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

#include <RBSegmentMover.hh>

Public Member Functions
	RBSegmentMover ()
	constructor More...

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

virtual void	apply (core::pose::Pose &pose)=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...

virtual std::string	get_name () const
	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	~Mover ()

virtual MoverSP	create ()

virtual void	apply (core::io::serialization::PipeMap &pmap)

virtual void	parse_state (SerializableState const &state)

virtual void	parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)

virtual void	save_state (SerializableState &state)

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

	Mover (Mover const &other)

Mover &	operator= (Mover const &other)
	assignment operator More...

virtual core::Real	last_proposal_density_ratio ()

std::string const &	type () const

void	set_type (std::string const &setting)

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...

void	set_current_tag (std::string const &new_tag)

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	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...

void	type (const std::string &type_in)

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

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

std::string	get_type () const

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...

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 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...

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

jobdist::BasicJobCOP	get_current_job () const

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

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

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

inline

constructor

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

inline

constructor

Member Function Documentation

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

pure 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.

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 numeric::conversions::radians(), rotation, sa, numeric::xyzMatrix< class >::xx(), numeric::xyzMatrix< class >::xy(), numeric::xyzMatrix< class >::xz(), numeric::xyzMatrix< class >::yx(), numeric::xyzMatrix< class >::yy(), numeric::xyzMatrix< class >::yz(), numeric::xyzMatrix< class >::zx(), numeric::xyzMatrix< class >::zy(), and numeric::xyzMatrix< class >::zz().

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

Apply an arbitrary rotation specified by a rotation matrix.

References core::pose::Pose::batch_set_xyz(), end, numeric::inverse(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), protocols::loops::start, core::pose::Pose::total_residue(), and core::pose::Pose::xyz().

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.

References numeric::conversions::radians(), rotation, and numeric::rotation_matrix().

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(), end, numeric::inverse(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), protocols::loops::start, core::pose::Pose::total_residue(), and core::pose::Pose::xyz().

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(), end, core::conformation::Residue::natoms(), core::pose::Pose::residue(), protocols::loops::start, core::pose::Pose::total_residue(), and core::pose::Pose::xyz().

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 numeric::xyzMatrix< class >::col_x(), numeric::xyzMatrix< class >::col_y(), numeric::xyzMatrix< class >::col_z(), numeric::xyzVector< class >::cross(), numeric::xyzVector< class >::normalize(), numeric::xyzVector< class >::project_normal(), and trans().

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

virtual

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.

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 end, N, core::pose::Pose::residue(), protocols::loops::start, core::pose::Pose::total_residue(), and core::conformation::Residue::xyz().

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.

References numeric::xyzMatrix< class >::clear(), numeric::xyzMatrix< class >::xx(), numeric::xyzMatrix< class >::yy(), and numeric::xyzMatrix< class >::zz().

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

Get the the starting and ending residues of transform.

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

inline

Print debugging info.

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