#include <SmallMinCCDTrial.hh>

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

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

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

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

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

virtual	~SmallMinCCDTrial ()

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

virtual void	apply (Pose &)

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

virtual protocols::moves::MoverOP	clone () const
	clone has to be overridden only if clone invocation is expected. More...

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

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

virtual void	show (std::ostream &out=std::cout)

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)

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...

virtual	~LoopRefineInnerCycle ()

	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	~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

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)

virtual void	parse_my_tag (TagPtr const tag, DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

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
	this function informs the job distributor (august 08 vintage) whether this object needs to be freshly regenerated on each use. More...

void	set_current_job (protocols::jobdist::BasicJobCOP job)

jobdist::BasicJobCOP	get_current_job () const

Static Public Member Functions
static void	register_options ()
	Associates relevant options with the LoopRefineInnerCycle class. More...

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. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. 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::TagPtr	TagPtr

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

typedef protocols::filters::Filters_map	Filters_map

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)

Detailed Description

Definition at line 42 of file SmallMinCCDTrial.hh.

Constructor & Destructor Documentation

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

default constructor

Definition at line 67 of file SmallMinCCDTrial.cc.

References init().

Referenced by clone(), and fresh_instance().

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

copy constructor

Definition at line 73 of file SmallMinCCDTrial.cc.

References init_for_equal_operator_and_copy_constructor().

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

virtual

Definition at line 88 of file SmallMinCCDTrial.cc.

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

Definition at line 127 of file SmallMinCCDTrial.cc.

References init().

Member Function Documentation

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

virtual

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

Definition at line 137 of file SmallMinCCDTrial.cc.

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().

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

virtual

clone has to be overridden only if clone invocation is expected.

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.

Definition at line 98 of file SmallMinCCDTrial.cc.

References SmallMinCCDTrial().

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

private

Definition at line 344 of file SmallMinCCDTrial.cc.

References protocols::loops::loop_mover::refine::LoopRefineInnerCycle::debug(), core::pose::Pose::dump_pdb(), core::pose::Pose::energies(), 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().

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

private

Definition at line 334 of file SmallMinCCDTrial.cc.

References protocols::loops::loop_mover::refine::LoopRefineInnerCycle::debug(), core::pose::Pose::dump_pdb(), core::pose::Pose::energies(), 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().

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

private

Definition at line 296 of file SmallMinCCDTrial.cc.

References protocols::loops::loop_mover::refine::LoopRefineInnerCycle::debug(), core::pose::Pose::dump_pdb(), core::pose::Pose::energies(), 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().

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

private

Definition at line 324 of file SmallMinCCDTrial.cc.

References protocols::loops::loop_mover::refine::LoopRefineInnerCycle::debug(), core::pose::Pose::dump_pdb(), core::pose::Pose::energies(), 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().

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

private

Definition at line 310 of file SmallMinCCDTrial.cc.

References protocols::loops::loop_mover::refine::LoopRefineInnerCycle::debug(), core::pose::Pose::dump_pdb(), core::pose::Pose::energies(), 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().

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

private

Definition at line 285 of file SmallMinCCDTrial.cc.

References protocols::loops::loop_mover::refine::LoopRefineInnerCycle::debug(), core::pose::Pose::dump_pdb(), core::pose::Pose::energies(), 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().

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

virtual

fresh_instance returns a default-constructed object for JD2

Reimplemented from protocols::moves::Mover.

Definition at line 105 of file SmallMinCCDTrial.cc.

References SmallMinCCDTrial().

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

virtual

Each derived class must specify its name.

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

Definition at line 91 of file SmallMinCCDTrial.cc.

References protocols::moves::Mover::type().

Referenced by protocols::loops::loop_mover::refine::operator<<().

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

private

Definition at line 209 of file SmallMinCCDTrial.cc.

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

Referenced by SmallMinCCDTrial().

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

private

Definition at line 219 of file SmallMinCCDTrial.cc.

References minimizer_.

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

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

private

Definition at line 228 of file SmallMinCCDTrial.cc.

Referenced by init().

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

private

Definition at line 237 of file SmallMinCCDTrial.cc.

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

Referenced by apply().

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

Definition at line 260 of file SmallMinCCDTrial.cc.

References minimizer_options_.

Referenced by set_minimizer_options().

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

Definition at line 250 of file SmallMinCCDTrial.cc.

References nmoves_.

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

assignment operator

Definition at line 79 of file SmallMinCCDTrial.cc.

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

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

static

Associates relevant options with the LoopRefineInnerCycle class.

Definition at line 116 of file SmallMinCCDTrial.cc.

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

virtual

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.

Definition at line 111 of file SmallMinCCDTrial.cc.

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

Definition at line 265 of file SmallMinCCDTrial.cc.

References minimizer_options(), and minimizer_options_.

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

Definition at line 255 of file SmallMinCCDTrial.cc.

References nmoves_.

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

private

Definition at line 202 of file SmallMinCCDTrial.cc.

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

Referenced by apply().

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

virtual

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

Definition at line 271 of file SmallMinCCDTrial.cc.

Friends And Related Function Documentation

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

friend

Definition at line 276 of file SmallMinCCDTrial.cc.

Member Data Documentation

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

mutableprivate

Definition at line 98 of file SmallMinCCDTrial.hh.

Referenced by init_for_equal_operator_and_copy_constructor(), and minimizer().

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

private

Definition at line 97 of file SmallMinCCDTrial.hh.

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

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

private

Definition at line 96 of file SmallMinCCDTrial.hh.

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

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation