#include <AbscriptStageMover.hh>

Inheritance diagram for protocols::abinitio::abscript::AbscriptStageMover:

[legend]

Public Member Functions
	AbscriptStageMover (StageID stage, moves::MonteCarloOP mc, core::scoring::ScoreFunctionOP score, core::Size cycles)

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

void	yield_submovers (MoverSet &set) const

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

bool	setup_stage (core::pose::Pose &pose, core::Real const &progress)

void	add_submover (ClientMoverOP mover, core::Real weight)

void	add_preparer (StagePreparerOP mover)

void	set_cycles_adjust (core::Real in)

void	set_seq_sep_ramping (core::Real const slope, core::Real const intercept)

void	set_chainbreak_ramping (core::Real const slope, core::Real const intercept)

core::Real const &	seq_sep_intercept ()

core::scoring::ScoreFunctionCOP	scorefxn () const

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 MoverOP	clone () const
	Return a clone of the Mover object. 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...

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

virtual void	parse_my_tag (TagCOP tag, basic::datacache::DataMap &data)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

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...

Private Types
typedef environment::ClientMoverOP	ClientMoverOP

typedef std::set< ClientMoverOP >	MoverSet

typedef std::set< StagePreparerOP >	PreparerSet

Private Member Functions
void	update_max_seq_sep (core::pose::Pose &pose, core::Real const &progress)

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

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 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

◆ ClientMoverOP

typedef environment::ClientMoverOP protocols::abinitio::abscript::AbscriptStageMover::ClientMoverOP

private

◆ MoverSet

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

private

◆ PreparerSet

typedef std::set< StagePreparerOP > protocols::abinitio::abscript::AbscriptStageMover::PreparerSet

private

Constructor & Destructor Documentation

◆ AbscriptStageMover()

protocols::abinitio::abscript::AbscriptStageMover::AbscriptStageMover	(	StageID	stage,
		moves::MonteCarloOP	mc,
		core::scoring::ScoreFunctionOP	score,
		core::Size	cycles
	)

References random_mover_.

Member Function Documentation

◆ add_preparer()

void protocols::abinitio::abscript::AbscriptStageMover::add_preparer ( StagePreparerOP mover )

References preparers_.

◆ add_submover()

void protocols::abinitio::abscript::AbscriptStageMover::add_submover	(	ClientMoverOP	mover,
		core::Real	weight
	)

References movers_, and random_mover_.

◆ apply()

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

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References protocols::moves::RepeatMover::apply(), core::pose::Pose::constraint_set(), cycles_, cycles_adjust_, protocols::abinitio::abscript::I, mc_, random_mover_, and stage_.

Referenced by protocols::abinitio::abscript::AbscriptMover::StageTracker::do_step().

◆ get_name()

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

overridevirtual

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

Implements protocols::moves::Mover.

References stage_, and core::id::to_string().

◆ scorefxn()

core::scoring::ScoreFunctionCOP protocols::abinitio::abscript::AbscriptStageMover::scorefxn ( ) const

inline

References score_.

◆ seq_sep_intercept()

core::Real const& protocols::abinitio::abscript::AbscriptStageMover::seq_sep_intercept ( )

inline

References seqsep_intcpt_.

◆ set_chainbreak_ramping()

void protocols::abinitio::abscript::AbscriptStageMover::set_chainbreak_ramping	(	core::Real const	slope,
		core::Real const	intercept
	)

References chbreak_intcpt_, and chbreak_slope_.

◆ set_cycles_adjust()

void protocols::abinitio::abscript::AbscriptStageMover::set_cycles_adjust ( core::Real in )

References cycles_adjust_, and core::conformation::membrane::in.

◆ set_seq_sep_ramping()

void protocols::abinitio::abscript::AbscriptStageMover::set_seq_sep_ramping	(	core::Real const	slope,
		core::Real const	intercept
	)

References seqsep_intcpt_, and seqsep_slope_.

◆ setup_stage()

bool protocols::abinitio::abscript::AbscriptStageMover::setup_stage	(	core::pose::Pose &	pose,
		core::Real const &	progress
	)

References protocols::abinitio::abscript::I, mc_, preparers_, score_, protocols::abinitio::abscript::score_cst(), stage_, temperature_, and update_max_seq_sep().

Referenced by protocols::abinitio::abscript::AbscriptMover::StageTracker::do_step().

◆ update_max_seq_sep()

void protocols::abinitio::abscript::AbscriptStageMover::update_max_seq_sep	(	core::pose::Pose &	pose,
		core::Real const &	progress
	)

private

◆ yield_submovers()

void protocols::abinitio::abscript::AbscriptStageMover::yield_submovers ( MoverSet & set ) const

References movers_, and preparers_.

Member Data Documentation

◆ chbreak_intcpt_

core::Real protocols::abinitio::abscript::AbscriptStageMover::chbreak_intcpt_

private

Referenced by set_chainbreak_ramping(), and update_max_seq_sep().

◆ chbreak_slope_

core::Real protocols::abinitio::abscript::AbscriptStageMover::chbreak_slope_

private

Referenced by set_chainbreak_ramping(), and update_max_seq_sep().

◆ constraints_

constraints_additional::MaxSeqSepConstraintSetOP protocols::abinitio::abscript::AbscriptStageMover::constraints_

private

Referenced by update_max_seq_sep().

◆ cycles_

core::Size const protocols::abinitio::abscript::AbscriptStageMover::cycles_

private

Referenced by apply().

◆ cycles_adjust_

core::Real protocols::abinitio::abscript::AbscriptStageMover::cycles_adjust_

private

Referenced by apply(), and set_cycles_adjust().

◆ mc_

moves::MonteCarloOP protocols::abinitio::abscript::AbscriptStageMover::mc_

private

Referenced by apply(), setup_stage(), and update_max_seq_sep().

◆ movers_

MoverSet protocols::abinitio::abscript::AbscriptStageMover::movers_

private

Referenced by add_submover(), and yield_submovers().

◆ preparers_

PreparerSet protocols::abinitio::abscript::AbscriptStageMover::preparers_

private

Referenced by add_preparer(), setup_stage(), and yield_submovers().

◆ random_mover_

moves::RandomMoverOP protocols::abinitio::abscript::AbscriptStageMover::random_mover_

private

Referenced by AbscriptStageMover(), add_submover(), and apply().

◆ score_

core::scoring::ScoreFunctionOP protocols::abinitio::abscript::AbscriptStageMover::score_

private

Referenced by scorefxn(), setup_stage(), and update_max_seq_sep().

◆ seqsep_intcpt_

core::Real protocols::abinitio::abscript::AbscriptStageMover::seqsep_intcpt_

private

Referenced by seq_sep_intercept(), set_seq_sep_ramping(), and update_max_seq_sep().

◆ seqsep_slope_

core::Real protocols::abinitio::abscript::AbscriptStageMover::seqsep_slope_

private

Referenced by set_seq_sep_ramping(), and update_max_seq_sep().

◆ stage_

StageID protocols::abinitio::abscript::AbscriptStageMover::stage_

private

Referenced by apply(), get_name(), setup_stage(), and update_max_seq_sep().

◆ temperature_

core::Real protocols::abinitio::abscript::AbscriptStageMover::temperature_

private

Referenced by setup_stage().

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

src/protocols/abinitio/abscript/AbscriptStageMover.hh
src/protocols/abinitio/abscript/AbscriptStageMover.cc

Private Attributes
StageID	stage_

moves::RandomMoverOP	random_mover_

MoverSet	movers_

PreparerSet	preparers_

core::Size const	cycles_

core::Real	cycles_adjust_

core::scoring::ScoreFunctionOP	score_

moves::MonteCarloOP	mc_

core::Real	temperature_

core::Real	seqsep_slope_

core::Real	seqsep_intcpt_

core::Real	chbreak_slope_

core::Real	chbreak_intcpt_

constraints_additional::MaxSeqSepConstraintSetOP	constraints_

Public Member Functions

Private Types

Private Member Functions

Private Attributes

Additional Inherited Members

Member Typedef Documentation

◆ ClientMoverOP

◆ MoverSet

◆ PreparerSet

Constructor & Destructor Documentation

◆ AbscriptStageMover()

Member Function Documentation

◆ add_preparer()

◆ add_submover()

◆ apply()

◆ get_name()

◆ scorefxn()

◆ seq_sep_intercept()

◆ set_chainbreak_ramping()

◆ set_cycles_adjust()

◆ set_seq_sep_ramping()

◆ setup_stage()

◆ update_max_seq_sep()

◆ yield_submovers()

Member Data Documentation

◆ chbreak_intcpt_

◆ chbreak_slope_

◆ constraints_

◆ cycles_

◆ cycles_adjust_

◆ mc_

◆ movers_

◆ preparers_

◆ random_mover_

◆ score_

◆ seqsep_intcpt_

◆ seqsep_slope_

◆ stage_

◆ temperature_