#include <AbscriptMover.hh>

Inheritance diagram for protocols::abinitio::abscript::AbscriptMover:

Classes
class	StageTracker

Public Member Functions
	AbscriptMover ()

	AbscriptMover (AbscriptMover const &)

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

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

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

void	initialize (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	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...

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

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	stage_complex_namer (std::string)

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...

Private Types
typedef environment::claims::EnvClaims	EnvClaims

typedef environment::ClientMoverOP	ClientMoverOP

typedef std::set< ClientMoverOP >	MoverSet

typedef std::map< StageID, MoverSet >	IDMoverSetMap

Private Member Functions
void	add_frags (std::string const &small_frags, std::string const &large_frags, core::select::residue_selector::ResidueSelectorCOP=nullptr, bool initialize=true)

void	parse_subtags (utility::vector0< utility::tag::TagPtr > const &, basic::datacache::DataMap &data)

void	register_submover (protocols::moves::MoverOP, StageIDs const &, core::Real weight)

void	register_preparer (protocols::moves::MoverOP, StageIDs const &)

std::map< core::Size, core::Size >	calculate_iterations (core::pose::Pose const &)

StageIDs	parse_stage_id (std::string const &) const

Private Attributes
std::map< std::string, StageID >	id_map_

std::map< StageID, AbscriptStageMoverOP >	stage_movers_

moves::MonteCarloOP	mc_

environment::claims::EnvClaims	claims_

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

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	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...

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...

Member Typedef Documentation

typedef environment::ClientMoverOP protocols::abinitio::abscript::AbscriptMover::ClientMoverOP

private

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

private

typedef std::map< StageID, MoverSet > protocols::abinitio::abscript::AbscriptMover::IDMoverSetMap

private

typedef std::set<ClientMoverOP> protocols::abinitio::abscript::AbscriptMover::MoverSet

private

Constructor & Destructor Documentation

protocols::abinitio::abscript::AbscriptMover::AbscriptMover ( )

References protocols::abinitio::abscript::DEFAULT_TEMP, protocols::abinitio::abscript::I, id_map_, protocols::abinitio::abscript::II, protocols::abinitio::abscript::IIIa, protocols::abinitio::abscript::IIIb, protocols::abinitio::abscript::IVa, protocols::abinitio::abscript::IVb, core::scoring::linear_chainbreak, mc_, protocols::canonical_sampling::mc_convergence_checks::setup_convergence_checks_from_cmdline(), protocols::abinitio::abscript::setup_score(), and stage_movers_.

protocols::abinitio::abscript::AbscriptMover::AbscriptMover ( AbscriptMover const & src )

Member Function Documentation

void protocols::abinitio::abscript::AbscriptMover::add_frags	(	std::string const &	small_frags,
		std::string const &	large_frags,
		core::select::residue_selector::ResidueSelectorCOP	selector = `nullptr`,
		bool	initialize = `true`
	)

private

References protocols::abinitio::abscript::I, protocols::abinitio::abscript::IIIb, protocols::abinitio::abscript::increment_stageid(), protocols::abinitio::abscript::IVa, protocols::abinitio::abscript::IVb, core::fragment::FragmentIO::read_data(), and stage_movers_.

Referenced by parse_my_tag().

void protocols::abinitio::abscript::AbscriptMover::apply ( core::pose::Pose & )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

std::map< core::Size, core::Size > protocols::abinitio::abscript::AbscriptMover::calculate_iterations ( core::pose::Pose const & pose )

private

References core::pose::Pose::constraint_set(), core::pose::Pose::fold_tree(), protocols::abinitio::abscript::I, protocols::mean_field::min(), core::pose::Pose::size(), and stage_movers_.

Referenced by apply().

moves::MoverOP protocols::abinitio::abscript::AbscriptMover::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.

Referenced by parse_my_tag().

moves::MoverOP protocols::abinitio::abscript::AbscriptMover::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.

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

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

Referenced by parse_my_tag().

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

inlineoverridevirtual

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.

std::string protocols::abinitio::abscript::AbscriptMover::mover_name ( )

static

Referenced by get_name(), protocols::abinitio::abscript::AbscriptMoverCreator::keyname(), and provide_xml_schema().

void protocols::abinitio::abscript::AbscriptMover::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 add_frags(), clone(), get_name(), protocols::abinitio::abscript::I, id_map_, protocols::abinitio::abscript::II, protocols::abinitio::abscript::IIIa, protocols::abinitio::abscript::IIIb, protocols::abinitio::abscript::increment_stageid(), protocols::abinitio::abscript::IVa, protocols::abinitio::abscript::IVb, protocols::moves::Mover::name(), protocols::rosetta_scripts::parse_mover_or_null(), parse_stage_id(), register_preparer(), register_submover(), stage_movers_, core::id::to_string(), and tr().

StageIDs protocols::abinitio::abscript::AbscriptMover::parse_stage_id ( std::string const & id_str ) const

private

References id_map_, protocols::abinitio::abscript::increment_stageid(), protocols::sic_dock::range(), and protocols::abinitio::abscript::verify_stage_ID().

Referenced by parse_my_tag().

void protocols::abinitio::abscript::AbscriptMover::parse_subtags	(	utility::vector0< utility::tag::TagPtr > const &	,
		basic::datacache::DataMap &	data
	)

private

void protocols::abinitio::abscript::AbscriptMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References mover_name(), stage_complex_namer(), and protocols::moves::xsd_type_definition_w_attributes_and_repeatable_subelements().

Referenced by protocols::abinitio::abscript::AbscriptMoverCreator::provide_xml_schema().

void protocols::abinitio::abscript::AbscriptMover::register_preparer	(	protocols::moves::MoverOP	mover,
		StageIDs const &	ids
	)

private

References stage_movers_, and tr().

Referenced by parse_my_tag().

void protocols::abinitio::abscript::AbscriptMover::register_submover	(	protocols::moves::MoverOP	mover_in,
		StageIDs const &	ids,
		core::Real	weight
	)

private

References stage_movers_, and tr().

Referenced by parse_my_tag().

std::string protocols::abinitio::abscript::AbscriptMover::stage_complex_namer ( std::string tag_name )

static

Referenced by provide_xml_schema().

EnvClaims protocols::abinitio::abscript::AbscriptMover::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 claims_.

void protocols::abinitio::abscript::AbscriptMover::yield_submovers ( std::set< ClientMoverOP > & ) const

overridevirtual

this method is used to make sure any movers contained in this mover (that want to make claims) also get registered with the environment.

Reimplemented from protocols::environment::ClientMover.

References stage_movers_.