#include <HelixRotate.hh>

Inheritance diagram for protocols::nonlocal::HelixRotate:

[legend]

Public Member Functions
	HelixRotate ()

	HelixRotate (const protocols::loops::Loop &helix, core::Real degrees)

void	apply (core::pose::Pose &pose) override
	Rotates the helix by the specified number of degrees. More...

std::string	get_name () const override
	Returns the protocol's name. More...

moves::MoverOP	clone () const override
	Creates a new instance with the copy constructor. More...

moves::MoverOP	fresh_instance () const override
	Creates a new instance with the default constructor. More...

const protocols::loops::Loop &	get_helix () const
	Returns the helix to be modified. More...

core::Real	get_degrees () const
	Returns the number of degrees to rotate the helix. More...

void	set_helix (const protocols::loops::Loop &helix)
	Updates the helix to be modified. More...

void	set_degrees (core::Real degrees)
	Updates the number of degrees to rotate the helix. 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...

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
void	initialize (const protocols::loops::Loop &helix, core::Real degrees)
	Shared initialization routine. More...

bool	is_valid () const
	Returns true if this instance is valid and fully configured. More...

void	decompose_structure (unsigned num_residues, protocols::loops::Loops *chunks) const
	Partitions the structure such that the helix to be rotated belongs to its own chunk, which will be subsequently connected to the star fold tree by its own jump. More...

unsigned	jump_containing_helix (const protocols::loops::Loops &chunks) const
	Searches chunks for the member representing the helix, returning its index. More...

void	get_rotation_parameters (const core::pose::Pose &pose, numeric::xyzVector< core::Real > axis, numeric::xyzVector< core::Real > point) const
	Computes rotational parameters– axis and point. More...

Private Attributes
protocols::loops::Loop	helix_
	Stretch of contiguous residues representing the helix to be rotated. More...

core::Real	degrees_
	Number of degrees to rotate the helix. More...

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::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...

Constructor & Destructor Documentation

◆ HelixRotate() [1/2]

protocols::nonlocal::HelixRotate::HelixRotate ( )

References initialize().

◆ HelixRotate() [2/2]

protocols::nonlocal::HelixRotate::HelixRotate	(	const protocols::loops::Loop &	helix,
		core::Real	degrees
	)

References protocols::loops::loop_closure::ccd::helix, and initialize().

Member Function Documentation

◆ apply()

void protocols::nonlocal::HelixRotate::apply ( core::pose::Pose & pose )

overridevirtual

Rotates the helix by the specified number of degrees.

Implements protocols::moves::Mover.

References core::pose::Pose::conformation(), decompose_structure(), core::pose::Pose::fold_tree(), get_degrees(), get_helix(), get_rotation_parameters(), is_valid(), core::pose::Pose::jump(), jump_containing_helix(), core::kinematics::Jump::rotation_by_axis(), core::pose::Pose::set_jump(), protocols::nonlocal::StarTreeBuilder::set_up(), core::pose::Pose::size(), protocols::nonlocal::StarTreeBuilder::tear_down(), protocols::nonlocal::TR(), and core::conformation::Conformation::upstream_jump_stub().

◆ clone()

moves::MoverOP protocols::nonlocal::HelixRotate::clone ( ) const

overridevirtual

Creates a new instance with the copy constructor.

Reimplemented from protocols::moves::Mover.

◆ decompose_structure()

void protocols::nonlocal::HelixRotate::decompose_structure	(	unsigned	num_residues,
		protocols::loops::Loops *	chunks
	)		const

private

Partitions the structure such that the helix to be rotated belongs to its own chunk, which will be subsequently connected to the star fold tree by its own jump.

References protocols::loops::Loops::add_loop(), get_helix(), protocols::loops::Loops::sequential_order(), protocols::loops::Loop::start(), protocols::loops::start, protocols::loops::Loop::stop(), and protocols::loops::stop.

Referenced by apply().

◆ fresh_instance()

moves::MoverOP protocols::nonlocal::HelixRotate::fresh_instance ( ) const

overridevirtual

Creates a new instance with the default constructor.

Reimplemented from protocols::moves::Mover.

◆ get_degrees()

core::Real protocols::nonlocal::HelixRotate::get_degrees ( ) const

Returns the number of degrees to rotate the helix.

References degrees_.

Referenced by apply().

◆ get_helix()

const protocols::loops::Loop & protocols::nonlocal::HelixRotate::get_helix ( ) const

Returns the helix to be modified.

References helix_.

Referenced by apply(), and decompose_structure().

◆ get_name()

std::string protocols::nonlocal::HelixRotate::get_name ( ) const

overridevirtual

Returns the protocol's name.

Implements protocols::moves::Mover.

◆ get_rotation_parameters()

void protocols::nonlocal::HelixRotate::get_rotation_parameters	(	const core::pose::Pose &	pose,
		numeric::xyzVector< core::Real > *	axis,
		numeric::xyzVector< core::Real > *	point
	)		const

private

Computes rotational parameters– axis and point.

References core::pose::motif::a(), protocols::nonlocal::avg_ca_position(), protocols::match::upstream::b, helix_, protocols::loops::Loop::length(), protocols::loops::Loop::midpoint(), protocols::loops::Loop::start(), protocols::loops::Loop::stop(), and core::pose::Pose::xyz().

Referenced by apply().

◆ initialize()

void protocols::nonlocal::HelixRotate::initialize	(	const protocols::loops::Loop &	helix,
		core::Real	degrees
	)

private

Shared initialization routine.

References degrees_, protocols::loops::loop_closure::ccd::helix, and helix_.

Referenced by HelixRotate().

◆ is_valid()

bool protocols::nonlocal::HelixRotate::is_valid ( ) const

private

Returns true if this instance is valid and fully configured.

References helix_, protocols::loops::Loop::start(), and protocols::loops::Loop::stop().

Referenced by apply().

◆ jump_containing_helix()

unsigned protocols::nonlocal::HelixRotate::jump_containing_helix ( const protocols::loops::Loops & chunks ) const

private

Searches chunks for the member representing the helix, returning its index.

References helix_, protocols::loops::Loops::num_loop(), protocols::loops::Loop::start(), and protocols::loops::start.

Referenced by apply().

◆ set_degrees()

void protocols::nonlocal::HelixRotate::set_degrees ( core::Real degrees )

Updates the number of degrees to rotate the helix.

References degrees_.

◆ set_helix()

void protocols::nonlocal::HelixRotate::set_helix ( const protocols::loops::Loop & helix )

Updates the helix to be modified.

References protocols::loops::loop_closure::ccd::helix, and helix_.

Member Data Documentation

◆ degrees_

core::Real protocols::nonlocal::HelixRotate::degrees_

private

Number of degrees to rotate the helix.

Referenced by get_degrees(), initialize(), and set_degrees().

◆ helix_

protocols::loops::Loop protocols::nonlocal::HelixRotate::helix_

private

Stretch of contiguous residues representing the helix to be rotated.

Referenced by get_helix(), get_rotation_parameters(), initialize(), is_valid(), jump_containing_helix(), and set_helix().

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

src/protocols/nonlocal/HelixRotate.hh
src/protocols/nonlocal/HelixRotate.cc

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ HelixRotate() [1/2]

◆ HelixRotate() [2/2]

Member Function Documentation

◆ apply()

◆ clone()

◆ decompose_structure()

◆ fresh_instance()

◆ get_degrees()

◆ get_helix()

◆ get_name()

◆ get_rotation_parameters()

◆ initialize()

◆ is_valid()

◆ jump_containing_helix()

◆ set_degrees()

◆ set_helix()

Member Data Documentation

◆ degrees_

◆ helix_