protocols::toolbox::task_operations::StoreCompoundTaskMover Class Reference

#include <StoreCompoundTaskMover.hh>

Public Types
typedef std::vector< std::pair < core::pack::task::PackerTaskOP, boolean_operations > >	CompoundTask
typedef CompoundTask::iterator	task_iterator
typedef CompoundTask::const_iterator	const_task_iterator
typedef std::vector< std::pair < core::pack::task::TaskFactoryOP, boolean_operations > >	CompoundFactory
typedef CompoundFactory::iterator	factory_iterator
typedef CompoundFactory::const_iterator	const_factory_iterator
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

Public Member Functions
	StoreCompoundTaskMover ()
	~StoreCompoundTaskMover ()
void	CompoundPackableTask (core::pose::Pose const &pose, core::Size &total_residue, core::pack::task::PackerTaskOP &task)
void	CompoundDesignableTask (core::pose::Pose const &pose, core::Size &total_residue, core::pack::task::PackerTaskOP &task)
virtual 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	task_clear ()
task_iterator	task_begin ()
const_task_iterator	task_begin () const
task_iterator	task_end ()
const_task_iterator	task_end () const
void	factory_clear ()
factory_iterator	factory_begin ()
const_factory_iterator	factory_begin () const
factory_iterator	factory_end ()
const_factory_iterator	factory_end () const
void	task_name (std::string const tn)
void	mode (std::string const md)
void	true_behavior (std::string const tb)
void	false_behavior (std::string const fb)
void	invert (bool const inv)
void	verbose (bool const verb)
void	overwrite (bool const ow)
void	parse_my_tag (TagCOP tag, basic::datacache::DataMap &data_map, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &pose)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
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...

Private Attributes
CompoundTask	compound_task_
CompoundFactory	compound_factory_
std::string	task_name_
std::string	mode_
std::string	true_behavior_
std::string	false_behavior_
bool	invert_
bool	verbose_
bool	overwrite_

Additional Inherited Members
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

typedef std::vector< std::pair< core::pack::task::TaskFactoryOP, boolean_operations > > protocols::toolbox::task_operations::StoreCompoundTaskMover::CompoundFactory

typedef std::vector< std::pair< core::pack::task::PackerTaskOP, boolean_operations > > protocols::toolbox::task_operations::StoreCompoundTaskMover::CompoundTask

typedef CompoundFactory::const_iterator protocols::toolbox::task_operations::StoreCompoundTaskMover::const_factory_iterator

typedef CompoundTask::const_iterator protocols::toolbox::task_operations::StoreCompoundTaskMover::const_task_iterator

typedef CompoundFactory::iterator protocols::toolbox::task_operations::StoreCompoundTaskMover::factory_iterator

typedef CompoundTask::iterator protocols::toolbox::task_operations::StoreCompoundTaskMover::task_iterator

Constructor & Destructor Documentation

protocols::toolbox::task_operations::StoreCompoundTaskMover::StoreCompoundTaskMover

(

)

Referenced by clone(), and fresh_instance().

protocols::toolbox::task_operations::StoreCompoundTaskMover::~StoreCompoundTaskMover

(

)

Member Function Documentation

void protocols::toolbox::task_operations::StoreCompoundTaskMover::apply ( core::pose::Pose &  pose )

virtual

Implements protocols::moves::Mover.

References core::pack::task::PackerTask::clone(), compound_factory_, compound_task_, CompoundDesignableTask(), CompoundPackableTask(), core::pack::task::TaskFactory::create_packer_task(), core::pose::Pose::data(), basic::datacache::BasicDataCache::get_ptr(), basic::datacache::BasicDataCache::has(), protocols::toolbox::task_operations::STMStoredTask::has_task(), core::pose::symmetry::is_symmetric(), core::pack::make_symmetric_PackerTask_by_truncation(), mode_, overwrite_, runtime_assert, basic::datacache::BasicDataCache::set(), protocols::toolbox::task_operations::STMStoredTask::set_task(), core::pose::datacache::CacheableDataType::STM_STORED_TASKS, core::pose::symmetry::symmetry_info(), task_name_, core::pose::Pose::total_residue(), and utility_exit_with_message.

protocols::moves::MoverOP protocols::toolbox::task_operations::StoreCompoundTaskMover::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 StoreCompoundTaskMover().

void protocols::toolbox::task_operations::StoreCompoundTaskMover::CompoundDesignableTask	(	core::pose::Pose const &	pose,
		core::Size &	total_residue,
		core::pack::task::PackerTaskOP &	task
	)

References protocols::toolbox::task_operations::AND, protocols::toolbox::task_operations::ANDNOT, compound_task_, false_behavior_, invert_, protocols::toolbox::task_operations::NAND, core::pack::task::PackerTask::nonconst_residue_task(), protocols::toolbox::task_operations::NOR, protocols::toolbox::task_operations::NOT, basic::options::option, protocols::toolbox::task_operations::OR, protocols::toolbox::task_operations::ORNOT, core::pose::Pose::pdb_info(), core::pack::task::ResidueLevelTask::prevent_repacking(), basic::options::OptionKeys::out::file::renumber_pdb, resi, core::pack::task::ResidueLevelTask::restrict_to_repacking(), task_name_, protocols::toolbox::task_operations::TR, true_behavior_, verbose_, and protocols::toolbox::task_operations::XOR.

Referenced by apply().

void protocols::toolbox::task_operations::StoreCompoundTaskMover::CompoundPackableTask	(	core::pose::Pose const &	pose,
		core::Size &	total_residue,
		core::pack::task::PackerTaskOP &	task
	)

References protocols::toolbox::task_operations::AND, protocols::toolbox::task_operations::ANDNOT, compound_task_, false_behavior_, invert_, protocols::toolbox::task_operations::NAND, core::pack::task::PackerTask::nonconst_residue_task(), protocols::toolbox::task_operations::NOR, protocols::toolbox::task_operations::NOT, basic::options::option, protocols::toolbox::task_operations::OR, protocols::toolbox::task_operations::ORNOT, core::pose::Pose::pdb_info(), core::pack::task::ResidueLevelTask::prevent_repacking(), basic::options::OptionKeys::out::file::renumber_pdb, resi, core::pack::task::ResidueLevelTask::restrict_to_repacking(), task_name_, protocols::toolbox::task_operations::TR, true_behavior_, verbose_, and protocols::toolbox::task_operations::XOR.

Referenced by apply().

StoreCompoundTaskMover::factory_iterator protocols::toolbox::task_operations::StoreCompoundTaskMover::factory_begin

(

)

References compound_factory_.

StoreCompoundTaskMover::const_factory_iterator protocols::toolbox::task_operations::StoreCompoundTaskMover::factory_begin

(

)

const

References compound_factory_.

void protocols::toolbox::task_operations::StoreCompoundTaskMover::factory_clear

(

)

References compound_factory_.

StoreCompoundTaskMover::factory_iterator protocols::toolbox::task_operations::StoreCompoundTaskMover::factory_end

(

)

References compound_factory_.

StoreCompoundTaskMover::const_factory_iterator protocols::toolbox::task_operations::StoreCompoundTaskMover::factory_end

(

)

const

References compound_factory_.

void protocols::toolbox::task_operations::StoreCompoundTaskMover::false_behavior

(

std::string const

fb

)

References false_behavior_.

protocols::moves::MoverOP protocols::toolbox::task_operations::StoreCompoundTaskMover::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 StoreCompoundTaskMover().

std::string protocols::toolbox::task_operations::StoreCompoundTaskMover::get_name ( ) const

virtual

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

Implements protocols::moves::Mover.

void protocols::toolbox::task_operations::StoreCompoundTaskMover::invert

(

bool const

inv

)

References invert_.

void protocols::toolbox::task_operations::StoreCompoundTaskMover::mode

(

std::string const

md

)

References mode_.

void protocols::toolbox::task_operations::StoreCompoundTaskMover::overwrite

(

bool const

ow

)

References overwrite_.

void protocols::toolbox::task_operations::StoreCompoundTaskMover::parse_my_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 protocols::toolbox::task_operations::AND, protocols::toolbox::task_operations::ANDNOT, core::pack::task::TaskFactory::clone(), compound_factory_, end, false_behavior_, basic::datacache::DataMap::get(), basic::datacache::DataMap::has(), invert_, mode_, protocols::toolbox::task_operations::NAND, protocols::toolbox::task_operations::NOR, protocols::toolbox::task_operations::NOT, protocols::toolbox::task_operations::OR, protocols::toolbox::task_operations::ORNOT, overwrite_, core::pack::task::TaskFactory::push_back(), runtime_assert, utility::string_split(), task_name_, protocols::toolbox::task_operations::TR, true_behavior_, utility_exit_with_message, verbose_, and protocols::toolbox::task_operations::XOR.

StoreCompoundTaskMover::task_iterator protocols::toolbox::task_operations::StoreCompoundTaskMover::task_begin

(

)

References compound_task_.

StoreCompoundTaskMover::const_task_iterator protocols::toolbox::task_operations::StoreCompoundTaskMover::task_begin

(

)

const

References compound_task_.

void protocols::toolbox::task_operations::StoreCompoundTaskMover::task_clear

(

)

References compound_task_.

StoreCompoundTaskMover::task_iterator protocols::toolbox::task_operations::StoreCompoundTaskMover::task_end

(

)

References compound_task_.

StoreCompoundTaskMover::const_task_iterator protocols::toolbox::task_operations::StoreCompoundTaskMover::task_end

(

)

const

References compound_task_.

void protocols::toolbox::task_operations::StoreCompoundTaskMover::task_name

(

std::string const

tn

)

References task_name_.

void protocols::toolbox::task_operations::StoreCompoundTaskMover::true_behavior

(

std::string const

tb

)

References true_behavior_.

void protocols::toolbox::task_operations::StoreCompoundTaskMover::verbose

(

bool const

verb

)

References verbose_.

Member Data Documentation

CompoundFactory protocols::toolbox::task_operations::StoreCompoundTaskMover::compound_factory_

private

Referenced by apply(), factory_begin(), factory_clear(), factory_end(), and parse_my_tag().

CompoundTask protocols::toolbox::task_operations::StoreCompoundTaskMover::compound_task_

private

Referenced by apply(), CompoundDesignableTask(), CompoundPackableTask(), task_begin(), task_clear(), and task_end().

std::string protocols::toolbox::task_operations::StoreCompoundTaskMover::false_behavior_

private

Referenced by CompoundDesignableTask(), CompoundPackableTask(), false_behavior(), and parse_my_tag().

bool protocols::toolbox::task_operations::StoreCompoundTaskMover::invert_

private

Referenced by CompoundDesignableTask(), CompoundPackableTask(), invert(), and parse_my_tag().

std::string protocols::toolbox::task_operations::StoreCompoundTaskMover::mode_

private

Referenced by apply(), mode(), and parse_my_tag().

bool protocols::toolbox::task_operations::StoreCompoundTaskMover::overwrite_

private

Referenced by apply(), overwrite(), and parse_my_tag().

std::string protocols::toolbox::task_operations::StoreCompoundTaskMover::task_name_

private

Referenced by apply(), CompoundDesignableTask(), CompoundPackableTask(), parse_my_tag(), and task_name().

std::string protocols::toolbox::task_operations::StoreCompoundTaskMover::true_behavior_

private

Referenced by CompoundDesignableTask(), CompoundPackableTask(), parse_my_tag(), and true_behavior().

bool protocols::toolbox::task_operations::StoreCompoundTaskMover::verbose_

private

Referenced by CompoundDesignableTask(), CompoundPackableTask(), parse_my_tag(), and verbose().

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

• src/protocols/toolbox/task_operations/StoreCompoundTaskMover.hh
• src/protocols/toolbox/task_operations/StoreCompoundTaskMover.cc