#include <LoopRelaxMover.hh>

Inheritance diagram for protocols::relax::loop::LoopRelaxMover:

[legend]

Public Member Functions
	LoopRelaxMover ()

	LoopRelaxMover (std::string const &remodel, std::string const &intermedrelax, std::string const &refine, std::string const &relax, loops::Loops const &loops)
	Alternative constructor. BE WARNED: THIS CONSTRUCTOR DOES NOT CALL SET_DEFAULTS(). AS A RESULT, THE SCORE FUNCTIONS (AMONG OTHER THINGS) WILL NOT BE INITIALIZED. More...

	LoopRelaxMover (std::string const &remodel, std::string const &intermedrelax, std::string const &refine, std::string const &relax, loops::LoopsFileData const &loops_from_file)
	Unresolved-loop-index constructor. BE WARNED: THIS CONSTRUCTOR DOES NOT CALL SET_DEFAULTS(). AS A RESULT, THE SCORE FUNCTIONS (AMONG OTHER THINGS) WILL NOT BE INITIALIZED. More...

	LoopRelaxMover (std::string const &remodel, std::string const &intermedrelax, std::string const &refine, std::string const &relax, loops::GuardedLoopsFromFileOP guarded_loops)
	GuardedLoopsOP constructor. This constructor copies the pointer to a GuardedLoops object; Loop indices must be resolved by the time that the guarded_loops_ object is accessed, but, they need not have been resolved at the time of this object's construction. BE WARNED: THIS CONSTRUCTOR DOES NOT CALL SET_DEFAULTS(). AS A RESULT, THE SCORE FUNCTIONS (AMONG OTHER THINGS) WILL NOT BE INITIALIZED. More...

void	apply (core::pose::Pose &pose) override
	Apply the loop-relax protocol to a Pose. At the call to this function, the loop indices originating from the loop file (which may list indices with PDB identifiers i.e. res+insertioncode+chain ) will be resolved. Until this point, the Loops object in the LoopRelaxMover cannot be used. More...

void	scorefxns (core::scoring::ScoreFunctionOP cen_scorefxn, core::scoring::ScoreFunctionOP fa_scorefxn)

void	fa_scorefxn (core::scoring::ScoreFunctionOP fa_scorefxn)

void	cen_scorefxn (core::scoring::ScoreFunctionOP cen_scorefxn)

void	cmd_line_csts (bool setting)

void	copy_sidechains (bool setting)

void	rebuild_filter (core::Real setting)

void	n_rebuild_tries (core::Size setting)

void	remodel (std::string const &val)

void	intermedrelax (std::string const &val)

void	refine (std::string const &val)

void	relax (std::string const &val)

void	resolve_loopfile_indices (core::pose::Pose const &pose)
	Must be called before the Loops data can be read from. More...

void	loops (protocols::loops::LoopsOP const val)
	set the Loops object (with resolved indices) directly. This would override the unresolved-indices held in the LoopsFileData if that data were set in the constructor More...

void	loops_file_data (loops::LoopsFileData const &loopfiledata)
	Set the loop file data. This will require that a Pose be presented to the LoopRelax object before get_loops() can be called. More...

void	frag_libs (utility::vector1< core::fragment::FragSetOP > new_libs)

bool	cmd_line_csts () const

bool	copy_sidechains () const

core::Size	n_rebuild_tries () const

core::Real	rebuild_filter () const

protocols::loops::LoopsOP	get_loops ()
	Loops accessor. May only be retrieved after the loop indices have been resolved in a call to apply. More...

protocols::loops::LoopsCOP	get_loops () const
	Loops accessor. May only be retrieved after the loop indices have been resolved in a call to apply. More...

std::string	remodel () const

std::string	relax () const

std::string	intermedrelax () const

std::string	refine () const

utility::vector1< core::fragment::FragSetOP >	frag_libs () const

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	compute_rmsd (bool const c)

bool	compute_rmsd () const

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

Private Attributes
bool	cmd_line_csts_

bool	copy_sidechains_

core::Size	n_rebuild_tries_

core::Real	rebuild_filter_

std::string	remodel_

std::string	intermedrelax_

std::string	refine_

std::string	relax_

loops::GuardedLoopsFromFileOP	guarded_loops_

core::scoring::ScoreFunctionOP	cen_scorefxn_

core::scoring::ScoreFunctionOP	fa_scorefxn_

utility::vector1< core::fragment::FragSetOP >	frag_libs_

bool	compute_rmsd_

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

◆ LoopRelaxMover() [1/4]

protocols::relax::loop::LoopRelaxMover::LoopRelaxMover ( )

References set_defaults_().

◆ LoopRelaxMover() [2/4]

protocols::relax::loop::LoopRelaxMover::LoopRelaxMover	(	std::string const &	remodel,
		std::string const &	intermedrelax,
		std::string const &	refine,
		std::string const &	relax,
		loops::Loops const &	loops
	)

Alternative constructor. BE WARNED: THIS CONSTRUCTOR DOES NOT CALL SET_DEFAULTS(). AS A RESULT, THE SCORE FUNCTIONS (AMONG OTHER THINGS) WILL NOT BE INITIALIZED.

◆ LoopRelaxMover() [3/4]

protocols::relax::loop::LoopRelaxMover::LoopRelaxMover	(	std::string const &	remodel,
		std::string const &	intermedrelax,
		std::string const &	refine,
		std::string const &	relax,
		loops::LoopsFileData const &	loops_from_file
	)

Unresolved-loop-index constructor. BE WARNED: THIS CONSTRUCTOR DOES NOT CALL SET_DEFAULTS(). AS A RESULT, THE SCORE FUNCTIONS (AMONG OTHER THINGS) WILL NOT BE INITIALIZED.

◆ LoopRelaxMover() [4/4]

protocols::relax::loop::LoopRelaxMover::LoopRelaxMover	(	std::string const &	remodel,
		std::string const &	intermedrelax,
		std::string const &	refine,
		std::string const &	relax,
		loops::GuardedLoopsFromFileOP	guarded_loops
	)

GuardedLoopsOP constructor. This constructor copies the pointer to a GuardedLoops object; Loop indices must be resolved by the time that the guarded_loops_ object is accessed, but, they need not have been resolved at the time of this object's construction. BE WARNED: THIS CONSTRUCTOR DOES NOT CALL SET_DEFAULTS(). AS A RESULT, THE SCORE FUNCTIONS (AMONG OTHER THINGS) WILL NOT BE INITIALIZED.

Member Function Documentation

◆ apply()

void protocols::relax::loop::LoopRelaxMover::apply ( core::pose::Pose & pose )

overridevirtual

Apply the loop-relax protocol to a Pose. At the call to this function, the loop indices originating from the loop file (which may list indices with PDB identifiers i.e. res+insertioncode+chain ) will be resolved. Until this point, the Loops object in the LoopRelaxMover cannot be used.

Implements protocols::moves::Mover.

Referenced by protocols::loop_build::LoopBuildMover::apply(), protocols::protein_interface_design::movers::LoopMoverFromCommandLine::apply(), protocols::rbsegment_relax::RBSegmentRelax::apply(), protocols::medal::MedalMover::do_loop_closure(), and protocols::mpi_refinement::WorkUnit_KicCloser::run().

◆ cen_scorefxn()

void protocols::relax::loop::LoopRelaxMover::cen_scorefxn ( core::scoring::ScoreFunctionOP cen_scorefxn )

References cen_scorefxn_.

Referenced by parse_my_tag(), and scorefxns().

◆ clone()

protocols::moves::MoverOP protocols::relax::loop::LoopRelaxMover::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.

◆ cmd_line_csts() [1/2]

bool protocols::relax::loop::LoopRelaxMover::cmd_line_csts ( ) const

inline

References cmd_line_csts_.

Referenced by apply(), and parse_my_tag().

◆ cmd_line_csts() [2/2]

void protocols::relax::loop::LoopRelaxMover::cmd_line_csts ( bool setting )

inline

References cmd_line_csts_.

Referenced by protocols::rbsegment_relax::RBSegmentRelax::apply(), and protocols::medal::MedalMover::do_loop_closure().

◆ compute_rmsd() [1/2]

bool protocols::relax::loop::LoopRelaxMover::compute_rmsd ( ) const

inline

References compute_rmsd_.

Referenced by apply(), parse_my_tag(), and set_defaults_().

◆ compute_rmsd() [2/2]

void protocols::relax::loop::LoopRelaxMover::compute_rmsd ( bool const c )

inline

References compute_rmsd_.

Referenced by protocols::loop_build::LoopBuildMover::apply().

◆ copy_sidechains() [1/2]

bool protocols::relax::loop::LoopRelaxMover::copy_sidechains ( ) const

inline

References copy_sidechains_.

Referenced by apply(), and parse_my_tag().

◆ copy_sidechains() [2/2]

void protocols::relax::loop::LoopRelaxMover::copy_sidechains ( bool setting )

inline

References copy_sidechains_.

◆ fa_scorefxn()

void protocols::relax::loop::LoopRelaxMover::fa_scorefxn ( core::scoring::ScoreFunctionOP fa_scorefxn )

References fa_scorefxn_.

Referenced by protocols::rbsegment_relax::RBSegmentRelax::apply(), parse_my_tag(), and scorefxns().

◆ frag_libs() [1/2]

utility::vector1< core::fragment::FragSetOP > protocols::relax::loop::LoopRelaxMover::frag_libs ( ) const

References frag_libs_.

Referenced by apply().

◆ frag_libs() [2/2]

void protocols::relax::loop::LoopRelaxMover::frag_libs ( utility::vector1< core::fragment::FragSetOP > new_libs )

References frag_libs_.

Referenced by protocols::indel::IndelOptimizationMover::apply(), protocols::loop_build::LoopmodelWrapper::apply(), protocols::protein_interface_design::movers::LoopMoverFromCommandLine::apply(), protocols::rbsegment_relax::RBSegmentRelax::apply(), protocols::medal::MedalMover::do_loop_closure(), and protocols::loop_build::LoopBuild_main().

◆ fresh_instance()

protocols::moves::MoverOP protocols::relax::loop::LoopRelaxMover::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.

◆ get_loops() [1/2]

protocols::loops::LoopsOP protocols::relax::loop::LoopRelaxMover::get_loops ( void )

Loops accessor. May only be retrieved after the loop indices have been resolved in a call to apply.

References guarded_loops_.

Referenced by protocols::indel::IndelOptimizationMover::apply(), and apply().

◆ get_loops() [2/2]

protocols::loops::LoopsCOP protocols::relax::loop::LoopRelaxMover::get_loops ( void ) const

Loops accessor. May only be retrieved after the loop indices have been resolved in a call to apply.

References guarded_loops_.

◆ get_name()

std::string protocols::relax::loop::LoopRelaxMover::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

◆ intermedrelax() [1/2]

std::string protocols::relax::loop::LoopRelaxMover::intermedrelax ( ) const

inline

References intermedrelax_.

Referenced by apply(), and parse_my_tag().

◆ intermedrelax() [2/2]

void protocols::relax::loop::LoopRelaxMover::intermedrelax ( std::string const & val )

inline

References intermedrelax_, and protocols::hybridization::val.

Referenced by protocols::indel::IndelOptimizationMover::apply(), protocols::loop_build::LoopmodelWrapper::apply(), protocols::protein_interface_design::movers::LoopMoverFromCommandLine::apply(), protocols::rbsegment_relax::RBSegmentRelax::apply(), protocols::medal::MedalMover::do_loop_closure(), and protocols::loop_build::LoopBuild_main().

◆ loops()

void protocols::relax::loop::LoopRelaxMover::loops ( protocols::loops::LoopsOP const val )

set the Loops object (with resolved indices) directly. This would override the unresolved-indices held in the LoopsFileData if that data were set in the constructor

By setting the loops object directly, the requirement is relaxed that a Pose be first given to the LoopRelax object (through a call to apply() or resolve_loopfile_indices) before the get_loops() function may be called.

References guarded_loops_, and protocols::hybridization::val.

Referenced by protocols::indel::IndelOptimizationMover::apply(), protocols::protein_interface_design::movers::LoopMoverFromCommandLine::apply(), protocols::rbsegment_relax::RBSegmentRelax::apply(), apply(), and protocols::medal::MedalMover::do_loop_closure().

◆ loops_file_data()

void protocols::relax::loop::LoopRelaxMover::loops_file_data ( loops::LoopsFileData const & loopfiledata )

Set the loop file data. This will require that a Pose be presented to the LoopRelax object before get_loops() can be called.

Set the loop file data. This will require that.

References guarded_loops_.

Referenced by protocols::loop_build::LoopBuildMover::setup_loop_definition().

◆ mover_name()

std::string protocols::relax::loop::LoopRelaxMover::mover_name ( )

static

Referenced by get_name(), protocols::relax::loop::LoopRelaxMoverCreator::keyname(), and provide_xml_schema().

◆ n_rebuild_tries() [1/2]

core::Size protocols::relax::loop::LoopRelaxMover::n_rebuild_tries ( ) const

inline

References n_rebuild_tries_.

Referenced by apply(), and parse_my_tag().

◆ n_rebuild_tries() [2/2]

void protocols::relax::loop::LoopRelaxMover::n_rebuild_tries ( core::Size setting )

inline

References n_rebuild_tries_.

◆ parse_my_tag()

void protocols::relax::loop::LoopRelaxMover::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 cen_scorefxn(), cen_scorefxn_, cmd_line_csts(), compute_rmsd(), copy_sidechains(), fa_scorefxn(), frag_libs_, guarded_loops_, intermedrelax(), protocols::loops::loops_definers::load_loop_definitions(), protocols::loops::loop_mover::loops_set_chainbreak_weight(), n_rebuild_tries(), core::scoring::parse_score_function(), protocols::loops::read_loop_fragments(), rebuild_filter(), refine(), relax(), and remodel().