Performs a rigid-body movement on a segment of a protein Derived classes must implement 'getCoordinateTransform' and 'apply'. More...

#include <RBSegmentMover.hh>

Inheritance diagram for protocols::rbsegment_relax::RBSegmentMover:

[legend]

Public Member Functions
	RBSegmentMover ()
	constructor More...

	RBSegmentMover (RBSegment const &seg)
	constructor More...

void	apply (core::pose::Pose &pose) override=0
	Apply the rigid-body fragment mover to a pose. Must be defined by derived classes. More...

virtual void	set_segment (RBSegment const &seg)
	Set the segment this mover is working on. More...

std::string	get_name () const override
	Each derived class must specify its name. The class name. More...

virtual void	getCoordinateTransformation (core::pose::Pose const &, numeric::xyzVector< core::Real > &rotationCenter, numeric::xyzMatrix< core::Real > &coordinateTransform)
	Returns: (a) the matrix that rotates global coordinates into local fragment coordinates and (b) the center of rotation of the fragment. Default implementation sets them to global coords. More...

virtual void	set_movement (core::Real p1=0.0, core::Real p2=0.0, core::Real p3=0.0, core::Real p4=0.0)
	Set mover-specific movement parameters. Do nothing by default. More...

virtual void	set_movement (RBSegment const &rb)
	steal movement params from a segment definition More...

void	applyRotation (core::pose::Pose &pose, core::Real alpha, core::Real beta, core::Real gamma)
	Apply an arbitrary rotation specified by Euler angles (in degrees!) More...

void	applyRotation (core::pose::Pose &pose, numeric::xyzMatrix< core::Real > rotation)
	Apply an arbitrary rotation specified by a rotation matrix. More...

void	applyTranslation (core::pose::Pose &pose, numeric::xyzVector< core::Real > translation)
	Apply an arbitrary translation. More...

void	applyTransformation (core::pose::Pose &pose, numeric::xyzMatrix< core::Real > rotation, numeric::xyzVector< core::Real > translation)
	Apply a rotation followed by a translation (does not recompute coordinate transformation between the two!) More...

void	applySpin (core::pose::Pose &pose, numeric::xyzVector< core::Real > rotationAxis, core::Real degrees)
	Apply a spin of the specified angle (in degrees) about arbitrary axis. More...

void	setResidueRange (RBSegment const &seg)
	(re)set the starting and ending residues of this transform More...

RBSegment const &	getResidueRange ()
	Get the the starting and ending residues of transform. More...

void	print ()
	Print debugging info. More...

Public Member Functions inherited from protocols::moves::Mover
	Mover ()

virtual MoverOP	create ()

MoverCOP	get_self_ptr () const

MoverOP	get_self_ptr ()

MoverCAP	get_self_weak_ptr () const

MoverAP	get_self_weak_ptr ()

	Mover (std::string const &type_name)
	sets the type for a mover; name_ has been removed (2010/05/14) More...

virtual void	test_move (Pose &pose)
	: Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More...

virtual MoverOP	clone () const
	Return a clone of the Mover object. More...

virtual bool	reinitialize_for_each_job () const
	Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More...

virtual bool	reinitialize_for_new_input () const
	Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose). More...

virtual MoverOP	fresh_instance () const
	Generates a new Mover object freshly created with the default ctor. More...

MoverStatus	get_last_move_status () const
	end parser interface, start Job Distributor interface///////////// More...

void	reset_status ()
	resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More...

virtual core::pose::PoseOP	get_additional_output ()
	Mechanism by which a mover may return multiple output poses from a single input pose. More...

void	set_type (std::string const &setting)
	Set the 'type' string. More...

std::string	get_type () const

void	type (const std::string &type_in)
	Set the 'type' string. More...

std::string const &	type () const
	Get the set 'type' string. More...

virtual void	set_input_pose (PoseCOP pose)
	setter for poses contained for rms More...

virtual void	set_native_pose (PoseCOP pose)
	setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...

PoseCOP	get_input_pose () const

PoseCOP	get_native_pose () const

virtual void	parse_my_tag (TagCOP tag, basic::datacache::DataMap &data)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

void	set_current_job (protocols::jobdist::BasicJobCOP job)

jobdist::BasicJobCOP	get_current_job () const

virtual void	set_current_tag (std::string const &new_tag)

std::string	get_current_tag () const
	A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More...

virtual void	show (std::ostream &output=std::cout) const
	Outputs details about the Mover, including current settings. More...

virtual core::Real	last_proposal_density_ratio ()

virtual void	clear_info ()
	Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More...

virtual Strings &	info ()
	non-const accessor More...

virtual Strings const &	info () const
	const accessor More...

virtual void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

Protected Member Functions
numeric::xyzVector< core::Real >	getCoM (core::pose::Pose const &pose)
	Helper function computes center of mass of the segment in the pose. More...

Protected Member Functions inherited from protocols::moves::Mover
void	set_last_move_status (MoverStatus status)
	nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More...

Static Protected Member Functions
static numeric::xyzMatrix< core::Real >	coordTransformFromThreePoints (numeric::xyzVector< core::Real > ori, numeric::xyzVector< core::Real > zAxis, numeric::xyzVector< core::Real > xzPlane)
	Helper function to get a coordinate transformation from 3 points: the origin, a point specifying the +z axis, and a point specifying the x-z plane. More...

Protected Attributes
RBSegment	segment_

Additional Inherited Members
Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP	TagCOP

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

typedef std::list< std::string >	Strings

Static Public Member Functions inherited from protocols::moves::Mover
static std::string	name ()

static void	register_options ()
	Overload this static method if you access options within the mover. More...

Detailed Description

Performs a rigid-body movement on a segment of a protein Derived classes must implement 'getCoordinateTransform' and 'apply'.

Constructor & Destructor Documentation

◆ RBSegmentMover() [1/2]

protocols::rbsegment_relax::RBSegmentMover::RBSegmentMover ( )

inline

constructor

◆ RBSegmentMover() [2/2]

protocols::rbsegment_relax::RBSegmentMover::RBSegmentMover ( RBSegment const & seg )

inline

constructor

Member Function Documentation

◆ apply()

void protocols::rbsegment_relax::RBSegmentMover::apply ( core::pose::Pose & pose )

overridepure virtual

Apply the rigid-body fragment mover to a pose. Must be defined by derived classes.

Implements protocols::moves::Mover.

Implemented in protocols::rbsegment_relax::StrandTwistingMover, protocols::rbsegment_relax::GaussianRBSegmentMover, protocols::rbsegment_relax::SequenceShiftMover, and protocols::rbsegment_relax::HelicalGaussianMover.

◆ applyRotation() [1/2]

void protocols::rbsegment_relax::RBSegmentMover::applyRotation	(	core::pose::Pose &	pose,
		core::Real	alpha,
		core::Real	beta,
		core::Real	gamma
	)

inline

Apply an arbitrary rotation specified by Euler angles (in degrees!)

References core::scoring::sa.

◆ applyRotation() [2/2]

void protocols::rbsegment_relax::RBSegmentMover::applyRotation	(	core::pose::Pose &	pose,
		numeric::xyzMatrix< core::Real >	rotation
	)

Apply an arbitrary rotation specified by a rotation matrix.

◆ applySpin()

void protocols::rbsegment_relax::RBSegmentMover::applySpin	(	core::pose::Pose &	pose,
		numeric::xyzVector< core::Real >	rotationAxis,
		core::Real	degrees
	)

Apply a spin of the specified angle (in degrees) about arbitrary axis.

◆ applyTransformation()

void protocols::rbsegment_relax::RBSegmentMover::applyTransformation	(	core::pose::Pose &	pose,
		numeric::xyzMatrix< core::Real >	rotation,
		numeric::xyzVector< core::Real >	translation
	)

Apply a rotation followed by a translation (does not recompute coordinate transformation between the two!)

References core::pose::Pose::batch_set_xyz(), core::sequence::end, protocols::mean_field::max(), protocols::mean_field::min(), core::pose::Pose::residue(), core::pose::Pose::size(), protocols::loops::start, and core::pose::Pose::xyz().

◆ applyTranslation()

void protocols::rbsegment_relax::RBSegmentMover::applyTranslation	(	core::pose::Pose &	pose,
		numeric::xyzVector< core::Real >	translation
	)

Apply an arbitrary translation.

References core::pose::Pose::batch_set_xyz(), core::sequence::end, protocols::mean_field::max(), protocols::mean_field::min(), core::pose::Pose::residue(), core::pose::Pose::size(), protocols::loops::start, and core::pose::Pose::xyz().

◆ coordTransformFromThreePoints()

numeric::xyzMatrix< Real > protocols::rbsegment_relax::RBSegmentMover::coordTransformFromThreePoints	(	numeric::xyzVector< core::Real >	ori,
		numeric::xyzVector< core::Real >	zAxis,
		numeric::xyzVector< core::Real >	xzPlane
	)

staticprotected

Helper function to get a coordinate transformation from 3 points: the origin, a point specifying the +z axis, and a point specifying the x-z plane.

References trans().

◆ get_name()

std::string protocols::rbsegment_relax::RBSegmentMover::get_name ( ) const

overridevirtual

Each derived class must specify its name. The class name.

Implements protocols::moves::Mover.

Reimplemented in protocols::rbsegment_relax::StrandTwistingMover, protocols::rbsegment_relax::GaussianRBSegmentMover, protocols::rbsegment_relax::SequenceShiftMover, and protocols::rbsegment_relax::HelicalGaussianMover.

◆ getCoM()

numeric::xyzVector< Real > protocols::rbsegment_relax::RBSegmentMover::getCoM ( core::pose::Pose const & pose )

inlineprotected

Helper function computes center of mass of the segment in the pose.

References core::sequence::end, protocols::mean_field::max(), protocols::mean_field::min(), core::chemical::element::N, core::pose::Pose::residue(), core::pose::Pose::size(), protocols::loops::start, and core::conformation::Residue::xyz().

◆ getCoordinateTransformation()

virtual void protocols::rbsegment_relax::RBSegmentMover::getCoordinateTransformation	(	core::pose::Pose const &	,
		numeric::xyzVector< core::Real > &	rotationCenter,
		numeric::xyzMatrix< core::Real > &	coordinateTransform
	)

inlinevirtual

Returns: (a) the matrix that rotates global coordinates into local fragment coordinates and (b) the center of rotation of the fragment. Default implementation sets them to global coords.

Reimplemented in protocols::rbsegment_relax::StrandTwistingMover, protocols::rbsegment_relax::GaussianRBSegmentMover, and protocols::rbsegment_relax::HelicalGaussianMover.

◆ getResidueRange()

RBSegment const & protocols::rbsegment_relax::RBSegmentMover::getResidueRange ( )

Get the the starting and ending residues of transform.

◆ print()

void protocols::rbsegment_relax::RBSegmentMover::print ( )

inline

Print debugging info.

References protocols::rbsegment_relax::RBSegment::nContinuousSegments(), and segment_.

◆ set_movement() [1/2]

void protocols::rbsegment_relax::RBSegmentMover::set_movement	(	core::Real	p1 = `0.0`,
		core::Real	p2 = `0.0`,
		core::Real	p3 = `0.0`,
		core::Real	p4 = `0.0`
	)

virtual

Set mover-specific movement parameters. Do nothing by default.

Reimplemented in protocols::rbsegment_relax::SequenceShiftMover, protocols::rbsegment_relax::StrandTwistingMover, protocols::rbsegment_relax::GaussianRBSegmentMover, and protocols::rbsegment_relax::HelicalGaussianMover.

Referenced by set_movement().

◆ set_movement() [2/2]

virtual void protocols::rbsegment_relax::RBSegmentMover::set_movement ( RBSegment const & rb )

inlinevirtual

steal movement params from a segment definition

References protocols::rbsegment_relax::RBSegment::get_movement(), and set_movement().

◆ set_segment()

virtual void protocols::rbsegment_relax::RBSegmentMover::set_segment ( RBSegment const & seg )

inlinevirtual

Set the segment this mover is working on.

References segment_.

Referenced by protocols::rbsegment_relax::OptimizeThreadingMover::apply(), and protocols::rbsegment_relax::ConfChangeMover::stage1().

◆ setResidueRange()

void protocols::rbsegment_relax::RBSegmentMover::setResidueRange ( RBSegment const & seg )

(re)set the starting and ending residues of this transform

Member Data Documentation

◆ segment_

RBSegment protocols::rbsegment_relax::RBSegmentMover::segment_

protected

Referenced by print(), and set_segment().

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

src/protocols/rbsegment_relax/RBSegmentMover.hh
src/protocols/rbsegment_relax/RBSegmentMover.cc

Public Member Functions

Protected Member Functions

Static Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ RBSegmentMover() [1/2]

◆ RBSegmentMover() [2/2]

Member Function Documentation

◆ apply()

◆ applyRotation() [1/2]

◆ applyRotation() [2/2]

◆ applySpin()

◆ applyTransformation()

◆ applyTranslation()

◆ coordTransformFromThreePoints()

◆ get_name()

◆ getCoM()

◆ getCoordinateTransformation()

◆ getResidueRange()

◆ print()

◆ set_movement() [1/2]

◆ set_movement() [2/2]

◆ set_segment()

◆ setResidueRange()

Member Data Documentation

◆ segment_