#include <EnzRepackMinimize.hh>

Public Member Functions
	EnzRepackMinimize ()

	EnzRepackMinimize (std::string const name)

virtual	~EnzRepackMinimize ()

void	ensure_scofx_cstfication (core::pose::Pose const &pose)
	turns on constraint score terms in case the pose has an enzdes cst cache More...

void	minimize_in_stages (core::pose::Pose &pose, core::pack::task::PackerTaskCOP task, bool const &cstopt, bool const &min_sc, bool const &min_rb, bool const &min_lig)

void	apply (core::pose::Pose &pose)

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

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

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

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

utility::vector1< core::Size >	rb_min_jumps () const

void	rb_min_jumps (utility::vector1< core::Size > const )

void	set_min_rb (bool const min_rb)

bool	get_min_rb () const

void	set_min_sc (bool const min_sc)

bool	get_min_sc () const

void	set_min_lig (bool const min_lig)

bool	get_min_lig () const

void	set_min_bb (bool const min_bb)

bool	get_min_bb () const

bool	get_design () const

void	set_design (bool const des)

void	set_scorefxn_repack (core::scoring::ScoreFunctionCOP scorefxn)

void	set_scorefxn_minimize (core::scoring::ScoreFunctionCOP scorefxn)

core::scoring::ScoreFunctionOP	scorefxn_repack () const

core::scoring::ScoreFunctionOP	scorefxn_minimize () const

core::pack::task::PackerTaskOP	create_ptask (core::pose::Pose &pose)

void	task_factory (core::pack::task::TaskFactoryOP p)

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

void	set_type (std::string const &setting)

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)

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
	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...

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

jobdist::BasicJobCOP	get_current_job () const

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

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 protocols::filters::Filters_map	Filters_map

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...

Constructor & Destructor Documentation

protocols::enzdes::EnzRepackMinimize::EnzRepackMinimize ( )

Referenced by clone(), and fresh_instance().

protocols::enzdes::EnzRepackMinimize::EnzRepackMinimize ( std::string const name )

protocols::enzdes::EnzRepackMinimize::~EnzRepackMinimize ( )

virtual

Member Function Documentation

void protocols::enzdes::EnzRepackMinimize::apply ( core::pose::Pose & pose )

virtual

protocols::moves::MoverOP protocols::enzdes::EnzRepackMinimize::clone ( ) const

virtual

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.

References EnzRepackMinimize().

core::pack::task::PackerTaskOP protocols::enzdes::EnzRepackMinimize::create_ptask ( core::pose::Pose & pose )

References core::pack::task::TaskFactory::create_task_and_apply_taskoperations(), core::pack::task::TaskFactory::push_back(), task_factory_, and protocols::enzdes::TR.

Referenced by apply().

void protocols::enzdes::EnzRepackMinimize::ensure_scofx_cstfication ( core::pose::Pose const & pose )

turns on constraint score terms in case the pose has an enzdes cst cache

References protocols::enzdes::enzutil::enable_constraint_scoreterms(), protocols::toolbox::match_enzdes_util::get_enzdes_observer(), protocols::enzdes::enzutil::is_scofx_cstfied(), scorefxn_minimize_, scorefxn_repack_, protocols::enzdes::enzutil::scorefxn_update_from_options(), and protocols::enzdes::TR.

Referenced by apply().

protocols::moves::MoverOP protocols::enzdes::EnzRepackMinimize::fresh_instance ( ) const

virtual

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.

References EnzRepackMinimize().

bool protocols::enzdes::EnzRepackMinimize::get_design ( ) const

inline

References design_.

bool protocols::enzdes::EnzRepackMinimize::get_min_bb ( ) const

inline

References min_bb_.

bool protocols::enzdes::EnzRepackMinimize::get_min_lig ( ) const

inline

References min_lig_.

bool protocols::enzdes::EnzRepackMinimize::get_min_rb ( ) const

inline

References min_rb_.

bool protocols::enzdes::EnzRepackMinimize::get_min_sc ( ) const

inline

References min_sc_.

std::string protocols::enzdes::EnzRepackMinimize::get_name ( ) const

virtual

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

Implements protocols::moves::Mover.

References protocols::enzdes::EnzRepackMinimizeCreator::mover_name().

void protocols::enzdes::EnzRepackMinimize::minimize_in_stages	(	core::pose::Pose &	pose,
		core::pack::task::PackerTaskCOP	task,
		bool const &	cstopt,
		bool const &	min_sc,
		bool const &	min_rb,
		bool const &	min_lig
	)

References min_rb_, scorefxn_minimize(), and protocols::enzdes::TR.

Referenced by apply().

void protocols::enzdes::EnzRepackMinimize::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data,
		protocols::filters::Filters_map const &	filters,
		protocols::moves::Movers_map const &	movers,
		core::pose::Pose const &	pose
	)

virtual

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 stop executions. This, however, calls attention to the lack of this method, which could be due to something as silly as a wrong parameters definition.

Reimplemented from protocols::moves::Mover.

References backrub_, core::scoring::ScoreFunction::clone(), cst_opt_, design_, fix_catalytic_, protocols::rosetta_scripts::get_score_function_name(), min_bb_, minimize_in_stages_, minimize_prot_jumps_, n_cycles_, protocols::rosetta_scripts::parse_score_function(), protocols::rosetta_scripts::parse_task_operations(), rb_min_jumps(), repack_, scorefxn_minimize_, scorefxn_repack_, set_min_bb(), set_min_lig(), set_min_rb(), set_min_sc(), size(), task_factory(), task_factory_, protocols::enzdes::TR, and utility_exit_with_message.

utility::vector1< core::Size > protocols::enzdes::EnzRepackMinimize::rb_min_jumps ( ) const

References rb_min_jumps_.

Referenced by apply(), and parse_my_tag().

void protocols::enzdes::EnzRepackMinimize::rb_min_jumps ( utility::vector1< core::Size > const v )

References rb_min_jumps_.

core::scoring::ScoreFunctionOP protocols::enzdes::EnzRepackMinimize::scorefxn_minimize ( ) const

References scorefxn_minimize_.

Referenced by minimize_in_stages().

core::scoring::ScoreFunctionOP protocols::enzdes::EnzRepackMinimize::scorefxn_repack ( ) const

References scorefxn_repack_.

void protocols::enzdes::EnzRepackMinimize::set_design ( bool const des )

inline

References design_.

void protocols::enzdes::EnzRepackMinimize::set_min_bb ( bool const min_bb )

inline

References min_bb_.

Referenced by parse_my_tag().

void protocols::enzdes::EnzRepackMinimize::set_min_lig ( bool const min_lig )

inline

References min_lig_.

Referenced by parse_my_tag().

void protocols::enzdes::EnzRepackMinimize::set_min_rb ( bool const min_rb )

inline

References min_rb_.

Referenced by parse_my_tag().

void protocols::enzdes::EnzRepackMinimize::set_min_sc ( bool const min_sc )

inline

References min_sc_.

Referenced by parse_my_tag().

void protocols::enzdes::EnzRepackMinimize::set_scorefxn_minimize ( core::scoring::ScoreFunctionCOP scorefxn )

References scorefxn_minimize_.

void protocols::enzdes::EnzRepackMinimize::set_scorefxn_repack ( core::scoring::ScoreFunctionCOP scorefxn )

References scorefxn_repack_.

void protocols::enzdes::EnzRepackMinimize::task_factory ( core::pack::task::TaskFactoryOP p )

References task_factory_.

Referenced by parse_my_tag().

Member Data Documentation

bool protocols::enzdes::EnzRepackMinimize::backrub_

private

Referenced by apply(), and parse_my_tag().

bool protocols::enzdes::EnzRepackMinimize::cst_opt_

private

Referenced by apply(), and parse_my_tag().

bool protocols::enzdes::EnzRepackMinimize::design_

private

Referenced by apply(), get_design(), parse_my_tag(), and set_design().

bool protocols::enzdes::EnzRepackMinimize::fix_catalytic_

private

Referenced by apply(), and parse_my_tag().

bool protocols::enzdes::EnzRepackMinimize::min_bb_

private

Referenced by apply(), get_min_bb(), parse_my_tag(), and set_min_bb().

bool protocols::enzdes::EnzRepackMinimize::min_lig_

private

Referenced by apply(), get_min_lig(), and set_min_lig().

bool protocols::enzdes::EnzRepackMinimize::min_rb_

private

Referenced by apply(), get_min_rb(), minimize_in_stages(), and set_min_rb().

bool protocols::enzdes::EnzRepackMinimize::min_sc_

private

Referenced by apply(), get_min_sc(), and set_min_sc().

bool protocols::enzdes::EnzRepackMinimize::minimize_in_stages_

private

Referenced by apply(), and parse_my_tag().

bool protocols::enzdes::EnzRepackMinimize::minimize_prot_jumps_

private

Referenced by apply(), and parse_my_tag().

core::Size protocols::enzdes::EnzRepackMinimize::n_cycles_

private

Referenced by apply(), and parse_my_tag().

utility::vector1< core::Size > protocols::enzdes::EnzRepackMinimize::rb_min_jumps_

private

Referenced by rb_min_jumps().

bool protocols::enzdes::EnzRepackMinimize::repack_

private

Referenced by apply(), and parse_my_tag().

core::scoring::ScoreFunctionOP protocols::enzdes::EnzRepackMinimize::scorefxn_minimize_

private

Referenced by apply(), ensure_scofx_cstfication(), parse_my_tag(), scorefxn_minimize(), and set_scorefxn_minimize().

core::scoring::ScoreFunctionOP protocols::enzdes::EnzRepackMinimize::scorefxn_repack_

private

Referenced by apply(), ensure_scofx_cstfication(), parse_my_tag(), scorefxn_repack(), and set_scorefxn_repack().

core::pack::task::PackerTaskOP protocols::enzdes::EnzRepackMinimize::task_

private

Referenced by apply().

core::pack::task::TaskFactoryOP protocols::enzdes::EnzRepackMinimize::task_factory_

private

Referenced by apply(), create_ptask(), parse_my_tag(), and task_factory().

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

src/protocols/enzdes/EnzRepackMinimize.hh
src/protocols/enzdes/EnzRepackMinimize.cc

Private Attributes
core::scoring::ScoreFunctionOP	scorefxn_repack_

core::scoring::ScoreFunctionOP	scorefxn_minimize_

bool	cst_opt_

bool	design_

bool	repack_

bool	fix_catalytic_

bool	minimize_in_stages_

bool	min_rb_

bool	min_sc_

bool	min_bb_

bool	min_lig_

bool	minimize_prot_jumps_

bool	backrub_

core::pack::task::PackerTaskOP	task_

core::pack::task::TaskFactoryOP	task_factory_

core::Size	n_cycles_

utility::vector1< core::Size >	rb_min_jumps_

Public Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation