#include <ParsedProtocol.hh>

Inheritance diagram for protocols::rosetta_scripts::ParsedProtocol:

Collaboration diagram for protocols::rosetta_scripts::ParsedProtocol:

Public Types
typedef core::Real	Real

typedef core::pose::Pose	Pose

typedef std::pair< std::pair < protocols::moves::MoverOP, std::string > , protocols::filters::FilterOP >	mover_filter_pair

typedef utility::vector1 < mover_filter_pair >	MoverFilterVector

typedef MoverFilterVector::iterator	iterator

typedef MoverFilterVector::const_iterator	const_iterator

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

Public Member Functions
	ParsedProtocol ()

virtual void	apply (Pose &pose)

virtual core::pose::PoseOP	get_additional_output ()

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

void	add_mover (protocols::moves::MoverCOP mover, std::string const mover_name, protocols::filters::FilterOP filter)

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

core::scoring::ScoreFunctionCOP	final_scorefxn () const

void	final_score (core::pose::Pose &pose) const

void	report_all (Pose const &pose) const

void	report_filters_to_job (Pose const &pose) const

void	report_all_sm (std::map< std::string, core::Real > &score_map, Pose const &pose) const

protocols::moves::MoverCOP	get_mover (core::Size const mover_number) const

void	set_resid (core::Size const resid)

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

protocols::moves::MoverOP	fresh_instance () const
	this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More...

virtual void	parse_my_tag (utility::tag::TagPtr const, protocols::moves::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...

void	clear ()

std::string	mode () const

iterator	begin ()

const_iterator	begin () const

iterator	end ()

const_iterator	end () const

virtual	~ParsedProtocol ()

void	apply_probability (utility::vector1< core::Real > const a)

utility::vector1< core::Real >	apply_probability ()

core::Size	size ()

core::Size	last_attempted_mover_idx ()

void	last_attempted_mover_idx (core::Size const s)

bool	report_call_order () const

void	report_call_order (bool const c)

std::string	call_order () const

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)

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 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...

virtual bool	reinitialize_for_new_input () const
	this function informs 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

Public Member Functions inherited from protocols::moves::ResId
	ResId ()

	ResId (core::Size const r)

virtual core::Size	get_resid () const

virtual core::Size &	get_resid ()

virtual bool	modifiable () const
	should another method be able to modify resid_. This is used by modify_ResId_based_object as a test More...

virtual void	modifiable (bool const u)

virtual	~ResId ()

Private Member Functions
void	finish_protocol (Pose &pose)

bool	apply_mover_filter_pair (Pose &pose, mover_filter_pair const &mover_pair)

bool	apply_filter (Pose &pose, mover_filter_pair const &mover_pair)

void	sequence_protocol (Pose &pose, utility::vector1< mover_filter_pair >::const_iterator mover_it_in)

void	random_order_protocol (Pose &pose)

void	random_single_protocol (Pose &pose)

Private Attributes
MoverFilterVector	movers_

core::scoring::ScoreFunctionCOP	final_scorefxn_

std::string	mode_

utility::vector1< core::Real >	apply_probability_

core::Size	last_attempted_mover_idx_

bool	report_call_order_

std::string	call_order_

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. 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...

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...

Detailed Description

Definition at line 41 of file ParsedProtocol.hh.

Member Typedef Documentation

typedef MoverFilterVector::const_iterator protocols::rosetta_scripts::ParsedProtocol::const_iterator

Definition at line 49 of file ParsedProtocol.hh.

typedef MoverFilterVector::iterator protocols::rosetta_scripts::ParsedProtocol::iterator

Definition at line 48 of file ParsedProtocol.hh.

typedef std::pair< std::pair< protocols::moves::MoverOP, std::string >, protocols::filters::FilterOP > protocols::rosetta_scripts::ParsedProtocol::mover_filter_pair

Definition at line 46 of file ParsedProtocol.hh.

typedef utility::vector1< mover_filter_pair > protocols::rosetta_scripts::ParsedProtocol::MoverFilterVector

Definition at line 47 of file ParsedProtocol.hh.

typedef core::pose::Pose protocols::rosetta_scripts::ParsedProtocol::Pose

Definition at line 45 of file ParsedProtocol.hh.

typedef core::Real protocols::rosetta_scripts::ParsedProtocol::Real

Definition at line 44 of file ParsedProtocol.hh.

Constructor & Destructor Documentation

protocols::rosetta_scripts::ParsedProtocol::ParsedProtocol ( )

Definition at line 96 of file ParsedProtocol.cc.

protocols::rosetta_scripts::ParsedProtocol::~ParsedProtocol ( )

virtual

Definition at line 240 of file ParsedProtocol.cc.

Member Function Documentation

void protocols::rosetta_scripts::ParsedProtocol::add_mover	(	protocols::moves::MoverCOP	mover,
		std::string const	mover_name,
		protocols::filters::FilterOP	filter
	)

Tricky! movers are cloned into the protocol b/c their apply functions (which are nonconst) could accumulate state information. Filters are safe and are therefore merely registered. Under this state of affairs, a mover or filter may be called many times in the protocol, and it will be guaranteed to have no state accumulation.

Definition at line 164 of file ParsedProtocol.cc.

References movers_.

Referenced by parse_my_tag().

void protocols::rosetta_scripts::ParsedProtocol::apply ( Pose & pose)

virtual

Detailed: Takes care of the docking, design and filtering moves. pre_cycle and pose_cycle can: be setup in derived classes to setup variables before and after these cycles.

Implements protocols::moves::Mover.

Definition at line 107 of file ParsedProtocol.cc.

References apply_filter(), protocols::moves::FAIL_RETRY, final_score(), protocols::moves::Mover::get_last_move_status(), mode_, movers_, protocols::moves::MS_SUCCESS, random_order_protocol(), random_single_protocol(), sequence_protocol(), protocols::moves::Mover::set_last_move_status(), and core::pose::Pose::update_residue_neighbors().

bool protocols::rosetta_scripts::ParsedProtocol::apply_filter	(	Pose &	pose,
		mover_filter_pair const &	mover_pair
	)

private

Definition at line 419 of file ParsedProtocol.cc.

References end(), protocols::moves::FAIL_RETRY, protocols::moves::Mover::info(), protocols::moves::MS_SUCCESS, protocols::moves::Mover::set_last_move_status(), and core::pose::Pose::update_residue_neighbors().

Referenced by apply(), apply_mover_filter_pair(), and get_additional_output().

bool protocols::rosetta_scripts::ParsedProtocol::apply_mover_filter_pair	(	Pose &	pose,
		mover_filter_pair const &	mover_pair
	)

private

Definition at line 406 of file ParsedProtocol.cc.

References apply_filter(), and protocols::moves::Mover::get_native_pose().

Referenced by get_additional_output(), random_order_protocol(), random_single_protocol(), and sequence_protocol().

void protocols::rosetta_scripts::ParsedProtocol::apply_probability ( utility::vector1< core::Real > const a)

Definition at line 506 of file ParsedProtocol.cc.

References apply_probability_, and movers_.

utility::vector1< core::Real > protocols::rosetta_scripts::ParsedProtocol::apply_probability ( )

Definition at line 497 of file ParsedProtocol.cc.

References apply_probability_.

Referenced by parse_my_tag(), and random_single_protocol().

ParsedProtocol::iterator protocols::rosetta_scripts::ParsedProtocol::begin ( )

Definition at line 227 of file ParsedProtocol.cc.

References movers_.

ParsedProtocol::const_iterator protocols::rosetta_scripts::ParsedProtocol::begin ( ) const

Definition at line 232 of file ParsedProtocol.cc.

References movers_.

std::string protocols::rosetta_scripts::ParsedProtocol::call_order ( ) const

inline

Definition at line 88 of file ParsedProtocol.hh.

References call_order_.

void protocols::rosetta_scripts::ParsedProtocol::clear ( )

inline

Definition at line 74 of file ParsedProtocol.hh.

References movers_.

protocols::moves::MoverOP protocols::rosetta_scripts::ParsedProtocol::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 257 of file ParsedProtocol.cc.

ParsedProtocol::iterator protocols::rosetta_scripts::ParsedProtocol::end ( )

Definition at line 237 of file ParsedProtocol.cc.

References movers_.

Referenced by apply_filter().

ParsedProtocol::const_iterator protocols::rosetta_scripts::ParsedProtocol::end ( ) const

Definition at line 243 of file ParsedProtocol.cc.

References movers_.

void protocols::rosetta_scripts::ParsedProtocol::final_score ( core::pose::Pose & pose) const

Definition at line 182 of file ParsedProtocol.cc.

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

Referenced by apply().

void protocols::rosetta_scripts::ParsedProtocol::final_scorefxn ( core::scoring::ScoreFunctionCOP scorefxn)

Definition at line 171 of file ParsedProtocol.cc.

References final_scorefxn_.

core::scoring::ScoreFunctionCOP protocols::rosetta_scripts::ParsedProtocol::final_scorefxn ( ) const

Definition at line 176 of file ParsedProtocol.cc.

References final_scorefxn_.

Referenced by final_score().

void protocols::rosetta_scripts::ParsedProtocol::finish_protocol ( Pose & pose)

private

Definition at line 442 of file ParsedProtocol.cc.

References protocols::jd2::JobDistributor::current_job(), protocols::jd2::JobDistributor::get_instance(), movers_, protocols::moves::MS_SUCCESS, report_all(), report_call_order(), report_filters_to_job(), and protocols::moves::Mover::set_last_move_status().

Referenced by random_order_protocol(), random_single_protocol(), and sequence_protocol().

protocols::moves::MoverOP protocols::rosetta_scripts::ParsedProtocol::fresh_instance ( ) const

inlinevirtual

this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage).

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.

Definition at line 72 of file ParsedProtocol.hh.

core::pose::PoseOP protocols::rosetta_scripts::ParsedProtocol::get_additional_output ( )

virtual

Detailed: Looks for any submovers that have additional output poses to process.: If any are found, run remainder of parsed protocol.

Reimplemented from protocols::moves::Mover.

Definition at line 357 of file ParsedProtocol.cc.

References apply_filter(), apply_mover_filter_pair(), mode_, movers_, protocols::moves::MS_SUCCESS, report_all(), report_filters_to_job(), and protocols::moves::Mover::set_last_move_status().

protocols::moves::MoverCOP protocols::rosetta_scripts::ParsedProtocol::get_mover ( core::Size const mover_number) const

inline

Definition at line 66 of file ParsedProtocol.hh.

References movers_.

std::string protocols::rosetta_scripts::ParsedProtocol::get_name ( ) const

virtual

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

Implements protocols::moves::Mover.

Definition at line 156 of file ParsedProtocol.cc.

References protocols::rosetta_scripts::ParsedProtocolCreator::mover_name().

core::Size protocols::rosetta_scripts::ParsedProtocol::last_attempted_mover_idx ( )

inline

Definition at line 84 of file ParsedProtocol.hh.

References last_attempted_mover_idx_.

Referenced by random_single_protocol().

void protocols::rosetta_scripts::ParsedProtocol::last_attempted_mover_idx ( core::Size const s)

inline

Definition at line 85 of file ParsedProtocol.hh.

References last_attempted_mover_idx_.

std::string protocols::rosetta_scripts::ParsedProtocol::mode ( ) const

inline

Definition at line 75 of file ParsedProtocol.hh.

References mode_.

void protocols::rosetta_scripts::ParsedProtocol::parse_my_tag	(	utility::tag::TagPtr const	tag,
		protocols::moves::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.

Definition at line 263 of file ParsedProtocol.cc.

References protocols::moves::DataMap::add(), add_mover(), apply_probability(), protocols::moves::DataMap::get(), protocols::moves::DataMap::has(), mode_, and report_call_order().