#include <ShortBackrubMover.hh>

Inheritance diagram for protocols::simple_moves::ShortBackrubMover:

[legend]

Public Types
typedef protocols::moves::MoverOP	MoverOP

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

Public Member Functions
	ShortBackrubMover ()

	ShortBackrubMover (core::pose::PoseOP pose)
	constructor that sets input pose More...

	ShortBackrubMover (ShortBackrubMover const &rval)
	copy constructor More...

	~ShortBackrubMover () override
	destructor More...

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

protocols::moves::MoverOP	fresh_instance () const override
	create this type of object More...

void	apply (core::pose::Pose &pose) override
	Main Method. More...

void	set_resnum (core::Size resnum)

void	set_rotation_std_dev (core::Real rotation_std_dev)

void	set_randomize_resnum (bool randomize_resnum)

void	set_uniform_backrub (bool uniform_backrub)

void	set_input_pose (core::pose::PoseCOP pose) override
	setter for poses contained for rms More...

core::Size	get_resnum () const

core::Real	get_rotation_std_dev () const

bool	get_randomize_resnum () const

bool	get_uniform_backrub () const

protocols::backrub::BackrubMoverOP	get_backrubmover () const

void	parse_my_tag (TagCOP tag, basic::datacache::DataMap &data) override
	parse xml More...

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

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...

Static Public Member Functions
static std::string	mover_name ()

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

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...

Private Attributes
protocols::backrub::BackrubMoverOP	backrubmover_
	mover used for Backrub moves More...

core::Size	resnum_
	residue number specifying the center residue for the next Backrub move More...

core::Real	rotation_std_dev_
	standard deviation of rotation angle (degrees) used for Backrub moves More...

bool	randomize_resnum_
	if true, choose a random residue for the next move More...

bool	uniform_backrub_
	if true, sample rotation angle from a uniform distribution from -20 to 20 More...

Additional Inherited Members
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...

Member Typedef Documentation

◆ MoverOP

typedef protocols::moves::MoverOP protocols::simple_moves::ShortBackrubMover::MoverOP

Constructor & Destructor Documentation

◆ ShortBackrubMover() [1/3]

protocols::simple_moves::ShortBackrubMover::ShortBackrubMover ( )

References backrubmover_, randomize_resnum_, resnum_, rotation_std_dev_, protocols::moves::Mover::type(), and uniform_backrub_.

◆ ShortBackrubMover() [2/3]

protocols::simple_moves::ShortBackrubMover::ShortBackrubMover ( core::pose::PoseOP pose )

constructor that sets input pose

References backrubmover_, randomize_resnum_, resnum_, rotation_std_dev_, protocols::moves::Mover::type(), and uniform_backrub_.

◆ ShortBackrubMover() [3/3]

protocols::simple_moves::ShortBackrubMover::ShortBackrubMover ( ShortBackrubMover const & rval )

default

copy constructor

◆ ~ShortBackrubMover()

protocols::simple_moves::ShortBackrubMover::~ShortBackrubMover ( )

overridedefault

destructor

Member Function Documentation

◆ apply()

void protocols::simple_moves::ShortBackrubMover::apply ( core::pose::Pose & )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References backrubmover_, core::sequence::end, core::pose::Pose::fold_tree(), core::conformation::Residue::name1(), randomize_resnum_, core::pose::Pose::residue(), resnum_, core::scoring::rg, rotation_std_dev_, core::pose::Pose::size(), protocols::loops::start, uniform_backrub_, and core::conformation::Residue::xyz().

◆ clone()

ShortBackrubMover::MoverOP protocols::simple_moves::ShortBackrubMover::clone ( ) const

overridevirtual

clone this object

Reimplemented from protocols::moves::Mover.

◆ fresh_instance()

ShortBackrubMover::MoverOP protocols::simple_moves::ShortBackrubMover::fresh_instance ( ) const

overridevirtual

create this type of object

Reimplemented from protocols::moves::Mover.

◆ get_backrubmover()

protocols::backrub::BackrubMoverOP protocols::simple_moves::ShortBackrubMover::get_backrubmover ( ) const

References backrubmover_.

◆ get_name()

std::string protocols::simple_moves::ShortBackrubMover::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

◆ get_randomize_resnum()

bool protocols::simple_moves::ShortBackrubMover::get_randomize_resnum ( ) const

References randomize_resnum_.

◆ get_resnum()

core::Size protocols::simple_moves::ShortBackrubMover::get_resnum ( ) const

References resnum_.

◆ get_rotation_std_dev()

core::Real protocols::simple_moves::ShortBackrubMover::get_rotation_std_dev ( ) const

References rotation_std_dev_.

◆ get_uniform_backrub()

bool protocols::simple_moves::ShortBackrubMover::get_uniform_backrub ( ) const

References uniform_backrub_.

◆ mover_name()

std::string protocols::simple_moves::ShortBackrubMover::mover_name ( )

static

Referenced by get_name(), protocols::simple_moves::ShortBackrubMoverCreator::keyname(), and provide_xml_schema().

◆ parse_my_tag()

void protocols::simple_moves::ShortBackrubMover::parse_my_tag	(	TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

parse xml

Reimplemented from protocols::moves::Mover.

References backrubmover_.

◆ provide_xml_schema()

void protocols::simple_moves::ShortBackrubMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References mover_name(), and protocols::moves::xsd_type_definition_w_attributes().

Referenced by protocols::simple_moves::ShortBackrubMoverCreator::provide_xml_schema().

◆ set_input_pose()

void protocols::simple_moves::ShortBackrubMover::set_input_pose ( core::pose::PoseCOP pose )

overridevirtual

setter for poses contained for rms

Reimplemented from protocols::moves::Mover.

References backrubmover_.

◆ set_randomize_resnum()

void protocols::simple_moves::ShortBackrubMover::set_randomize_resnum ( bool randomize_resnum )

References randomize_resnum_.

◆ set_resnum()

void protocols::simple_moves::ShortBackrubMover::set_resnum ( core::Size resnum )

References resnum_.

◆ set_rotation_std_dev()

void protocols::simple_moves::ShortBackrubMover::set_rotation_std_dev ( core::Real rotation_std_dev )

References rotation_std_dev_.

◆ set_uniform_backrub()

void protocols::simple_moves::ShortBackrubMover::set_uniform_backrub ( bool uniform_backrub )

References uniform_backrub_.

Member Data Documentation

◆ backrubmover_

protocols::backrub::BackrubMoverOP protocols::simple_moves::ShortBackrubMover::backrubmover_

private

mover used for Backrub moves

Referenced by apply(), get_backrubmover(), parse_my_tag(), set_input_pose(), and ShortBackrubMover().

◆ randomize_resnum_

bool protocols::simple_moves::ShortBackrubMover::randomize_resnum_

private

if true, choose a random residue for the next move

Referenced by apply(), get_randomize_resnum(), set_randomize_resnum(), and ShortBackrubMover().

◆ resnum_

core::Size protocols::simple_moves::ShortBackrubMover::resnum_

private

residue number specifying the center residue for the next Backrub move

Referenced by apply(), get_resnum(), set_resnum(), and ShortBackrubMover().

◆ rotation_std_dev_

core::Real protocols::simple_moves::ShortBackrubMover::rotation_std_dev_

private

standard deviation of rotation angle (degrees) used for Backrub moves

Referenced by apply(), get_rotation_std_dev(), set_rotation_std_dev(), and ShortBackrubMover().

◆ uniform_backrub_

bool protocols::simple_moves::ShortBackrubMover::uniform_backrub_

private

if true, sample rotation angle from a uniform distribution from -20 to 20

Referenced by apply(), get_uniform_backrub(), set_uniform_backrub(), and ShortBackrubMover().

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

src/protocols/simple_moves/ShortBackrubMover.hh
src/protocols/simple_moves/ShortBackrubMover.cc

Public Types

Public Member Functions

Static Public Member Functions

Private Attributes

Additional Inherited Members

Member Typedef Documentation

◆ MoverOP

Constructor & Destructor Documentation

◆ ShortBackrubMover() [1/3]

◆ ShortBackrubMover() [2/3]

◆ ShortBackrubMover() [3/3]

◆ ~ShortBackrubMover()

Member Function Documentation

◆ apply()

◆ clone()

◆ fresh_instance()

◆ get_backrubmover()

◆ get_name()

◆ get_randomize_resnum()

◆ get_resnum()

◆ get_rotation_std_dev()

◆ get_uniform_backrub()

◆ mover_name()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ set_input_pose()

◆ set_randomize_resnum()

◆ set_resnum()

◆ set_rotation_std_dev()

◆ set_uniform_backrub()

Member Data Documentation

◆ backrubmover_

◆ randomize_resnum_

◆ resnum_

◆ rotation_std_dev_

◆ uniform_backrub_