core::kinematics::RT Class Reference

Rotation + translation class. More...

#include <RT.hh>

Public Types
typedef numeric::xyzVector< Real >	Vector
typedef numeric::xyzMatrix< Real >	Matrix
typedef void	iterator_category
typedef void	difference_type

Public Member Functions
	RT ()
	Default constructor. More...
	RT (Matrix const &rot, Vector const &vec)
	matrix/vector constructor More...
	RT (Stub const &stub1, Stub const &stub2)
	construct from two stubs More...
	RT (RT const &src)
	copy constructor More...
void	from_stubs (Stub const &stub1, Stub const &stub2)
	update from stubs More...
void	reverse ()
	reverse the "view" More...
void	inverse ()
	reverse the "view" More...
void	reset ()
	return to default-constructed state More...
void	identity_transform ()
	return to default-constructed state (another name) More...
void	set_translation (Vector const &t)
	set the tranlsation More...
void	set_rotation (Matrix const &r)
	set the rotation More...
Matrix const &	get_rotation () const
	get the rotation More...
Vector const &	get_translation () const
	get the translation More...
Real	distance_squared (RT const &b) const
void	fold_in_rb_deltas (utility::vector1< Real > const &rb, Vector const &rb_center)
	update the transform to include small additional rigid-body rotations and translations More...
void	make_jump (Stub const &stub1, Stub &stub2) const
	should be inverse of RT::from_stubs More...
RT &	operator= (RT const &)=default
	copy operator More...
bool	ortho_check () const
	check for orthogonality More...

Private Attributes
Matrix	rotation
	rotation matrix, written in stub1 frame More...
Vector	translation
	tranlsation vector, written in stub1 frame More...

Friends
std::ostream &	operator<< (std::ostream &os, RT const &rt)
	output operator More...
std::istream &	operator>> (std::istream &is, RT &rt)
	input operator More...
Real	distance (RT const &a, RT const &b)
	root squared devitation of two RTs More...

Detailed Description

Rotation + translation class.

Note

Used in jumps

Member Typedef Documentation

difference_type

typedef void core::kinematics::RT::difference_type

iterator_category

typedef void core::kinematics::RT::iterator_category

Matrix

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

Vector

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

Constructor & Destructor Documentation

RT() [1/4]

core::kinematics::RT::RT ( )

inline

Default constructor.

RT() [2/4]

core::kinematics::RT::RT ( Matrix const &  rot, Vector const &  vec  )

inline

matrix/vector constructor

RT() [3/4]

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

inline

construct from two stubs

References from_stubs().

RT() [4/4]

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

inline

copy constructor

Member Function Documentation

distance_squared()

Real core::kinematics::RT::distance_squared ( RT const &  b ) const

inline

References protocols::match::upstream::b, rotation, and translation.

Referenced by core::scoring::constraints::RTConstraint::dist(), and core::kinematics::AtomTree::insert_single_fragment().

fold_in_rb_deltas()

void core::kinematics::RT::fold_in_rb_deltas	(	utility::vector1< Real > const &	rb,
		Vector const &	rb_center
	)

update the transform to include small additional rigid-body rotations and translations

Note

PHIL: IT WOULD BE GOOD TO ELIMINATE ARGUMENT ARRAYS IN MINI BY USE OF APPROPRIATE LAYERED DATA STRUCTURES

rb are the small changes in translation and rotation, written in up-stream (jump_start) rb_center is the center of rotation, written in the down-stream (jump_end)

References rotation, and translation.

Referenced by core::kinematics::Jump::fold_in_rb_deltas(), and core::kinematics::Jump::make_jump().

from_stubs()

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

update from stubs

References core::kinematics::Stub::M, rotation, translation, and core::kinematics::Stub::v.

Referenced by core::kinematics::Jump::from_bond_cst(), core::kinematics::Jump::from_stubs(), and RT().

get_rotation()

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

inline

get the rotation

References rotation.

Referenced by core::kinematics::jacobian::calculate_error_twist(), protocols::cryst::crystRMSfast(), core::kinematics::find_stub_transform(), protocols::sic_dock::get_leap_6dof(), core::kinematics::Jump::get_rotation(), protocols::loophash::get_rt_over_leap(), protocols::loophash::get_rt_over_leap_fast(), protocols::loophash::get_rt_over_leap_without_foldtree_bs(), core::kinematics::AtomTree::insert_single_fragment(), core::scoring::constraints::RTConstraint::operator==(), protocols::hotspot_hashing::StubGenerator::placeResidueOnPose(), core::kinematics::Jump::rotation_by_matrix(), core::scoring::motif::rt_to_real6(), core::scoring::disulfides::DisulfideMatchingPotential::score_disulfide(), protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::update_current(), and core::kinematics::jacobian::ModuleType1::update_screw_vectors().

get_translation()

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

inline

get the translation

References translation.

Referenced by protocols::rigid::RigidBodyDofPerturbMover::apply(), core::kinematics::jacobian::calculate_error_twist(), protocols::sic_dock::count_linkers(), protocols::cryst::crystRMSfast(), core::kinematics::find_stub_transform(), protocols::sic_dock::get_leap_6dof(), protocols::loophash::get_rt_over_leap(), protocols::loophash::get_rt_over_leap_fast(), protocols::loophash::get_rt_over_leap_without_foldtree_bs(), core::kinematics::Jump::get_translation(), core::kinematics::AtomTree::insert_single_fragment(), core::scoring::constraints::RTConstraint::operator==(), protocols::hotspot_hashing::StubGenerator::placeResidueOnPose(), core::kinematics::Jump::rotation_by_matrix(), core::scoring::motif::rt_to_real6(), core::scoring::disulfides::DisulfideMatchingPotential::score_disulfide(), core::kinematics::Jump::translation_along_axis(), protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::update_current(), and core::kinematics::jacobian::ModuleType1::update_screw_vectors().

identity_transform()

void core::kinematics::RT::identity_transform ( )

inline

return to default-constructed state (another name)

References rotation, and translation.

Referenced by core::kinematics::Jump::identity_transform().

inverse()

void core::kinematics::RT::inverse ( )

inline

reverse the "view"

References reverse().

Referenced by core::scoring::constraints::RTConstraint::fill_f1_f2().

make_jump()

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

should be inverse of RT::from_stubs

References core::kinematics::Stub::M, rotation, translation, and core::kinematics::Stub::v.

Referenced by protocols::simple_filters::JumpEvaluator::apply(), core::kinematics::AtomTree::get_frag_local_stub(), core::kinematics::Jump::make_jump(), protocols::hotspot_hashing::ComposeSearchPatterns::Searchpoints(), and protocols::hotspot_hashing::SICPatternAtTransform::Searchpoints().

operator=()

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

default

copy operator

ortho_check()

bool core::kinematics::RT::ortho_check

(

)

const

check for orthogonality

References rotation.

Referenced by core::kinematics::Jump::ortho_check().

reset()

void core::kinematics::RT::reset ( )

inline

return to default-constructed state

References rotation, and translation.

Referenced by core::kinematics::Jump::reset().

reverse()

void core::kinematics::RT::reverse ( )

inline

reverse the "view"

References rotation, and translation.

Referenced by core::kinematics::Jump::fold_in_rb_deltas(), inverse(), core::kinematics::Jump::make_jump(), protocols::jumping::PairingLibrary::read_from_file(), core::kinematics::Jump::reverse(), and core::kinematics::AtomTree::set_stub_transform().

set_rotation()

void core::kinematics::RT::set_rotation ( Matrix const &  r )

inline

set the rotation

References rotation.

Referenced by protocols::jumping::dis_RT_from_epos(), core::kinematics::Jump::rotation_by_matrix(), protocols::jumping::RT_from_epos(), core::scoring::disulfides::RT_helper::RT_from_epos(), and core::kinematics::Jump::set_rotation().

set_translation()

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

inline

set the tranlsation

References protocols::hybridization::t, and translation.

Referenced by protocols::jumping::dis_RT_from_epos(), core::kinematics::Jump::random_trans(), core::kinematics::Jump::rotation_by_matrix(), protocols::jumping::RT_from_epos(), core::scoring::disulfides::RT_helper::RT_from_epos(), core::kinematics::Jump::set_translation(), and core::kinematics::Jump::translation_along_axis().

Friends And Related Function Documentation

distance

Real distance ( RT const &  a, RT const &  b  )

friend

root squared devitation of two RTs

operator<<

std::ostream& operator<< ( std::ostream &  os, RT const &  rt  )

friend

output operator

operator>>

std::istream& operator>> ( std::istream &  is, RT &  rt  )

friend

input operator

Member Data Documentation

rotation

Matrix core::kinematics::RT::rotation

private

rotation matrix, written in stub1 frame

Referenced by distance_squared(), fold_in_rb_deltas(), from_stubs(), get_rotation(), identity_transform(), make_jump(), ortho_check(), reset(), reverse(), and set_rotation().

translation

Vector core::kinematics::RT::translation

private

tranlsation vector, written in stub1 frame

Referenced by distance_squared(), fold_in_rb_deltas(), from_stubs(), get_translation(), identity_transform(), make_jump(), reset(), reverse(), and set_translation().

---

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

• src/core/kinematics/RT.hh
• src/core/kinematics/RT.cc