FloppyTail mover. More...

#include <FloppyTailMover.hh>

Inheritance diagram for protocols::floppy_tail::FloppyTailMover:

Collaboration diagram for protocols::floppy_tail::FloppyTailMover:

Public Member Functions
	FloppyTailMover ()
	ctor with no arguments More...

	FloppyTailMover (FloppyTailMover const &rhs)
	copy ctor More...

FloppyTailMover &	operator= (FloppyTailMover const &rhs)
	assignment operator More...

virtual	~FloppyTailMover ()

virtual void	set_movemap (core::kinematics::MoveMapOP const movemap)
	set the movemap instead of initializing it from cmd-line More...

virtual void	set_fa_scorefxn (core::scoring::ScoreFunctionOP const fa_scorefxn)

virtual void	set_cen_scorefxn (core::scoring::ScoreFunctionOP const cen_scorefunction)

virtual 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	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...

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...

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)

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

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

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...

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

jobdist::BasicJobCOP	get_current_job () const

Private Member Functions
virtual void	init_on_new_input (core::pose::Pose const &pose)
	init_on_new_input system allows for initializing these details the first time apply() is called. The job distributor will reinitialize the whole mover when the input changes (a freshly constructed mover, which will re-run this on first apply()). More...

Private Attributes
core::Size	start_

core::Size	stop_

bool	init_for_input_yet_

core::scoring::ScoreFunctionOP	centroid_scorefunction_

core::scoring::ScoreFunctionOP	fullatom_scorefunction_

core::pack::task::TaskFactoryOP	task_factory_

core::kinematics::MoveMapOP	movemap_

core::kinematics::MoveMapOP	movemap_lesstail_

core::kinematics::FoldTreeOP	foldtree_
	stored so that it can be generated in the init_on_new_input function More...

core::fragment::ConstantLengthFragSetOP	fragset3mer_

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...

Detailed Description

FloppyTail mover.

Definition at line 39 of file FloppyTailMover.hh.

Constructor & Destructor Documentation

protocols::floppy_tail::FloppyTailMover::FloppyTailMover ( )

protocols::floppy_tail::FloppyTailMover::FloppyTailMover ( FloppyTailMover const & rhs)

copy ctor

Definition at line 146 of file FloppyTailMover.cc.

protocols::floppy_tail::FloppyTailMover::~FloppyTailMover ( )

virtual

Definition at line 143 of file FloppyTailMover.cc.

Member Function Documentation

void protocols::floppy_tail::FloppyTailMover::apply ( core::pose::Pose & pose)

virtual

Implements protocols::moves::Mover.

Definition at line 358 of file FloppyTailMover.cc.

References core::scoring::constraints::add_constraints_from_cmdline_to_pose(), core::scoring::constraints::add_fa_constraints_from_cmdline_to_pose(), protocols::simple_moves::SwitchResidueTypeSetMover::apply(), protocols::simple_moves::ReturnSidechainMover::apply(), protocols::moves::PDBDumpMover::apply(), core::chemical::CENTROID, centroid_scorefunction_, protocols::floppy_tail::create_extra_output(), protocols::nonlocal::current_job(), core::pack::interaction_graph::debug, core::pose::Pose::fold_tree(), foldtree_, fragset3mer_, fullatom_scorefunction_, init_for_input_yet_, init_on_new_input(), movemap_, movemap_lesstail_, protocols::moves::MS_SUCCESS, core::pose::Pose::remove_constraints(), protocols::moves::Mover::set_last_move_status(), core::kinematics::simple_visualize_fold_tree_and_movemap(), stop_, task_factory_, core::pose::Pose::total_residue(), and protocols::TR().

virtual protocols::moves::MoverOP protocols::floppy_tail::FloppyTailMover::fresh_instance ( ) const

inlinevirtual

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.

Definition at line 65 of file FloppyTailMover.hh.

References FloppyTailMover().

virtual std::string protocols::floppy_tail::FloppyTailMover::get_name ( ) const

inlinevirtual

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

Implements protocols::moves::Mover.

Definition at line 63 of file FloppyTailMover.hh.

void protocols::floppy_tail::FloppyTailMover::init_on_new_input ( core::pose::Pose const & pose)

privatevirtual

init_on_new_input system allows for initializing these details the first time apply() is called. The job distributor will reinitialize the whole mover when the input changes (a freshly constructed mover, which will re-run this on first apply()).

init_on_new_input system allows for initializing these details the first time apply() is called. the job distributor will reinitialize the whole mover when the input changes (a freshly constructed mover, which will re-run this on first apply().

Definition at line 184 of file FloppyTailMover.cc.

References core::sequence::end, core::pose::Pose::fold_tree(), foldtree_, init_for_input_yet_, core::pose::metrics::CalculatorFactory::Instance(), core::kinematics::linearize_fold_tree(), movemap_, movemap_lesstail_, core::pose::Pose::pdb_info(), core::pose::metrics::CalculatorFactory::register_calculator(), core::pose::metrics::CalculatorFactory::remove_calculator(), start_, stop_, task_factory_, core::pose::Pose::total_residue(), and protocols::TR().

Referenced by apply().

FloppyTailMover & protocols::floppy_tail::FloppyTailMover::operator= ( FloppyTailMover const & rhs)

assignment operator

Definition at line 152 of file FloppyTailMover.cc.

References centroid_scorefunction_, foldtree_, fragset3mer_, fullatom_scorefunction_, init_for_input_yet_, movemap_, movemap_lesstail_, start_, stop_, and task_factory_.

virtual bool protocols::floppy_tail::FloppyTailMover::reinitialize_for_each_job ( ) const

inlinevirtual

this function informs the job distributor (august 08 vintage) whether this object needs to be freshly regenerated on each use.

Movers default to not regenerating

Reimplemented from protocols::moves::Mover.

Definition at line 67 of file FloppyTailMover.hh.

virtual bool protocols::floppy_tail::FloppyTailMover::reinitialize_for_new_input ( ) const

inlinevirtual

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).

Movers default to not regenerating

Reimplemented from protocols::moves::Mover.

Definition at line 69 of file FloppyTailMover.hh.

void protocols::floppy_tail::FloppyTailMover::set_cen_scorefxn ( core::scoring::ScoreFunctionOP const cen_scorefunction)

virtual

Definition at line 179 of file FloppyTailMover.cc.

References centroid_scorefunction_.

void protocols::floppy_tail::FloppyTailMover::set_fa_scorefxn ( core::scoring::ScoreFunctionOP const fa_scorefxn)

virtual

Definition at line 175 of file FloppyTailMover.cc.

References fullatom_scorefunction_.

void protocols::floppy_tail::FloppyTailMover::set_movemap ( core::kinematics::MoveMapOP const movemap)