loop_graph::evaluator::SixDTransRotPotential::get_derivative(), core::scoring::loop_graph::evaluator::SixDTransRotPotentialEvaluator::get_f1_f2(), operator==(), protocols::rna::denovo::output::RNA_FragmentMonteCarloOutputter::output_jump_information(), protocols::forge::remodel::RemodelLoopMover::repeat_generation_with_additional_residue(), protocols::features::PoseConformationFeatures::report_features_implementation(), protocols::environment::ClientMover::sandboxed_copy(), protocols::loop_grower::SheetPositions::SheetPositions(), and protocols::ligand_docking::ga_ligand_dock::LigandConformer::update_conf().

◆ get_translation()

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

inline

get translation vector

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

Referenced by protocols::multistage_rosetta_scripts::cluster::metrics::JumpMetric::analyze(), protocols::rigid::UniformRigidBodyMover::apply(), protocols::cryst::UpdateCrystInfo::apply(), protocols::rigid::RigidBodyDofRandomizeMover::apply(), protocols::rigid::RigidBodyDofTransMover::apply(), protocols::matdes::SymDofMover::apply(), protocols::simple_moves::PeriodicBoxMover::apply(), core::kinematics::inverse::calculate_new_jump(), protocols::simple_moves::PeriodicBoxMover::change_volume_move(), protocols::matdes::GetRBDOFValues::compute(), protocols::simple_moves::PeriodicBoxMover::dump_ASU(), core::import_pose::atom_tree_diffs::dump_atom_tree_diff(), core::scoring::loop_graph::evaluator::SixDTransRotPotential::evaluate(), core::scoring::loop_graph::evaluator::SixDTransRotPotential::get_derivative(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::make_starting_pose_for_virtual_screening(), protocols::recces::sampler::rna::MC_RNA_OneJump::operator++(), operator==(), protocols::rna::denovo::output::RNA_FragmentMonteCarloOutputter::output_jump_information(), protocols::cryst::DockLatticeMover::perturb_lattice(), protocols::simple_moves::PeriodicBoxMover::perturb_molecule_move(), protocols::rna::denovo::movers::RNA_DeNovoMasterMover::randomize_rigid_body_orientations(), protocols::forge::remodel::RemodelLoopMover::repeat_generation_with_additional_residue(), protocols::features::PoseConformationFeatures::report_features_implementation(), protocols::simple_moves::PeriodicBoxMover::report_thermodynamics(), protocols::environment::ClientMover::sandboxed_copy(), protocols::loop_grower::SheetPositions::SheetPositions(), protocols::rna::denovo::coarse::MultipleDomainMover::slide_back_to_origin(), protocols::rna::denovo::coarse::MultipleDomainMover::try_to_slide_into_contact(), and protocols::ligand_docking::ga_ligand_dock::LigandConformer::update_conf().

◆ identity_transform()

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

reset to identity matrix, 0 translation

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

◆ make_jump()

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

References core::kinematics::RT::fold_in_rb_deltas(), invert_downstream_, invert_upstream_, core::kinematics::Stub::M, core::kinematics::RT::make_jump(), mirror_z_transform, rb_center, rb_delta, core::kinematics::RT::reverse(), and rt_.

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

◆ nonzero_deltas()

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

check whether there is rb_delta not being transformed.

References rb_delta, and core::simple_metrics::metrics::sum.

Referenced by rt().

◆ operator!=()

bool core::kinematics::Jump::operator!= ( Jump const & other ) const

inline

References operator==().

◆ operator=()

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

default

copy operator

◆ operator==()

bool core::kinematics::Jump::operator== ( Jump const & other ) const

References get_rotation(), and get_translation().

Referenced by operator!=().

◆ ortho_check()

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

check RT's orthogonality

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

Referenced by core::conformation::Conformation::set_jump().

◆ random_trans()

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

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

Referenced by protocols::topology_broker::BasicJumpClaimer::initialize_dofs().

◆ rb_index()

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

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

◆ reset()

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

reset RT, rb_delta and rb_center

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

◆ reverse()

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

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

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

Referenced by protocols::rigid::RigidBodyDofRandomizeMover::apply(), protocols::rigid::RigidBodyDofTransMover::apply(), protocols::rigid::RigidBodyDofPerturbMover::apply(), protocols::stepwise::sampler::protein::ProteinBetaAntiParallelStepWiseSampler::get_antiparallel_beta_jumps(), core::import_pose::libraries::RNA_JumpLibrary::read_jumps_from_file(), and reversed().

◆ reversed()

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

Return a new jump that is the inverse transformation.

References fold_in_rb_deltas(), and reverse().

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

◆ rotation_by_axis()

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

References core::conformation::membrane::center, fold_in_rb_deltas(), and rotation_by_matrix().

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

◆ rotation_by_matrix()

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.

References core::conformation::membrane::center, 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::docking::EllipsoidalRandomizationMover::apply(), protocols::rigid::RigidBodyRandomizeMover::apply(), protocols::toolbox::apply_superposition_transform_to_jump(), protocols::recces::sampler::rna::MC_RNA_OneJump::operator++(), protocols::ligand_docking::LigandDockProtocol::optimize_orientation3(), protocols::flexpep_docking::FlexPepDockingProtocol::place_peptide_on_binding_site(), protocols::hotspot_hashing::StubGenerator::placeResidueOnPose(), core::pose::symmetry::rotate_anchor_to_x_axis(), and rotation_by_axis().

◆ rt()

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

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

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

Referenced by protocols::rigid::RigidBodyDofPerturbMover::apply(), protocols::rna::denovo::output::RNA_FragmentMonteCarloOutputter::get_output_jump_RT(), protocols::loophash::get_rt_over_leap(), and protocols::loophash::get_rt_over_leap_fast().

◆ set_invert()

void core::kinematics::Jump::set_invert	(	bool	upstream,
		bool	downstream
	)

References invert_downstream_, and invert_upstream_.

Referenced by core::conformation::symmetry::MirrorSymmetricConformation::set_jump(), core::kinematics::tree::JumpAtom::steal_inversion(), and core::conformation::symmetry::MirrorSymmetricConformation::synch_mirror_jumps_with_atomtree().

◆ set_rb_center()

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)"

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

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

◆ set_rb_delta()

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

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().

◆ set_rb_deltas()

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

set rb_deltas by direction

References rb_delta, and rb_index().

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

◆ set_rotation()

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

set rotation matrix

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

Referenced by protocols::rigid::UniformRigidBodyMover::apply(), protocols::rigid::RigidBodyDofRandomizeMover::apply(), protocols::matdes::SymDofMover::apply(), protocols::loop_grower::LoopPartialSolution::apply_sheets(), core::kinematics::inverse::calculate_new_jump(), core::import_pose::atom_tree_diffs::pose_from_atom_tree_diff(), protocols::forge::remodel::RemodelLoopMover::repeat_generation_with_additional_residue(), protocols::toolbox::sample_around::sample_all_rotations_at_jump(), and protocols::ligand_docking::ga_ligand_dock::LigandConformer::to_pose().

◆ set_translation()

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

set translation vector

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

Referenced by protocols::rigid::UniformRigidBodyMover::apply(), protocols::dna::SeparateDnaFromNonDna::apply(), protocols::rigid::RigidBodyDofRandomizeMover::apply(), protocols::rigid::RigidBodyDofTransMover::apply(), protocols::rigid::RigidBodyDofPerturbMover::apply(), protocols::matdes::SymDofMover::apply(), protocols::loop_grower::LoopPartialSolution::apply_sheets(), core::kinematics::inverse::calculate_new_jump(), protocols::simple_moves::PeriodicBoxMover::change_volume_move(), protocols::toolbox::sample_around::do_xy_scan(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::make_starting_pose_for_virtual_screening(), protocols::recces::sampler::rna::MC_RNA_OneJump::operator++(), protocols::cryst::DockLatticeMover::perturb_lattice(), core::import_pose::atom_tree_diffs::pose_from_atom_tree_diff(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::prepare_ghost_pose(), protocols::rna::denovo::movers::RNA_DeNovoMasterMover::randomize_rigid_body_orientations(), protocols::forge::remodel::RemodelLoopMover::repeat_generation_with_additional_residue(), protocols::stepwise::monte_carlo::mover::AddMover::setup_initial_jump(), protocols::rna::denovo::coarse::MultipleDomainMover::slide_back_to_origin(), protocols::stepwise::modeler::split_pose(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::to_pose(), and protocols::rna::denovo::coarse::MultipleDomainMover::try_to_slide_into_contact().

◆ translation_along_axis()

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

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

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

Friends And Related Function Documentation

◆ distance

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

friend

RT root squared deviation.

Referenced by from_bond_cst().

◆ operator<<

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

friend

stream output operator

◆ operator>>

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

friend

stream input operator

Member Data Documentation

◆ invert_downstream_

bool core::kinematics::Jump::invert_downstream_

private

Referenced by get_invert_downstream(), make_jump(), reset(), and set_invert().

◆ invert_upstream_

bool core::kinematics::Jump::invert_upstream_

private

are the upstream or downstream residues an inverted coordinate system (Z <- -X cross Y)

Referenced by get_invert_upstream(), make_jump(), reset(), and set_invert().

◆ mirror_z_transform

numeric::xyzMatrix< core::Real > core::kinematics::Jump::mirror_z_transform = numeric::xyzMatrix< core::Real >::rows( 1.,0.,0., 0.,1.,0., 0.,0.,-1. )

static

Referenced by core::kinematics::tree::JumpAtom::get_dof_axis_and_end_pos(), make_jump(), core::conformation::symmetry::SymmetryTransform::set_mirror_z(), core::kinematics::tree::JumpAtom::update_internal_coords(), core::kinematics::tree::JumpAtom::update_stub(), core::kinematics::tree::BondedAtom::update_xyz_coords(), and core::kinematics::tree::JumpAtom::update_xyz_coords().

◆ rb_center

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.

Referenced by fold_in_rb_deltas(), get_rb_center(), identity_transform(), make_jump(), reset(), and set_rb_center().

◆ rb_delta

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.

Referenced by fold_in_rb_deltas(), from_bond_cst(), from_stubs(), get_rb_delta(), identity_transform(), make_jump(), nonzero_deltas(), reset(), set_rb_delta(), and set_rb_deltas().

◆ ROT_X

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

static

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

◆ ROT_Y

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

static

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

◆ ROT_Z

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

static

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

◆ rt_

RT core::kinematics::Jump::rt_

private

translation and rotation

Referenced by fold_in_rb_deltas(), from_bond_cst(), from_stubs(), get_rotation(), get_translation(), identity_transform(), make_jump(), ortho_check(), random_trans(), reset(), reverse(), rotation_by_matrix(), rt(), set_rotation(), set_translation(), and translation_along_axis().

◆ TRANS_X

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

static

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

◆ TRANS_Y

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

static

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

◆ TRANS_Z

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

static

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

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

◆ Matrix

◆ Vector

Constructor & Destructor Documentation

◆ Jump() [1/4]

◆ Jump() [2/4]

◆ Jump() [3/4]

◆ Jump() [4/4]

Member Function Documentation

◆ fold_in_rb_deltas()

◆ from_bond_cst()

◆ from_stubs()

◆ gaussian_move()

◆ gaussian_move_single_rb()

◆ get_invert_downstream()

◆ get_invert_upstream()

◆ get_rb_center()

◆ get_rb_delta() [1/2]

◆ get_rb_delta() [2/2]

◆ get_rotation()

◆ get_translation()

◆ identity_transform()

◆ make_jump()

◆ nonzero_deltas()

◆ operator!=()

◆ operator=()

◆ operator==()

◆ ortho_check()

◆ random_trans()

◆ rb_index()

◆ reset()

◆ reverse()

◆ reversed()

◆ rotation_by_axis()

◆ rotation_by_matrix()

◆ rt()

◆ set_invert()

◆ set_rb_center()

◆ set_rb_delta()

◆ set_rb_deltas()

◆ set_rotation()

◆ set_translation()

◆ translation_along_axis()

Friends And Related Function Documentation

◆ distance

◆ operator<<

◆ operator>>

Member Data Documentation

◆ invert_downstream_

◆ invert_upstream_

◆ mirror_z_transform

◆ rb_center

◆ rb_delta

◆ ROT_X

◆ ROT_Y

◆ ROT_Z

◆ rt_

◆ TRANS_X

◆ TRANS_Y

◆ TRANS_Z