#include <RBInMover.hh>

Inheritance diagram for protocols::splice::RBInMover:

[legend]

Public Member Functions
	RBInMover ()

	~RBInMover () override

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

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

protocols::moves::MoverOP	fresh_instance () const override
	Generates a new Mover object freshly created with the default ctor. 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...

std::string	RBDatabase_fname () const

void	RBDatabase_fname (std::string const &s)

void	RB_dbase (std::string const &s)

std::string	RB_dbase () const

core::Size	from_entry () const

void	from_entry (core::Size const s)

void	to_entry (core::Size const s)

core::Size	to_entry () const

bool	randomize () const

void	randomize (bool const b)

utility::vector1< std::pair< std::string, core::kinematics::Jump > >	jump_library () const

void	jump_library (utility::vector1< std::pair< std::string, core::kinematics::Jump > > j)

void	checkpointing_file (std::string const &s)

std::string	checkpointing_file () const

void	set_fold_tree (core::pose::Pose &pose)

void	modify_foldtree (bool const m)

bool	modify_foldtree () const

void	find_disulfide_postions (core::pose::Pose const &pose, utility::vector1< core::Size > &cys_pos)

core::Size	find_vl_vh_cut (core::pose::Pose pose) const

utility::vector1< std::array< int, 3 > >	set_fold_tree_nodes (core::pose::Pose const &pose, utility::vector1< core::Size > &cys_pos, core::Size vl_vh_cut)

void	db_entry (std::string s)

std::string	db_entry ()

void	select_entry_by_name ()

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_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 Member Functions
void	init ()

bool	checkpoint_recovery ()
	sets the entry order; if the jump_library is already populated returns without doing anything More...

bool	checkpoint () const
	recover from checkpointing. If checkpointing is off, does nothing. Returns true if recovered from checkpoint More...

Private Attributes
std::string	RB_dbase_

core::Size	from_entry_

core::Size	to_entry_

core::Size	current_entry_

bool	randomize_

utility::vector1< std::pair< std::string, core::kinematics::Jump > >	jump_library_

std::string	checkpointing_file_

bool	modify_foldtree_

std::string	db_entry_

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

◆ RBInMover()

protocols::splice::RBInMover::RBInMover ( )

References jump_library_.

◆ ~RBInMover()

protocols::splice::RBInMover::~RBInMover ( )

overridedefault

Member Function Documentation

◆ apply()

void protocols::splice::RBInMover::apply ( core::pose::Pose & )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References core::pose::add_comment(), checkpoint(), current_entry_, jump_library_, modify_foldtree(), select_entry_by_name(), set_fold_tree(), core::pose::Pose::set_jump(), and protocols::splice::TR().

◆ checkpoint()

bool protocols::splice::RBInMover::checkpoint ( ) const

private

recover from checkpointing. If checkpointing is off, does nothing. Returns true if recovered from checkpoint

References checkpointing_file(), checkpointing_file_, current_entry_, jump_library(), core::conformation::membrane::out, and protocols::splice::TR().

Referenced by apply(), and init().

◆ checkpoint_recovery()

bool protocols::splice::RBInMover::checkpoint_recovery ( )

private

sets the entry order; if the jump_library is already populated returns without doing anything

Referenced by init().

◆ checkpointing_file() [1/2]

std::string protocols::splice::RBInMover::checkpointing_file ( ) const

inline

References checkpointing_file_.

Referenced by checkpoint(), and parse_my_tag().

◆ checkpointing_file() [2/2]

void protocols::splice::RBInMover::checkpointing_file ( std::string const & s )

inline

References checkpointing_file_.

◆ clone()

moves::MoverOP protocols::splice::RBInMover::clone ( ) const

overridevirtual

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.

◆ db_entry() [1/2]

std::string protocols::splice::RBInMover::db_entry ( )

inline

References db_entry_.

Referenced by parse_my_tag(), and select_entry_by_name().

◆ db_entry() [2/2]

void protocols::splice::RBInMover::db_entry ( std::string s )

inline

References db_entry_.

◆ find_disulfide_postions()

void protocols::splice::RBInMover::find_disulfide_postions	(	core::pose::Pose const &	pose,
		utility::vector1< core::Size > &	cys_pos
	)

References core::chemical::DISULFIDE, core::conformation::Residue::has_variant_type(), core::pose::Pose::residue(), and core::pose::Pose::total_residue().

Referenced by set_fold_tree().

◆ find_vl_vh_cut()

core::Size protocols::splice::RBInMover::find_vl_vh_cut ( core::pose::Pose pose ) const

References protocols::simple_moves::CutChainMover::chain_cut().

Referenced by set_fold_tree().

◆ fresh_instance()

moves::MoverOP protocols::splice::RBInMover::fresh_instance ( ) const

overridevirtual

Generates a new Mover object freshly created with the default ctor.

fresh_instance is meant to return a new object of this class, created with the default constructor. 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. This is used by the August 08 job distributor.

Reimplemented from protocols::moves::Mover.

◆ from_entry() [1/2]

core::Size protocols::splice::RBInMover::from_entry ( ) const

inline

References from_entry_.

Referenced by init(), and parse_my_tag().

◆ from_entry() [2/2]

void protocols::splice::RBInMover::from_entry ( core::Size const s )

inline

References from_entry_.

◆ get_name()

std::string protocols::splice::RBInMover::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

◆ init()

void protocols::splice::RBInMover::init ( void )

private

References checkpoint(), checkpoint_recovery(), current_entry_, from_entry(), jump_library_, randomize(), RB_dbase_, core::scoring::rg, protocols::sparta::split(), to_entry(), and protocols::splice::TR().

Referenced by parse_my_tag().

◆ jump_library() [1/2]

utility::vector1< std::pair< std::string, core::kinematics::Jump > > protocols::splice::RBInMover::jump_library ( ) const

References jump_library_.

Referenced by checkpoint().

◆ jump_library() [2/2]

void protocols::splice::RBInMover::jump_library ( utility::vector1< std::pair< std::string, core::kinematics::Jump > > j )

References jump_library_.

◆ modify_foldtree() [1/2]

bool protocols::splice::RBInMover::modify_foldtree ( ) const

inline

References modify_foldtree_.

Referenced by apply(), and parse_my_tag().

◆ modify_foldtree() [2/2]

void protocols::splice::RBInMover::modify_foldtree ( bool const m )

inline

References modify_foldtree_.

◆ mover_name()

std::string protocols::splice::RBInMover::mover_name ( )

static

Referenced by get_name(), protocols::splice::RBInMoverCreator::keyname(), and provide_xml_schema().

◆ parse_my_tag()

void protocols::splice::RBInMover::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 checkpointing_file(), db_entry(), from_entry(), init(), modify_foldtree(), randomize(), RB_dbase(), and to_entry().

◆ provide_xml_schema()

void protocols::splice::RBInMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

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

Referenced by protocols::splice::RBInMoverCreator::provide_xml_schema().

◆ randomize() [1/2]

bool protocols::splice::RBInMover::randomize ( ) const

inline

References randomize_.

Referenced by init(), and parse_my_tag().

◆ randomize() [2/2]

void protocols::splice::RBInMover::randomize ( bool const b )

inline

References protocols::match::upstream::b, and randomize_.

◆ RB_dbase() [1/2]

std::string protocols::splice::RBInMover::RB_dbase ( ) const

inline

References RB_dbase_.

Referenced by parse_my_tag().

◆ RB_dbase() [2/2]

void protocols::splice::RBInMover::RB_dbase ( std::string const & s )

inline

References RB_dbase_.

◆ RBDatabase_fname() [1/2]

std::string protocols::splice::RBInMover::RBDatabase_fname ( ) const

inline

References RB_dbase_.

◆ RBDatabase_fname() [2/2]

void protocols::splice::RBInMover::RBDatabase_fname ( std::string const & s )

inline

References RB_dbase_.

◆ select_entry_by_name()

void protocols::splice::RBInMover::select_entry_by_name ( )

References current_entry_, db_entry(), db_entry_, and jump_library_.

Referenced by apply().

◆ set_fold_tree()

void protocols::splice::RBInMover::set_fold_tree ( core::pose::Pose & pose )

References core::kinematics::FoldTree::add_edge(), core::kinematics::FoldTree::check_fold_tree(), core::kinematics::FoldTree::clear(), core::kinematics::FoldTree::delete_self_edges(), find_disulfide_postions(), find_vl_vh_cut(), core::pose::Pose::fold_tree(), core::kinematics::FoldTree::reorder(), set_fold_tree_nodes(), and protocols::splice::TR().

Referenced by apply(), protocols::splice::Splice::rb_adjust_template(), and protocols::splice::SpliceManager::rb_adjust_template().

◆ set_fold_tree_nodes()

utility::vector1< std::array< int, 3 > > protocols::splice::RBInMover::set_fold_tree_nodes	(	core::pose::Pose const &	pose,
		utility::vector1< core::Size > &	cys_pos,
		core::Size	vl_vh_cut
	)

References core::conformation::Conformation::chain_end(), and core::pose::Pose::conformation().

Referenced by set_fold_tree().

◆ to_entry() [1/2]

core::Size protocols::splice::RBInMover::to_entry ( ) const

inline

References to_entry_.

Referenced by init(), and parse_my_tag().

◆ to_entry() [2/2]

void protocols::splice::RBInMover::to_entry ( core::Size const s )

inline

References to_entry_.

Member Data Documentation

◆ checkpointing_file_

std::string protocols::splice::RBInMover::checkpointing_file_

private

Referenced by checkpoint(), and checkpointing_file().

◆ current_entry_

core::Size protocols::splice::RBInMover::current_entry_

private

Referenced by apply(), checkpoint(), init(), and select_entry_by_name().

◆ db_entry_

std::string protocols::splice::RBInMover::db_entry_

private

Referenced by db_entry(), and select_entry_by_name().

◆ from_entry_

core::Size protocols::splice::RBInMover::from_entry_

private

Referenced by from_entry().

◆ jump_library_

utility::vector1< std::pair <std::string,core::kinematics::Jump> > protocols::splice::RBInMover::jump_library_

private

Referenced by apply(), init(), jump_library(), RBInMover(), and select_entry_by_name().

◆ modify_foldtree_

bool protocols::splice::RBInMover::modify_foldtree_

private

Referenced by modify_foldtree().

◆ randomize_

bool protocols::splice::RBInMover::randomize_

private

Referenced by randomize().

◆ RB_dbase_

std::string protocols::splice::RBInMover::RB_dbase_

private

Referenced by init(), RB_dbase(), and RBDatabase_fname().

◆ to_entry_

core::Size protocols::splice::RBInMover::to_entry_

private

Referenced by to_entry().

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

src/protocols/splice/RBInMover.hh
src/protocols/splice/RBInMover.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ RBInMover()

◆ ~RBInMover()

Member Function Documentation

◆ apply()

◆ checkpoint()

◆ checkpoint_recovery()

◆ checkpointing_file() [1/2]

◆ checkpointing_file() [2/2]

◆ clone()

◆ db_entry() [1/2]

◆ db_entry() [2/2]

◆ find_disulfide_postions()

◆ find_vl_vh_cut()

◆ fresh_instance()

◆ from_entry() [1/2]

◆ from_entry() [2/2]

◆ get_name()

◆ init()

◆ jump_library() [1/2]

◆ jump_library() [2/2]

◆ modify_foldtree() [1/2]

◆ modify_foldtree() [2/2]

◆ mover_name()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ randomize() [1/2]

◆ randomize() [2/2]

◆ RB_dbase() [1/2]

◆ RB_dbase() [2/2]

◆ RBDatabase_fname() [1/2]

◆ RBDatabase_fname() [2/2]

◆ select_entry_by_name()

◆ set_fold_tree()

◆ set_fold_tree_nodes()

◆ to_entry() [1/2]

◆ to_entry() [2/2]

Member Data Documentation

◆ checkpointing_file_

◆ current_entry_

◆ db_entry_

◆ from_entry_

◆ jump_library_

◆ modify_foldtree_

◆ randomize_

◆ RB_dbase_

◆ to_entry_