#include <CoMTrackerCM.hh>

Inheritance diagram for protocols::environment::CoMTrackerCM:

[legend]

Public Member Functions
	CoMTrackerCM ()

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

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

	~CoMTrackerCM () override=default

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

void	initialize (core::pose::Pose &pose) override
	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...

void	apply (core::pose::Pose &) override
	Main Method. More...

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
	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)

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

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

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

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

	ClientMover (ClientMover const &)

	~ClientMover () override

virtual void	yield_submovers (std::set< ClientMoverOP > &) 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...

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...

Protected Member Functions
void	passport_updated () override
	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...

Protected Member Functions inherited from protocols::environment::ClientMover
void	sandboxed_copy (core::pose::Pose const &sandbox_pose, core::pose::Pose &true_pose) const
	convience method that copies all changes from an unprotected pose to a protected pose. More...

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::select::residue_selector::ResidueSubset	mobile_residues_

core::select::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 std::list< std::string >	Strings

Member Typedef Documentation

◆ EnvClaims

typedef environment::claims::EnvClaims protocols::environment::CoMTrackerCM::EnvClaims

private

◆ JumpNumber

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

private

Constructor & Destructor Documentation

◆ CoMTrackerCM() [1/3]

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

◆ CoMTrackerCM() [2/3]

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

◆ CoMTrackerCM() [3/3]

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

◆ ~CoMTrackerCM()

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

overridedefault

Member Function Documentation

◆ apply()

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

overridevirtual

Main Method.

Implements protocols::moves::Mover.

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

◆ clone()

moves::MoverOP protocols::environment::CoMTrackerCM::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.

◆ fresh_instance()

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

overridevirtual

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

Implements protocols::moves::Mover.

◆ initialize()

void protocols::environment::CoMTrackerCM::initialize ( core::pose::Pose & conf )

overridevirtual

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::ClientMover.

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

◆ mover_name()

std::string protocols::environment::CoMTrackerCM::mover_name ( )

static

Referenced by protocols::environment::CoMTrackerCMCreator::keyname().

◆ name() [1/2]

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

inline

References name_.

◆ name() [2/2]

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

inline

References name(), and name_.

Referenced by name().

◆ parse_my_tag()

void protocols::environment::CoMTrackerCM::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 protocols::environment::GENERATE_STATIONARY_ATTACHMENT_POINT.

◆ passport_updated()

void protocols::environment::CoMTrackerCM::passport_updated ( )

overrideprotectedvirtual

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::ClientMover.

References protocols::environment::ClientMover::active_environment(), core::scoring::env, and protocols::environment::ClientMover::has_passport().

◆ provide_xml_schema()

void protocols::environment::CoMTrackerCM::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References protocols::environment::GENERATE_STATIONARY_ATTACHMENT_POINT, and protocols::moves::xsd_type_definition_w_attributes().

Referenced by protocols::environment::CoMTrackerCMCreator::provide_xml_schema().

◆ update_com()

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

private

References protocols::membrane::com(), protocols::environment::com_calc(), and core::scoring::env.

◆ update_tracking_residue()

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(), core::kinematics::FoldTree::downstream_jump_residue(), core::conformation::Conformation::downstream_jump_stub(), core::pose::Pose::fold_tree(), core::conformation::Residue::name(), core::pose::Pose::residue(), core::kinematics::FoldTree::root(), core::pose::Pose::set_jump(), core::pose::Pose::size(), core::kinematics::FoldTree::upstream_jump_residue(), core::conformation::Conformation::upstream_jump_stub(), core::kinematics::Stub::v, and core::conformation::Residue::xyz().

◆ yield_claims()

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

overridevirtual

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::ClientMover.

References protocols::environment::GENERATE_STATIONARY_ATTACHMENT_POINT, core::chemical::rdkit::get_name(), and protocols::environment::claims::MUST_CONTROL.

Member Data Documentation

◆ com_jump_name_

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

private

◆ com_name_

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

private

◆ mobile_residues_

core::select::residue_selector::ResidueSubset protocols::environment::CoMTrackerCM::mobile_residues_

private

◆ mobile_selector_

core::select::residue_selector::ResidueSelectorCOP protocols::environment::CoMTrackerCM::mobile_selector_

private

◆ name_

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

private

Referenced by name().

◆ stationary_label_

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

Static Public Member Functions

Protected Member Functions

Private Types

Private Member Functions

Private Attributes

Additional Inherited Members

Member Typedef Documentation

◆ EnvClaims

◆ JumpNumber

Constructor & Destructor Documentation

◆ CoMTrackerCM() [1/3]

◆ CoMTrackerCM() [2/3]

◆ CoMTrackerCM() [3/3]

◆ ~CoMTrackerCM()

Member Function Documentation

◆ apply()

◆ clone()

◆ fresh_instance()

◆ get_name()

◆ initialize()

◆ mover_name()

◆ name() [1/2]

◆ name() [2/2]

◆ parse_my_tag()

◆ passport_updated()

◆ provide_xml_schema()

◆ update_com()

◆ update_tracking_residue()

◆ yield_claims()

Member Data Documentation

◆ com_jump_name_

◆ com_name_

◆ mobile_residues_

◆ mobile_selector_

◆ name_

◆ stationary_label_