#include <FragmentCM.hh>

Public Member Functions
	FragmentCM ()

	FragmentCM (simple_moves::FragmentMoverOP, std::string const &)

virtual void	set_label (std::string const &label)

virtual void	set_mover (simple_moves::FragmentMoverOP mover)

virtual	~FragmentCM ()

virtual EnvClaims	yield_claims (core::pose::Pose &)
	Returns a list of claims for this mover. More...

virtual void	initialize (Pose &pose)
	this method is called by the broking system in response to a successful initialization claim by this mover. The passport will prevent any unauthorized changes. More...

virtual void	apply (Pose &pose)

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

std::string const &	label () const

Public Member Functions inherited from protocols::environment::ClaimingMover
	ClaimingMover ()

	ClaimingMover (ClaimingMover const &)

virtual	~ClaimingMover ()

virtual void	yield_submovers (std::set< ClaimingMoverOP > &) const
	this method is used to make sure any movers contained in this mover (that want to make claims) also get registered with the environment. More...

virtual bool	is_loop_closer () const
	indicate to the environment that this mover would like to close the loops after the environment closes. Perhaps this could be replaced by a claim type? 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
	Return a clone of the Mover object. More...

virtual void	parse_my_tag (TagCOP tag, basic::datacache::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...

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...

virtual MoverOP	fresh_instance () const
	Generates a new Mover object freshly created with the default ctor. More...

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

jobdist::BasicJobCOP	get_current_job () const

virtual void	show (std::ostream &output=std::cout) const
	Outputs details about the Mover, including current settings. More...

Protected Member Functions
virtual void	passport_updated ()
	hook that is called each time the passport status is updated (presumably because there's a new subenvironment, or the sub- environment has expired) More...

simple_moves::FragmentMoverOP	mover () const

Protected Member Functions inherited from protocols::environment::ClaimingMover
virtual void	broking_finished (EnvClaimBroker::BrokerResult const &)
	hook that provides information about the final result of broking at the very end, though this BrokerResult construct. More...

core::environment::DofPassportCOP	passport () const
	read-only access to the top passport in the passport stack. More...

bool	has_passport () const

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...

Private Types
typedef environment::claims::EnvClaims	EnvClaims

Private Attributes
simple_moves::FragmentMoverOP	mover_

std::string	label_

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 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. More...

Member Typedef Documentation

typedef environment::claims::EnvClaims protocols::abinitio::abscript::FragmentCM::EnvClaims

private

Constructor & Destructor Documentation

protocols::abinitio::abscript::FragmentCM::FragmentCM ( )

protocols::abinitio::abscript::FragmentCM::FragmentCM	(	simple_moves::FragmentMoverOP	mover,
		std::string const &	label
	)

References set_mover().

protocols::abinitio::abscript::FragmentCM::~FragmentCM ( )

virtual

Member Function Documentation

void protocols::abinitio::abscript::FragmentCM::apply ( Pose & pose )

virtual

Implements protocols::moves::Mover.

References core::pose::Pose::conformation(), core::conformation::Conformation::is_protected(), mover(), and protocols::environment::ClaimingMover::passport().

std::string protocols::abinitio::abscript::FragmentCM::get_name ( ) const

virtual

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

Implements protocols::moves::Mover.

Reimplemented in protocols::abinitio::abscript::FragmentJumpCM.

References mover().

Referenced by set_mover().

void protocols::abinitio::abscript::FragmentCM::initialize ( Pose & conf )

virtual

this method is called by the broking system in response to a successful initialization claim by this mover. The passport will prevent any unauthorized changes.

Reimplemented from protocols::environment::ClaimingMover.

References core::pose::Pose::conformation(), mover(), and protocols::environment::ClaimingMover::passport().

std::string const& protocols::abinitio::abscript::FragmentCM::label ( ) const

inline

References label_.

Referenced by protocols::abinitio::abscript::FragmentJumpCM::build_claims(), protocols::abinitio::abscript::FragmentJumpCM::parse_my_tag(), set_label(), and yield_claims().

simple_moves::FragmentMoverOP protocols::abinitio::abscript::FragmentCM::mover ( ) const

inlineprotected

Referenced by apply(), protocols::abinitio::abscript::FragmentJumpCM::FragmentJumpCM(), protocols::abinitio::abscript::FragmentJumpCM::get_name(), get_name(), initialize(), passport_updated(), set_mover(), protocols::abinitio::abscript::FragmentJumpCM::set_topology(), protocols::abinitio::abscript::FragmentJumpCM::setup_fragments(), yield_claims(), and protocols::abinitio::abscript::FragmentJumpCM::yield_claims().

void protocols::abinitio::abscript::FragmentCM::passport_updated ( )

protectedvirtual

hook that is called each time the passport status is updated (presumably because there's a new subenvironment, or the sub- environment has expired)

Reimplemented from protocols::environment::ClaimingMover.

References protocols::environment::ClaimingMover::has_passport(), mover(), and protocols::environment::ClaimingMover::passport().

void protocols::abinitio::abscript::FragmentCM::set_label ( std::string const & label )

virtual

References label(), and label_.

Referenced by protocols::abinitio::abscript::FragmentJumpCM::parse_my_tag().

void protocols::abinitio::abscript::FragmentCM::set_mover ( simple_moves::FragmentMoverOP mover )

virtual

References get_name(), mover(), mover_, and protocols::moves::Mover::type().

Referenced by FragmentCM(), and protocols::abinitio::abscript::FragmentJumpCM::setup_fragments().

claims::EnvClaims protocols::abinitio::abscript::FragmentCM::yield_claims ( core::pose::Pose & )

virtual

Returns a list of claims for this mover.

The pose passed as an argument is used for reference informational purposes only (for example, you want to know the sequence) or access the pose cache. Any changes to the conformation will get overwritten!

Implements protocols::environment::ClaimingMover.

Reimplemented in protocols::abinitio::abscript::FragmentJumpCM.

References protocols::environment::claims::CAN_CONTROL, protocols::environment::claims::DOES_NOT_INITIALIZE, fragments, label(), mover(), and ss.