#include <RBSegmentMover.hh>

Inheritance diagram for protocols::rbsegment_relax::SequenceShiftMover:

[legend]

Public Member Functions
	SequenceShiftMover (RBSegment const &seg, core::Size magnitude=4)
	constructor More...

	SequenceShiftMover (core::pose::Pose const &pose_in, RBSegment const &seg, core::Size magnitude=4)
	constructor More...

	SequenceShiftMover (RBResidueRange const &rb, core::Size magnitude=4)
	constructor More...

	SequenceShiftMover ()

protocols::moves::MoverOP	clone () const override
	clone this object More...

void	set_movement (core::Real, core::Real, core::Real, core::Real) override
	set movement parameters. ignore all input args More...

void	apply (core::pose::Pose &pose) override
	Apply a + or - residue "shift" to this helix. More...

void	apply (core::pose::Pose &pose, int shift)
	Apply a + or - residue "shift" to this helix. More...

void	set_extra_penalty (utility::vector1< bool > const &penalty_res)
	Set an extra block-shift penalty at certain residues. More...

void	trigger_accept ()
	Last move accepted; update offsets_. More...

int	score (bool step_fn=false)
	Return a score: the minimum number of block shifts accumulated. More...

void	set_verbose (bool inval)

loops::LoopsOP	get_residues_to_rebuild ()
	IF ref_pose is given, get a list of residues to rebuild via fragment insertion. More...

Public Member Functions inherited from protocols::rbsegment_relax::RBSegmentMover
	RBSegmentMover ()
	constructor More...

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

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

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

Private Attributes
core::Size	magnitude_

int	last_move_

core::pose::Pose	ref_pose_

utility::vector1< int >	offsets_

utility::vector1< bool >	penalty_res_

bool	verbose_

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...

Protected Member Functions inherited from protocols::rbsegment_relax::RBSegmentMover
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 inherited from protocols::rbsegment_relax::RBSegmentMover
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 inherited from protocols::rbsegment_relax::RBSegmentMover
RBSegment	segment_

Detailed Description

"Register shift" a segment by one amino-acid Works in both centroid and all-atom

Constructor & Destructor Documentation

◆ SequenceShiftMover() [1/4]

protocols::rbsegment_relax::SequenceShiftMover::SequenceShiftMover	(	RBSegment const &	seg,
		core::Size	magnitude = `4`
	)

inline

constructor

◆ SequenceShiftMover() [2/4]

protocols::rbsegment_relax::SequenceShiftMover::SequenceShiftMover	(	core::pose::Pose const &	pose_in,
		RBSegment const &	seg,
		core::Size	magnitude = `4`
	)

inline

constructor

References protocols::hybridization::get_num_residues_nonvirt(), and offsets_.

◆ SequenceShiftMover() [3/4]

protocols::rbsegment_relax::SequenceShiftMover::SequenceShiftMover	(	RBResidueRange const &	rb,
		core::Size	magnitude = `4`
	)

inline

constructor

◆ SequenceShiftMover() [4/4]

protocols::rbsegment_relax::SequenceShiftMover::SequenceShiftMover ( )

inline

Member Function Documentation

◆ apply() [1/2]

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

overridevirtual

Apply a + or - residue "shift" to this helix.

Apply a "register shift" move to this fragment.

Implements protocols::rbsegment_relax::RBSegmentMover.

References core::scoring::rg.

Referenced by protocols::rbsegment_relax::OptimizeThreadingMover::apply().

◆ apply() [2/2]

void protocols::rbsegment_relax::SequenceShiftMover::apply	(	core::pose::Pose &	pose,
		int	shift
	)

Apply a + or - residue "shift" to this helix.

References core::conformation::Residue::atom(), core::pose::Pose::batch_set_xyz(), core::sequence::end, protocols::hybridization::get_num_residues_nonvirt(), core::conformation::Residue::is_protein(), protocols::mean_field::max(), protocols::mean_field::min(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), protocols::loops::start, protocols::rbsegment_relax::TR(), core::conformation::Atom::xyz(), and core::pose::Pose::xyz().

◆ clone()

protocols::moves::MoverOP protocols::rbsegment_relax::SequenceShiftMover::clone ( ) const

inlineoverridevirtual

clone this object

Reimplemented from protocols::moves::Mover.

◆ get_name()

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

overrideprivatevirtual

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

Reimplemented from protocols::rbsegment_relax::RBSegmentMover.

◆ get_residues_to_rebuild()

loops::LoopsOP protocols::rbsegment_relax::SequenceShiftMover::get_residues_to_rebuild ( )

IF ref_pose is given, get a list of residues to rebuild via fragment insertion.

Referenced by protocols::rbsegment_relax::OptimizeThreadingMover::apply().

◆ score()

int protocols::rbsegment_relax::SequenceShiftMover::score ( bool step_fn = false )

Return a score: the minimum number of block shifts accumulated.

References protocols::loops::start.

Referenced by protocols::rbsegment_relax::OptimizeThreadingMover::apply().

◆ set_extra_penalty()

void protocols::rbsegment_relax::SequenceShiftMover::set_extra_penalty ( utility::vector1< bool > const & penalty_res )

inline

Set an extra block-shift penalty at certain residues.

References penalty_res_.

Referenced by protocols::rbsegment_relax::OptimizeThreadingMover::apply().

◆ set_movement()

void protocols::rbsegment_relax::SequenceShiftMover::set_movement	(	core::Real	,
		core::Real	,
		core::Real	,
		core::Real
	)

inlineoverridevirtual

set movement parameters. ignore all input args

Reimplemented from protocols::rbsegment_relax::RBSegmentMover.

◆ set_verbose()

void protocols::rbsegment_relax::SequenceShiftMover::set_verbose ( bool inval )

inline

References verbose_.

◆ trigger_accept()

void protocols::rbsegment_relax::SequenceShiftMover::trigger_accept ( )

Last move accepted; update offsets_.

References protocols::loops::start.

Referenced by protocols::rbsegment_relax::OptimizeThreadingMover::apply().

Member Data Documentation

◆ last_move_

int protocols::rbsegment_relax::SequenceShiftMover::last_move_

private

◆ magnitude_

core::Size protocols::rbsegment_relax::SequenceShiftMover::magnitude_

private

◆ offsets_

utility::vector1< int > protocols::rbsegment_relax::SequenceShiftMover::offsets_

private

Referenced by SequenceShiftMover().

◆ penalty_res_

utility::vector1< bool > protocols::rbsegment_relax::SequenceShiftMover::penalty_res_

private

Referenced by set_extra_penalty().

◆ ref_pose_

core::pose::Pose protocols::rbsegment_relax::SequenceShiftMover::ref_pose_

private

◆ verbose_

bool protocols::rbsegment_relax::SequenceShiftMover::verbose_

private

Referenced by set_verbose().

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

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ SequenceShiftMover() [1/4]

◆ SequenceShiftMover() [2/4]

◆ SequenceShiftMover() [3/4]

◆ SequenceShiftMover() [4/4]

Member Function Documentation

◆ apply() [1/2]

◆ apply() [2/2]

◆ clone()

◆ get_name()

◆ get_residues_to_rebuild()

◆ score()

◆ set_extra_penalty()

◆ set_movement()

◆ set_verbose()

◆ trigger_accept()

Member Data Documentation

◆ last_move_

◆ magnitude_

◆ offsets_

◆ penalty_res_

◆ ref_pose_

◆ verbose_