#include <SetupNCSMover.hh>

Inheritance diagram for protocols::symmetry::SetupNCSMover:

[legend]

Public Member Functions
	SetupNCSMover ()

	SetupNCSMover (std::string src, std::string tgt)

	SetupNCSMover (std::string src, utility::vector1< std::string > tgt)

	SetupNCSMover (utility::vector1< std::string > src, utility::vector1< std::string > tgt)

	~SetupNCSMover () override

void	add_group (std::string src, std::string tgt)

void	add_groupE (std::string src, std::string tgt)

void	add_groupD (std::string src, std::string tgt)

void	set_defaults ()

moves::MoverOP	clone () const override
	Return a clone of the Mover object. More...

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

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

void	set_bb (bool bb_in)

bool	bb ()

void	set_chi (bool chi_in)

bool	chi ()

void	set_symmetric_sequence (bool symmetric_sequence_in)

bool	symmetric_sequence ()

bool	distance_pair ()

void	set_limit (core::Real limit_in)

core::Real	limit ()

void	set_weight (core::Real wt_in)

core::Real	weight ()

void	set_sd (core::Real sd_in)

core::Real	sd ()

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...

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

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
utility::vector1< std::string >	src_

utility::vector1< std::string >	tgt_

utility::vector1< std::string >	srcE_

utility::vector1< std::string >	tgtE_

utility::vector1< std::string >	srcD_

utility::vector1< std::string >	tgtD_

bool	bb_

bool	chi_

bool	symmetric_sequence_

bool	distance_pair_

core::Real	limit_

core::Real	wt_

core::Real	sd_

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

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

◆ SetupNCSMover() [1/4]

protocols::symmetry::SetupNCSMover::SetupNCSMover ( )

References set_defaults().

◆ SetupNCSMover() [2/4]

protocols::symmetry::SetupNCSMover::SetupNCSMover	(	std::string	src,
		std::string	tgt
	)

References add_group(), and set_defaults().

◆ SetupNCSMover() [3/4]

protocols::symmetry::SetupNCSMover::SetupNCSMover	(	std::string	src,
		utility::vector1< std::string >	tgt
	)

References add_group(), and set_defaults().

◆ SetupNCSMover() [4/4]

protocols::symmetry::SetupNCSMover::SetupNCSMover	(	utility::vector1< std::string >	src,
		utility::vector1< std::string >	tgt
	)

References add_group(), and set_defaults().

◆ ~SetupNCSMover()

protocols::symmetry::SetupNCSMover::~SetupNCSMover ( )

overridedefault

Member Function Documentation

◆ add_group()

void protocols::symmetry::SetupNCSMover::add_group	(	std::string	src,
		std::string	tgt
	)

References src_, and tgt_.

Referenced by protocols::forge::remodel::RemodelMover::apply(), protocols::forge::remodel::RemodelMover::design_refine_cart_relax(), protocols::forge::remodel::RemodelMover::design_refine_seq_relax(), protocols::forge::remodel::RemodelLoopMover::generate_ncs_csts(), parse_my_tag(), and SetupNCSMover().

◆ add_groupD()

void protocols::symmetry::SetupNCSMover::add_groupD	(	std::string	src,
		std::string	tgt
	)

References srcD_, and tgtD_.

Referenced by parse_my_tag().

◆ add_groupE()

void protocols::symmetry::SetupNCSMover::add_groupE	(	std::string	src,
		std::string	tgt
	)

References srcE_, and tgtE_.

Referenced by parse_my_tag().

◆ apply()

void protocols::symmetry::SetupNCSMover::apply ( core::pose::Pose & )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References core::conformation::Residue::aa(), core::pose::Pose::add_constraint(), core::conformation::Residue::atom_index(), core::id::AtomID::atomno(), core::id::BB, bb_, core::chemical::rna::CHI, chi_, core::pose::Pose::conformation(), core::pose::Pose::data(), distance_pair_, core::pose::get_resnum_list_ordered(), core::conformation::Conformation::get_torsion_angle_atom_ids(), limit_, core::conformation::Residue::mainchain_torsions(), core::conformation::Residue::nchi(), core::pose::datacache::CacheableDataType::NCS_RESIDUE_MAPPING, core::pose::Pose::replace_residue(), core::pose::Pose::residue(), sd_, src_, srcD_, srcE_, symmetric_sequence_, tgt_, tgtD_, tgtE_, protocols::symmetry::TZ(), and wt_.

Referenced by protocols::forge::remodel::RemodelMover::apply(), protocols::forge::remodel::RemodelMover::design_refine_cart_relax(), and protocols::forge::remodel::RemodelMover::design_refine_seq_relax().

◆ bb()

bool protocols::symmetry::SetupNCSMover::bb ( )

inline

References bb_.

◆ chi()

bool protocols::symmetry::SetupNCSMover::chi ( )

inline

References chi_.

◆ clone()

moves::MoverOP protocols::symmetry::SetupNCSMover::clone ( ) const

inlineoverridevirtual

Return a clone of the Mover object.

clone is meant to return an OP'ed deep copy of this object. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function.

Reimplemented from protocols::moves::Mover.

◆ distance_pair()

bool protocols::symmetry::SetupNCSMover::distance_pair ( )

inline

References distance_pair_.

◆ get_name()

std::string protocols::symmetry::SetupNCSMover::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

◆ limit()

core::Real protocols::symmetry::SetupNCSMover::limit ( )

inline

References limit_.

◆ mover_name()

std::string protocols::symmetry::SetupNCSMover::mover_name ( )

static

Referenced by get_name(), protocols::symmetry::SetupNCSMoverCreator::keyname(), and provide_xml_schema().

◆ parse_my_tag()

void protocols::symmetry::SetupNCSMover::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Some movers need not be parsed, so we shouldn't force people to reimplement this method. However, we should be chatty about the fact that someone is using a RosettaScripts interface to a mover which didn't define parse_my_tag()

Reimplemented from protocols::moves::Mover.

References add_group(), add_groupD(), add_groupE(), bb_, chi_, distance_pair_, limit_, sd_, symmetric_sequence_, protocols::symmetry::TZ(), and wt_.

◆ provide_xml_schema()

void protocols::symmetry::SetupNCSMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

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

Referenced by protocols::symmetry::SetupNCSMoverCreator::provide_xml_schema().

◆ sd()

core::Real protocols::symmetry::SetupNCSMover::sd ( )

inline

References sd_.

◆ set_bb()

void protocols::symmetry::SetupNCSMover::set_bb ( bool bb_in )

inline

References bb_.

Referenced by protocols::forge::remodel::RemodelMover::design_refine_cart_relax().

◆ set_chi()

void protocols::symmetry::SetupNCSMover::set_chi ( bool chi_in )

inline

References chi_.

◆ set_defaults()

void protocols::symmetry::SetupNCSMover::set_defaults ( )

References bb_, chi_, distance_pair_, limit_, sd_, symmetric_sequence_, and wt_.

Referenced by SetupNCSMover().

◆ set_limit()

void protocols::symmetry::SetupNCSMover::set_limit ( core::Real limit_in )

inline

References limit_.

◆ set_sd()

void protocols::symmetry::SetupNCSMover::set_sd ( core::Real sd_in )

inline

References sd_.

◆ set_symmetric_sequence()

void protocols::symmetry::SetupNCSMover::set_symmetric_sequence ( bool symmetric_sequence_in )

inline

References symmetric_sequence_.

◆ set_weight()

void protocols::symmetry::SetupNCSMover::set_weight ( core::Real wt_in )

inline

References wt_.

◆ symmetric_sequence()

bool protocols::symmetry::SetupNCSMover::symmetric_sequence ( )

inline

References symmetric_sequence_.

◆ weight()

core::Real protocols::symmetry::SetupNCSMover::weight ( )

inline

References wt_.

Member Data Documentation

◆ bb_

bool protocols::symmetry::SetupNCSMover::bb_

private

Referenced by apply(), bb(), parse_my_tag(), set_bb(), and set_defaults().

◆ chi_

bool protocols::symmetry::SetupNCSMover::chi_

private

Referenced by apply(), chi(), parse_my_tag(), set_chi(), and set_defaults().

◆ distance_pair_

bool protocols::symmetry::SetupNCSMover::distance_pair_

private

Referenced by apply(), distance_pair(), parse_my_tag(), and set_defaults().

◆ limit_

core::Real protocols::symmetry::SetupNCSMover::limit_

private

Referenced by apply(), limit(), parse_my_tag(), set_defaults(), and set_limit().

◆ sd_

core::Real protocols::symmetry::SetupNCSMover::sd_

private

Referenced by apply(), parse_my_tag(), sd(), set_defaults(), and set_sd().

◆ src_

utility::vector1< std::string > protocols::symmetry::SetupNCSMover::src_

private

Referenced by add_group(), and apply().

◆ srcD_

utility::vector1< std::string > protocols::symmetry::SetupNCSMover::srcD_

private

Referenced by add_groupD(), and apply().

◆ srcE_

utility::vector1< std::string > protocols::symmetry::SetupNCSMover::srcE_

private

Referenced by add_groupE(), and apply().

◆ symmetric_sequence_

bool protocols::symmetry::SetupNCSMover::symmetric_sequence_

private

Referenced by apply(), parse_my_tag(), set_defaults(), set_symmetric_sequence(), and symmetric_sequence().

◆ tgt_

utility::vector1< std::string > protocols::symmetry::SetupNCSMover::tgt_

private

Referenced by add_group(), and apply().

◆ tgtD_

utility::vector1< std::string > protocols::symmetry::SetupNCSMover::tgtD_

private

Referenced by add_groupD(), and apply().

◆ tgtE_

utility::vector1< std::string > protocols::symmetry::SetupNCSMover::tgtE_

private

Referenced by add_groupE(), and apply().

◆ wt_

core::Real protocols::symmetry::SetupNCSMover::wt_

private

Referenced by apply(), parse_my_tag(), set_defaults(), set_weight(), and weight().

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

src/protocols/symmetry/SetupNCSMover.hh
src/protocols/symmetry/SetupNCSMover.cc

Public Member Functions

Static Public Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ SetupNCSMover() [1/4]

◆ SetupNCSMover() [2/4]

◆ SetupNCSMover() [3/4]

◆ SetupNCSMover() [4/4]

◆ ~SetupNCSMover()

Member Function Documentation

◆ add_group()

◆ add_groupD()

◆ add_groupE()

◆ apply()

◆ bb()

◆ chi()

◆ clone()

◆ distance_pair()

◆ get_name()

◆ limit()

◆ mover_name()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ sd()

◆ set_bb()

◆ set_chi()

◆ set_defaults()

◆ set_limit()

◆ set_sd()

◆ set_symmetric_sequence()

◆ set_weight()

◆ symmetric_sequence()

◆ weight()

Member Data Documentation

◆ bb_

◆ chi_

◆ distance_pair_

◆ limit_

◆ sd_

◆ src_

◆ srcD_

◆ srcE_

◆ symmetric_sequence_

◆ tgt_

◆ tgtD_

◆ tgtE_

◆ wt_