#include <CloseFold.hh>

Inheritance diagram for protocols::seeded_abinitio::CloseFold:

[legend]

Public Member Functions
	CloseFold ()

	~CloseFold () 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 &) 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
protocols::loops::LoopsOP	find_loops (core::pose::Pose &pose, std::string secstr, core::Size offset, protocols::loops::Loops seeds)
	functions More...

bool	is_cut (utility::vector1< core::Size > &cut_points, core::Size residue)

bool	chainbreakweights ()

void	add_chainbreakweights (bool acbw)

bool	use_cutpoints ()

void	use_cutpoints (bool uc)

core::Size	trials ()

void	set_trials (core::Size trials_quick_ccd)

void	initialize_fragments ()

void	fast_loopclose (core::pose::Pose &pose, protocols::loops::LoopsOP const loops, bool kic)

void	quick_closure (core::pose::Pose &pose, protocols::loops::LoopsOP const loops)

Private Attributes
core::fragment::FragSetOP	fragments_
	data More...

boost::unordered_map< core::Size, core::fragment::Frame >	library_
	index-based access to the data contained in the FragSet More...

core::pose::PoseOP	template_pdb_

std::string	secstructure_

utility::vector1< core::Size >	chains_

bool	use_cutpoints_

utility::vector1< std::pair< std::string, std::string > >	seed_vector_
	residues specifying the seeds More...

protocols::loops::LoopsOP	loops_

bool	chainbreakweights_
	add cutpoint variants for closure More...

core::Size	trials_
	option for quick ccd protocol, how many attempts More...

bool	idealize_
	options for fast_ccd protocol More...

bool	kic_
	should kinematic loop mover be used after the fast ccd More...

bool	ccd_

core::scoring::ScoreFunctionOP	cen_scorefxn_

core::scoring::ScoreFunctionOP	fa_scorefxn_

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

◆ CloseFold()

protocols::seeded_abinitio::CloseFold::CloseFold ( )

References chainbreakweights_, chains_, idealize_, kic_, secstructure_, seed_vector_, trials_, and use_cutpoints_.

◆ ~CloseFold()

protocols::seeded_abinitio::CloseFold::~CloseFold ( )

overridedefault

Member Function Documentation

◆ add_chainbreakweights()

void protocols::seeded_abinitio::CloseFold::add_chainbreakweights ( bool acbw )

private

References chainbreakweights_.

◆ apply()

void protocols::seeded_abinitio::CloseFold::apply ( core::pose::Pose & )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References ccd_, core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), chains_, core::pose::Pose::conformation(), fast_loopclose(), find_loops(), core::pose::Pose::fold_tree(), kic_, loops_, protocols::seeded_abinitio::parse_seeds(), quick_closure(), core::pose::Pose::secstruct(), secstructure_, seed_vector_, core::pose::Pose::split_by_chain(), and protocols::seeded_abinitio::TR().

◆ chainbreakweights()

bool protocols::seeded_abinitio::CloseFold::chainbreakweights ( )

private

References chainbreakweights_.

Referenced by find_loops().

◆ clone()

protocols::moves::MoverOP protocols::seeded_abinitio::CloseFold::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.

◆ fast_loopclose()

void protocols::seeded_abinitio::CloseFold::fast_loopclose	(	core::pose::Pose &	pose,
		protocols::loops::LoopsOP const	loops,
		bool	kic
	)

private

References cen_scorefxn_, fa_scorefxn_, protocols::loops::loop_mover::perturb::fast_ccd_close_loops(), core::pose::Pose::fold_tree(), core::util::remove_cutpoint_variants(), protocols::loops::set_extended_torsions(), protocols::loops::set_move_map_for_centroid_loop(), protocols::forge::methods::set_single_loop_fold_tree(), and trials().

Referenced by apply().

◆ find_loops()

protocols::loops::LoopsOP protocols::seeded_abinitio::CloseFold::find_loops	(	core::pose::Pose &	pose,
		std::string	secstr,
		core::Size	offset,
		protocols::loops::Loops	seeds
	)

private

functions

References protocols::loops::Loops::add_loop(), core::pose::add_variant_type_to_pose_residue(), core::conformation::Conformation::chain_endings(), chainbreakweights(), core::pose::Pose::conformation(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::sequence::end, core::pose::Pose::fold_tree(), is_cut(), protocols::loops::Loops::is_loop_residue(), core::pose::Pose::size(), protocols::loops::Loops::size(), protocols::seeded_abinitio::TR(), use_cutpoints(), and use_cutpoints_.

Referenced by apply().

◆ fresh_instance()

protocols::moves::MoverOP protocols::seeded_abinitio::CloseFold::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_name()

std::string protocols::seeded_abinitio::CloseFold::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

◆ initialize_fragments()

void protocols::seeded_abinitio::CloseFold::initialize_fragments ( )

private

References fragments_, and library_.

◆ is_cut()

bool protocols::seeded_abinitio::CloseFold::is_cut	(	utility::vector1< core::Size > &	cut_points,
		core::Size	residue
	)

private

References protocols::loops::cut_point.

Referenced by find_loops().

◆ mover_name()

std::string protocols::seeded_abinitio::CloseFold::mover_name ( )

static

Referenced by get_name(), protocols::seeded_abinitio::CloseFoldCreator::keyname(), and provide_xml_schema().

◆ parse_my_tag()

void protocols::seeded_abinitio::CloseFold::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 ccd_, cen_scorefxn_, chainbreakweights_, chains_, protocols::simple_filters::dssp(), fa_scorefxn_, fragments_, idealize_, kic_, loops_, core::scoring::parse_score_function(), core::import_pose::PDB_file, core::import_pose::pose_from_file(), secstructure_, seed_vector_, template_pdb_, protocols::seeded_abinitio::TR(), trials_, and use_cutpoints_.