#include <SmallMinCCDTrial.hh>

Inheritance diagram for protocols::loops::loop_mover::refine::SmallMinCCDTrial:

[legend]

Public Member Functions
	SmallMinCCDTrial ()
	default constructor More...

	SmallMinCCDTrial (SmallMinCCDTrial const &rhs)
	copy constructor More...

SmallMinCCDTrial &	operator= (SmallMinCCDTrial const &rhs)
	assignment operator More...

	~SmallMinCCDTrial () override

	SmallMinCCDTrial (LoopMover_Refine_CCDAP loop_mover, moves::MonteCarloOP mc, core::scoring::ScoreFunctionOP scorefxn, core::pack::task::TaskFactoryOP tf)

void	apply (Pose &) override
	Main Method. More...

protocols::moves::MoverOP	clone () const override
	Each derived class must specify its name. More...

protocols::moves::MoverOP	fresh_instance () const override
	fresh_instance returns a default-constructed object for JD2 More...

bool	reinitialize_for_new_input () const override
	This mover retains state such that a fresh version is needed if the input Pose is about to change. More...

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

core::Size	number_of_moves () const

void	set_number_of_moves (core::Size nmoves)

core::optimization::MinimizerOptionsOP	minimizer_options () const

void	set_minimizer_options (core::optimization::MinimizerOptionsOP minimizer_options)

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

Public Member Functions inherited from protocols::loops::loop_mover::refine::LoopRefineInnerCycle
	LoopRefineInnerCycle ()
	default constructor More...

	LoopRefineInnerCycle (LoopRefineInnerCycle const &rhs)
	copy constructor More...

LoopRefineInnerCycle &	operator= (LoopRefineInnerCycle const &rhs)
	assignment operator More...

	~LoopRefineInnerCycle () override

	LoopRefineInnerCycle (LoopMover_Refine_CCDAP loop_mover, moves::MonteCarloOP mc, core::scoring::ScoreFunctionOP scorefxn, core::pack::task::TaskFactoryOP tf)

bool	debug () const

void	set_debug (bool debug)

moves::MonteCarloOP	mc () const

virtual void	set_mc (moves::MonteCarloOP mc)

core::scoring::ScoreFunctionOP	scorefxn () const

virtual void	set_scorefxn (core::scoring::ScoreFunctionOP scorefxn)

core::pack::task::TaskFactoryOP	task_factory () const

virtual void	set_task_factory (core::pack::task::TaskFactoryOP tf)

LoopMover_Refine_CCDAP	loop_mover () const

virtual void	set_loop_mover (LoopMover_Refine_CCDAP new_owner_in_town)

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...

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 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 void	register_options ()
	Associates relevant options with the LoopRefineInnerCycle class. More...

static std::string	mover_name ()

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

Static Public Member Functions inherited from protocols::loops::loop_mover::refine::LoopRefineInnerCycle
static void	register_options ()
	Associates relevant options with the LoopRefineInnerCycle class. More...

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 Member Functions
void	setup_objects (Pose const &pose)

void	init ()

void	init_for_equal_operator_and_copy_constructor (SmallMinCCDTrial &lhs, SmallMinCCDTrial const &rhs)

void	init_options ()

core::optimization::AtomTreeMinimizerOP	minimizer (core::pose::Pose const &pose) const

void	debug_zero (Pose &pose)

void	debug_one (Pose &pose)

void	debug_two (Pose &pose)

void	debug_three (Pose &pose)

void	debug_four (Pose &pose)

void	debug_five (Pose &pose)

Private Attributes
core::Size	nmoves_

core::optimization::MinimizerOptionsOP	minimizer_options_

core::optimization::AtomTreeMinimizerOP	minimizer_

Friends
std::ostream &	operator<< (std::ostream &out, SmallMinCCDTrial const &small_min_ccd_trial)

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::loops::loop_mover::refine::LoopRefineInnerCycle
core::kinematics::MoveMapOP	movemap () const

void	set_movemap (core::kinematics::MoveMapOP movemap)

Loops	get_one_random_loop () const

void	setup_objects (Pose const &pose)

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...

Constructor & Destructor Documentation

◆ SmallMinCCDTrial() [1/3]

protocols::loops::loop_mover::refine::SmallMinCCDTrial::SmallMinCCDTrial ( )

default constructor

References init().

◆ SmallMinCCDTrial() [2/3]

protocols::loops::loop_mover::refine::SmallMinCCDTrial::SmallMinCCDTrial ( SmallMinCCDTrial const & rhs )

copy constructor

References init_for_equal_operator_and_copy_constructor().

◆ ~SmallMinCCDTrial()

protocols::loops::loop_mover::refine::SmallMinCCDTrial::~SmallMinCCDTrial ( )

overridedefault

◆ SmallMinCCDTrial() [3/3]

protocols::loops::loop_mover::refine::SmallMinCCDTrial::SmallMinCCDTrial	(	LoopMover_Refine_CCDAP	loop_mover,
		moves::MonteCarloOP	mc,
		core::scoring::ScoreFunctionOP	scorefxn,
		core::pack::task::TaskFactoryOP	tf
	)

References init().

Member Function Documentation

◆ apply()

void protocols::loops::loop_mover::refine::SmallMinCCDTrial::apply ( Pose & )

overridevirtual

Main Method.

Implements protocols::loops::loop_mover::refine::LoopRefineInnerCycle.

References protocols::loops::add_loop_flank_residues_bb_to_movemap(), protocols::simple_moves::BackboneMover::apply(), protocols::loops::ccd_close_loops(), debug_five(), debug_four(), debug_one(), debug_three(), debug_two(), debug_zero(), protocols::loops::loop_mover::refine::LoopRefineInnerCycle::get_one_random_loop(), protocols::loops::loop_mover::refine::LoopRefineInnerCycle::loop_mover(), protocols::loops::loop_mover::refine::LoopRefineInnerCycle::mc(), minimizer(), minimizer_options_, protocols::loops::loop_mover::refine::LoopRefineInnerCycle::movemap(), nmoves_, core::pack::rotamer_trials(), protocols::loops::loop_mover::refine::LoopRefineInnerCycle::scorefxn(), setup_objects(), protocols::loops::Loops::size(), and protocols::loops::loop_mover::refine::LoopRefineInnerCycle::task_factory().

◆ clone()

protocols::moves::MoverOP protocols::loops::loop_mover::refine::SmallMinCCDTrial::clone ( ) const

overridevirtual

Each derived class must specify its name.

Reimplemented from protocols::moves::Mover.

◆ debug_five()

void protocols::loops::loop_mover::refine::SmallMinCCDTrial::debug_five ( Pose & pose )

private

References protocols::loops::loop_mover::refine::LoopRefineInnerCycle::debug(), core::pose::Pose::dump_pdb(), core::pose::Pose::energies(), core::chemical::element::F, protocols::moves::Mover::get_native_pose(), protocols::loops::loop_mover::refine::LoopRefineInnerCycle::loop_mover(), protocols::loops::loop_rmsd(), protocols::loops::loop_mover::refine::LoopRefineInnerCycle::scorefxn(), core::scoring::Energies::total_energies(), protocols::loops::loop_mover::refine::TR(), and core::scoring::EMapVector::weighted_string_of().

Referenced by apply().

◆ debug_four()

void protocols::loops::loop_mover::refine::SmallMinCCDTrial::debug_four ( Pose & pose )

private

References protocols::loops::loop_mover::refine::LoopRefineInnerCycle::debug(), core::pose::Pose::dump_pdb(), core::pose::Pose::energies(), core::chemical::element::F, protocols::moves::Mover::get_native_pose(), protocols::loops::loop_mover::refine::LoopRefineInnerCycle::loop_mover(), protocols::loops::loop_rmsd(), protocols::loops::loop_mover::refine::LoopRefineInnerCycle::scorefxn(), core::scoring::Energies::total_energies(), protocols::loops::loop_mover::refine::TR(), and core::scoring::EMapVector::weighted_string_of().

Referenced by apply().

◆ debug_one()

void protocols::loops::loop_mover::refine::SmallMinCCDTrial::debug_one ( Pose & pose )

private

References protocols::loops::loop_mover::refine::LoopRefineInnerCycle::debug(), core::pose::Pose::dump_pdb(), core::pose::Pose::energies(), core::chemical::element::F, protocols::moves::Mover::get_native_pose(), protocols::loops::loop_mover::refine::LoopRefineInnerCycle::loop_mover(), protocols::loops::loop_rmsd(), core::conformation::membrane::out, protocols::loops::loop_mover::refine::LoopRefineInnerCycle::scorefxn(), core::scoring::Energies::total_energies(), protocols::loops::loop_mover::refine::TR(), and core::scoring::EMapVector::weighted_string_of().

Referenced by apply().

◆ debug_three()

void protocols::loops::loop_mover::refine::SmallMinCCDTrial::debug_three ( Pose & pose )

private

References protocols::loops::loop_mover::refine::LoopRefineInnerCycle::debug(), core::pose::Pose::dump_pdb(), core::pose::Pose::energies(), core::chemical::element::F, protocols::moves::Mover::get_native_pose(), protocols::loops::loop_mover::refine::LoopRefineInnerCycle::loop_mover(), protocols::loops::loop_rmsd(), protocols::loops::loop_mover::refine::LoopRefineInnerCycle::scorefxn(), core::scoring::Energies::total_energies(), protocols::loops::loop_mover::refine::TR(), and core::scoring::EMapVector::weighted_string_of().

Referenced by apply().

◆ debug_two()

void protocols::loops::loop_mover::refine::SmallMinCCDTrial::debug_two ( Pose & pose )

private

References protocols::loops::loop_mover::refine::LoopRefineInnerCycle::debug(), core::pose::Pose::dump_pdb(), core::pose::Pose::energies(), core::chemical::element::F, protocols::moves::Mover::get_native_pose(), protocols::loops::loop_mover::refine::LoopRefineInnerCycle::loop_mover(), protocols::loops::loop_rmsd(), core::conformation::membrane::out, protocols::loops::loop_mover::refine::LoopRefineInnerCycle::scorefxn(), core::scoring::Energies::total_energies(), protocols::loops::loop_mover::refine::TR(), and core::scoring::EMapVector::weighted_string_of().

Referenced by apply().

◆ debug_zero()

void protocols::loops::loop_mover::refine::SmallMinCCDTrial::debug_zero ( Pose & pose )

private

References protocols::loops::loop_mover::refine::LoopRefineInnerCycle::debug(), core::pose::Pose::dump_pdb(), core::pose::Pose::energies(), core::chemical::element::F, protocols::moves::Mover::get_native_pose(), protocols::loops::loop_mover::refine::LoopRefineInnerCycle::loop_mover(), protocols::loops::loop_rmsd(), protocols::loops::loop_mover::refine::LoopRefineInnerCycle::scorefxn(), core::scoring::Energies::total_energies(), protocols::loops::loop_mover::refine::TR(), and core::scoring::EMapVector::weighted_string_of().

Referenced by apply().

◆ fresh_instance()

protocols::moves::MoverOP protocols::loops::loop_mover::refine::SmallMinCCDTrial::fresh_instance ( ) const

overridevirtual

fresh_instance returns a default-constructed object for JD2

Reimplemented from protocols::moves::Mover.

◆ get_name()

std::string protocols::loops::loop_mover::refine::SmallMinCCDTrial::get_name ( ) const

overridevirtual

Each derived class must specify its name.

Reimplemented from protocols::loops::loop_mover::refine::LoopRefineInnerCycle.

References mover_name().

◆ init()

void protocols::loops::loop_mover::refine::SmallMinCCDTrial::init ( void )

private

References init_options(), minimizer_options_, nmoves_, and protocols::moves::Mover::type().

Referenced by SmallMinCCDTrial().

◆ init_for_equal_operator_and_copy_constructor()

void protocols::loops::loop_mover::refine::SmallMinCCDTrial::init_for_equal_operator_and_copy_constructor	(	SmallMinCCDTrial &	lhs,
		SmallMinCCDTrial const &	rhs
	)

private

References minimizer_.

Referenced by operator=(), and SmallMinCCDTrial().

◆ init_options()

void protocols::loops::loop_mover::refine::SmallMinCCDTrial::init_options ( )

private

Referenced by init().

◆ minimizer()

core::optimization::AtomTreeMinimizerOP protocols::loops::loop_mover::refine::SmallMinCCDTrial::minimizer ( core::pose::Pose const & pose ) const

private

References core::pose::symmetry::is_symmetric(), and minimizer_.

Referenced by apply().

◆ minimizer_options()

core::optimization::MinimizerOptionsOP protocols::loops::loop_mover::refine::SmallMinCCDTrial::minimizer_options ( ) const

References minimizer_options_.

Referenced by set_minimizer_options().

◆ mover_name()

std::string protocols::loops::loop_mover::refine::SmallMinCCDTrial::mover_name ( )

static

Referenced by get_name(), protocols::loops::loop_mover::refine::SmallMinCCDTrialCreator::keyname(), and provide_xml_schema().

◆ number_of_moves()

core::Size protocols::loops::loop_mover::refine::SmallMinCCDTrial::number_of_moves ( ) const

References nmoves_.

◆ operator=()

SmallMinCCDTrial & protocols::loops::loop_mover::refine::SmallMinCCDTrial::operator= ( SmallMinCCDTrial const & rhs )

assignment operator

References init_for_equal_operator_and_copy_constructor(), and protocols::loops::loop_mover::refine::LoopRefineInnerCycle::operator=().

◆ provide_xml_schema()

void protocols::loops::loop_mover::refine::SmallMinCCDTrial::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References mover_name(), and protocols::moves::xsd_type_definition_w_attributes().

Referenced by protocols::loops::loop_mover::refine::SmallMinCCDTrialCreator::provide_xml_schema().

◆ register_options()

void protocols::loops::loop_mover::refine::SmallMinCCDTrial::register_options ( )

static

Associates relevant options with the LoopRefineInnerCycle class.

◆ reinitialize_for_new_input()

bool protocols::loops::loop_mover::refine::SmallMinCCDTrial::reinitialize_for_new_input ( ) const

overridevirtual

This mover retains state such that a fresh version is needed if the input Pose is about to change.

Reimplemented from protocols::loops::loop_mover::refine::LoopRefineInnerCycle.

◆ set_minimizer_options()

void protocols::loops::loop_mover::refine::SmallMinCCDTrial::set_minimizer_options ( core::optimization::MinimizerOptionsOP minimizer_options )

References minimizer_options(), and minimizer_options_.

◆ set_number_of_moves()

void protocols::loops::loop_mover::refine::SmallMinCCDTrial::set_number_of_moves ( core::Size nmoves )

References nmoves_.

◆ setup_objects()

void protocols::loops::loop_mover::refine::SmallMinCCDTrial::setup_objects ( Pose const & pose )

private

References protocols::loops::loop_mover::refine::LoopRefineInnerCycle::setup_objects().

Referenced by apply().

◆ show()

void protocols::loops::loop_mover::refine::SmallMinCCDTrial::show ( std::ostream & output = std::cout ) const

overridevirtual

Outputs details about the Mover, including current settings.

Ideally, a child Mover should call Mover.show() and add additional information particular to that Mover.

Reimplemented from protocols::loops::loop_mover::refine::LoopRefineInnerCycle.

References core::conformation::membrane::out.

Friends And Related Function Documentation

◆ operator<<

std::ostream& operator<<	(	std::ostream &	out,
		SmallMinCCDTrial const &	small_min_ccd_trial
	)

friend

Member Data Documentation

◆ minimizer_

core::optimization::AtomTreeMinimizerOP protocols::loops::loop_mover::refine::SmallMinCCDTrial::minimizer_

mutableprivate

Referenced by init_for_equal_operator_and_copy_constructor(), and minimizer().

◆ minimizer_options_

core::optimization::MinimizerOptionsOP protocols::loops::loop_mover::refine::SmallMinCCDTrial::minimizer_options_

private

Referenced by apply(), init(), minimizer_options(), and set_minimizer_options().

◆ nmoves_

core::Size protocols::loops::loop_mover::refine::SmallMinCCDTrial::nmoves_

private

Referenced by apply(), init(), number_of_moves(), and set_number_of_moves().

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

src/protocols/loops/loop_mover/refine/SmallMinCCDTrial.hh
src/protocols/loops/loop_mover/refine/SmallMinCCDTrial.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Friends

Additional Inherited Members

Constructor & Destructor Documentation

◆ SmallMinCCDTrial() [1/3]

◆ SmallMinCCDTrial() [2/3]

◆ ~SmallMinCCDTrial()

◆ SmallMinCCDTrial() [3/3]

Member Function Documentation

◆ apply()

◆ clone()

◆ debug_five()

◆ debug_four()

◆ debug_one()

◆ debug_three()

◆ debug_two()

◆ debug_zero()

◆ fresh_instance()

◆ get_name()

◆ init()

◆ init_for_equal_operator_and_copy_constructor()

◆ init_options()

◆ minimizer()

◆ minimizer_options()

◆ mover_name()

◆ number_of_moves()

◆ operator=()

◆ provide_xml_schema()

◆ register_options()

◆ reinitialize_for_new_input()

◆ set_minimizer_options()

◆ set_number_of_moves()

◆ setup_objects()

◆ show()

Friends And Related Function Documentation

◆ operator<<

Member Data Documentation

◆ minimizer_

◆ minimizer_options_

◆ nmoves_