#include <CoMTrackerCM.hh>

Public Member Functions
	CoMTrackerCM ()

	CoMTrackerCM (std::string const &name, core::pack::task::residue_selector::ResidueSelectorCOP mobile_selector, std::string const &stationary_label)

	CoMTrackerCM (std::string const &name, core::pack::task::residue_selector::ResidueSelectorCOP mobile_selector)

virtual	~CoMTrackerCM ()

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

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

virtual void	initialize (core::pose::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 (core::pose::Pose &)

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

std::string const &	name () const

void	name (std::string const &name)

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

virtual moves::MoverOP	clone () const
	Return a clone of the Mover object. More...

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

void	set_type (std::string const &setting)

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
	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...

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). A conformation is provided for reference. More...

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...

EnvironmentCAP	active_environment () const
	return a pointer the active environment More...

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

bool	has_passport () const

bool	state_check (std::string const &method_name, bool test) const
	convienence method for failing a state-set call after brokering. 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...

Private Types
typedef environment::claims::EnvClaims	EnvClaims

typedef int	JumpNumber

Private Member Functions
void	update_tracking_residue (core::kinematics::RT::Vector new_position, core::Size tracking_residue_id, core::pose::Pose &pose) const

void	update_com (core::pose::Pose &) const

Private Attributes
std::string	name_

std::string	stationary_label_

std::string	com_name_

std::string	com_jump_name_

core::pack::task::residue_selector::ResidueSubset	mobile_residues_

core::pack::task::residue_selector::ResidueSelectorCOP	mobile_selector_

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::environment::CoMTrackerCM::EnvClaims

private

typedef int protocols::environment::CoMTrackerCM::JumpNumber

private

Constructor & Destructor Documentation

protocols::environment::CoMTrackerCM::CoMTrackerCM ( )

protocols::environment::CoMTrackerCM::CoMTrackerCM	(	std::string const &	name,
		core::pack::task::residue_selector::ResidueSelectorCOP	mobile_selector,
		std::string const &	stationary_label
	)

protocols::environment::CoMTrackerCM::CoMTrackerCM	(	std::string const &	name,
		core::pack::task::residue_selector::ResidueSelectorCOP	mobile_selector
	)

virtual protocols::environment::CoMTrackerCM::~CoMTrackerCM ( )

inlinevirtual

Member Function Documentation

void protocols::environment::CoMTrackerCM::apply ( core::pose::Pose & pose )

virtual

Implements protocols::moves::Mover.

References core::pose::Pose::conformation().

moves::MoverOP protocols::environment::CoMTrackerCM::clone ( ) const

virtual

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.

moves::MoverOP protocols::environment::CoMTrackerCM::fresh_instance ( ) const

virtual

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.

std::string protocols::environment::CoMTrackerCM::get_name ( ) const

virtual

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

Implements protocols::moves::Mover.

void protocols::environment::CoMTrackerCM::initialize ( core::pose::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().

std::string const& protocols::environment::CoMTrackerCM::name ( ) const

inline

References name_.

void protocols::environment::CoMTrackerCM::name ( std::string const & name )

inline

References name(), and name_.

Referenced by name().

void protocols::environment::CoMTrackerCM::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::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::environment::GENERATE_STATIONARY_ATTACHMENT_POINT, and basic::datacache::DataMap::get().

void protocols::environment::CoMTrackerCM::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). A conformation is provided for reference.

Reimplemented from protocols::environment::ClaimingMover.

References protocols::environment::ClaimingMover::active_environment(), and protocols::environment::ClaimingMover::has_passport().

void protocols::environment::CoMTrackerCM::update_com ( core::pose::Pose & pose ) const

private

References protocols::environment::com_calc().

void protocols::environment::CoMTrackerCM::update_tracking_residue	(	core::kinematics::RT::Vector	new_position,
		core::Size	tracking_residue_id,
		core::pose::Pose &	pose
	)		const

private

References core::pose::Pose::conformation(), numeric::xyzVector< class >::distance_squared(), core::kinematics::FoldTree::downstream_jump_residue(), core::conformation::Conformation::downstream_jump_stub(), core::pose::Pose::fold_tree(), core::conformation::Residue::name(), core::kinematics::FoldTree::num_jump(), core::pose::Pose::residue(), core::kinematics::FoldTree::root(), core::pose::Pose::set_jump(), core::kinematics::FoldTree::upstream_jump_residue(), core::conformation::Conformation::upstream_jump_stub(), core::kinematics::Stub::v, core::conformation::Residue::xyz(), and protocols::kinmatch::xyz().

claims::EnvClaims protocols::environment::CoMTrackerCM::yield_claims	(	core::pose::Pose const &	,
		basic::datacache::WriteableCacheableMapOP
	)

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.

References protocols::environment::GENERATE_STATIONARY_ATTACHMENT_POINT, utility::vector1< T, class >::index(), protocols::environment::claims::MUST_CONTROL, and core::pose::Pose::total_residue().

Member Data Documentation

std::string protocols::environment::CoMTrackerCM::com_jump_name_

private

std::string protocols::environment::CoMTrackerCM::com_name_

private

core::pack::task::residue_selector::ResidueSubset protocols::environment::CoMTrackerCM::mobile_residues_

private

core::pack::task::residue_selector::ResidueSelectorCOP protocols::environment::CoMTrackerCM::mobile_selector_

private

std::string protocols::environment::CoMTrackerCM::name_

private

Referenced by name().

std::string protocols::environment::CoMTrackerCM::stationary_label_

private

The documentation for this class was generated from the following files:

src/protocols/environment/CoMTrackerCM.hh
src/protocols/environment/CoMTrackerCM.cc

Public Member Functions

Protected Member Functions

Private Types

Private Member Functions

Private Attributes

Additional Inherited Members

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation