#include <CloseFold.hh>

Inheritance diagram for protocols::seeded_abinitio::CloseFold:

Collaboration diagram for protocols::seeded_abinitio::CloseFold:

Public Member Functions
	CloseFold ()

virtual	~CloseFold ()

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

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

virtual protocols::moves::MoverOP	clone () const
	clone has to be overridden only if clone invocation is expected. More...

virtual protocols::moves::MoverOP	fresh_instance () const
	this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More...

void	parse_my_tag (utility::tag::TagPtr const tag, protocols::moves::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

Public Member Functions inherited from protocols::moves::Mover
	Mover ()

virtual	~Mover ()

virtual MoverSP	create ()

virtual void	apply (core::io::serialization::PipeMap &pmap)

virtual void	parse_state (SerializableState const &state)

virtual void	parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)

virtual void	save_state (SerializableState &state)

	Mover (std::string const &type_name)
	sets the type for a mover; name_ has been removed (2010/05/14) More...

	Mover (Mover const &other)

Mover &	operator= (Mover const &other)
	assignment operator More...

virtual core::Real	last_proposal_density_ratio ()

std::string const &	type () const

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...

void	set_current_tag (std::string const &new_tag)

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

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...

void	type (const std::string &type_in)

std::string	get_type () const

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...

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 bool	reinitialize_for_each_job () const
	this function informs 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
	this function informs 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...

void	set_current_job (protocols::jobdist::BasicJobCOP job)

jobdist::BasicJobCOP	get_current_job () const

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< Size > &cut_points, 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::TagPtr	TagPtr

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

typedef protocols::filters::Filters_map	Filters_map

typedef std::list< std::string >	Strings

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. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. More...

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

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

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

Referenced by clone().

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

virtual

Member Function Documentation

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

private

References chainbreakweights_.

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

virtual

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(), secstructure_, seed_vector_, core::pose::Pose::split_by_chain(), and protocols::seeded_abinitio::TR().

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

private

References chainbreakweights_.

Referenced by find_loops().

protocols::moves::MoverOP protocols::seeded_abinitio::CloseFold::clone ( ) const

virtual

clone has to be overridden only if clone invocation is expected.

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.

References CloseFold().

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().

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(), protocols::loops::Loops::size(), core::pose::Pose::total_residue(), protocols::seeded_abinitio::TR(), use_cutpoints(), and use_cutpoints_.

Referenced by apply().

protocols::moves::MoverOP protocols::seeded_abinitio::CloseFold::fresh_instance ( ) const

virtual

this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage).

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.

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

virtual

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

Implements protocols::moves::Mover.

References protocols::seeded_abinitio::CloseFoldCreator::mover_name().

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

private

References fragments_, and library_.

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

private

Referenced by find_loops().

void protocols::seeded_abinitio::CloseFold::parse_my_tag	(	utility::tag::TagPtr const	tag,
		protocols::moves::DataMap &	data,
		protocols::filters::Filters_map const &	filters,
		protocols::moves::Movers_map const &	movers,
		core::pose::Pose const &	pose
	)

virtual

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 stop executions. This, however, calls attention to the lack of this method, which could be due to something as silly as a wrong parameters definition.

Reimplemented from protocols::moves::Mover.

References protocols::moves::DataMap::add(), ccd_, cen_scorefxn_, chainbreakweights_, chains_, core::pose::Pose::conformation(), fa_scorefxn_, fragments_, protocols::moves::DataMap::get(), idealize_, core::scoring::dssp::Dssp::insert_ss_into_pose(), kic_, loops_, core::conformation::Conformation::num_chains(), core::import_pose::pose_from_pdb(), core::pose::Pose::secstruct(), secstructure_, seed_vector_, template_pdb_, protocols::seeded_abinitio::TR(), trials_, and use_cutpoints_.