#include <ParsedProtocol.hh>

Inheritance diagram for protocols::rosetta_scripts::ParsedProtocol:

[legend]

Classes
struct	ParsedProtocolStep
	Represents a step in the ParsedProtocol Note that one or more of mover/filter/metrics may be null/empty. More...

Public Types
enum class	FilterReportTime { AT_END , AFTER_APPLY , NONE }

typedef core::Real	Real

typedef core::pose::Pose	Pose

typedef utility::vector1< ParsedProtocolStep >	ParsedProtocolStepVector

typedef ParsedProtocolStepVector::iterator	iterator

typedef ParsedProtocolStepVector::const_iterator	const_iterator

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

Public Member Functions
	ParsedProtocol ()

	~ParsedProtocol () override

void	apply (Pose &pose) override

core::pose::PoseOP	get_additional_output () override

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_pose (Pose &pose) const

void	add_values_to_job (Pose const &pose, protocols::jd2::Job &) const override

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

ParsedProtocolStep	get_step (core::Size const step_number) const

void	add_step (protocols::moves::MoverOP mover, std::string const &mover_name, protocols::filters::FilterOP filter, bool const report_filter_at_end=false)
	Add a mover-filter pair. More...

void	add_step (ParsedProtocolStep const &step)
	Add a step to the protocol. More...

void	set_resid (core::Size const resid) override

void	set_resid (core::pose::ResidueIndexDescriptionCOP r) override

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

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

void	parse_my_tag (utility::tag::TagCOP, basic::datacache::DataMap &) override
	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

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

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

void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const override
	Provide the citation. More...

core::Size	n_steps_passed_in_previous_run () const

bool	get_filter_status () const
	Get the status of any filters after running. More...

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...

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...

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...

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

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

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

	ResId (core::Size const r)

virtual	~ResId ()=default

virtual core::Size	get_resid (core::pose::Pose const &) const

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

void	modifiable (bool const u)

Public Member Functions inherited from protocols::jd2::JobOutputterObserver
virtual	~JobOutputterObserver ()=default

Static Public Member Functions
static std::string	mover_name ()

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

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	finish_protocol (Pose &pose)

bool	apply_step (Pose &pose, ParsedProtocolStep const &step, bool skip_mover=false)
	apply the components of the step More...

bool	apply_mover (Pose &pose, ParsedProtocolStep const &step)
	apply the mover of the step More...

bool	apply_filter (Pose &pose, ParsedProtocolStep const &step)
	apply the filter of the step More...

void	apply_metrics (Pose &pose, ParsedProtocolStep const &step)
	apply the metric of the step More...

void	sequence_protocol (Pose &pose, ParsedProtocolStepVector::const_iterator mover_it_in)

void	random_order_protocol (Pose &pose)

void	random_single_protocol (Pose &pose)

Private Attributes
ParsedProtocolStepVector	steps_

core::scoring::ScoreFunctionCOP	final_scorefxn_

std::string	mode_ = "sequence"

utility::vector1< core::Real >	apply_probability_

core::Size	last_attempted_mover_idx_ = 0

bool	report_call_order_ = false

std::string	call_order_

protocols::moves::MoverOP	last_mover_

bool	resume_support_ = false

core::Size	n_steps_passed_in_previous_run_ = 0

bool	filter_status_ = true

Additional Inherited Members
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

◆ const_iterator

typedef ParsedProtocolStepVector::const_iterator protocols::rosetta_scripts::ParsedProtocol::const_iterator

◆ iterator

typedef ParsedProtocolStepVector::iterator protocols::rosetta_scripts::ParsedProtocol::iterator

◆ ParsedProtocolStepVector

typedef utility::vector1< ParsedProtocolStep > protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStepVector

◆ Pose

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

◆ Real

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

Member Enumeration Documentation

◆ FilterReportTime

enum protocols::rosetta_scripts::ParsedProtocol::FilterReportTime

strong

Enumerator
AT_END
AFTER_APPLY
NONE

Constructor & Destructor Documentation

◆ ParsedProtocol()

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

◆ ~ParsedProtocol()

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

overridedefault

Member Function Documentation

◆ add_step() [1/2]

void protocols::rosetta_scripts::ParsedProtocol::add_step ( ParsedProtocolStep const & step )

Add a step to the protocol.

Indended for use OUTSIDE of a RosettaScripts context.

References steps_.

◆ add_step() [2/2]

void protocols::rosetta_scripts::ParsedProtocol::add_step	(	protocols::moves::MoverOP	mover,
		std::string const &	mover_name,
		protocols::filters::FilterOP	filter,
		bool const	report_filter_at_end = `false`
	)

Add a mover-filter pair.

Indended for use OUTSIDE of a RosettaScripts context.

Author: Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

References AFTER_APPLY, AT_END, mover_name(), and steps_.

Referenced by protocols::helical_bundle_predict::HBP_HelixCoilMoveGenerator::add_helix_update_moves(), and protocols::helical_bundle_predict::HBP_HelixCoilMoveGenerator::add_nonhelix_small_moves().

◆ add_values_to_job()

void protocols::rosetta_scripts::ParsedProtocol::add_values_to_job	(	Pose const &	pose,
		protocols::jd2::Job &	job
	)		const

overridevirtual

Implements protocols::jd2::JobOutputterObserver.

References protocols::jd2::Job::add_string_real_pair(), and steps_.

◆ apply()

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

overridevirtual

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.

References apply_step(), protocols::jd2::JobDistributor::current_job(), protocols::moves::FAIL_RETRY, final_score(), protocols::jd2::JobDistributor::get_instance(), protocols::moves::Mover::get_last_move_status(), protocols::moves::Mover::get_self_ptr(), protocols::jd2::jd2_used(), last_mover_, mode_, mover_name(), protocols::moves::MS_SUCCESS, n_steps_passed_in_previous_run_, random_order_protocol(), random_single_protocol(), resume_support_, sequence_protocol(), protocols::moves::Mover::set_last_move_status(), steps_, and protocols::rosetta_scripts::TR().

◆ apply_filter()

bool protocols::rosetta_scripts::ParsedProtocol::apply_filter	(	Pose &	pose,
		ParsedProtocolStep const &	step
	)

private

apply the filter of the step

Returns false on failure

References protocols::moves::FAIL_RETRY, protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep::filter, filter_status_, protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep::report_after_apply(), protocols::moves::Mover::set_last_move_status(), core::pose::setPoseExtraScore(), protocols::rosetta_scripts::TR(), protocols::rosetta_scripts::TR_report(), and core::pose::Pose::update_residue_neighbors().

Referenced by apply_step().

◆ apply_metrics()

void protocols::rosetta_scripts::ParsedProtocol::apply_metrics	(	Pose &	pose,
		ParsedProtocolStep const &	step
	)

private

apply the metric of the step

References protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep::metric_labels, protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep::metrics, and protocols::rosetta_scripts::TR().

Referenced by apply_step().

◆ apply_mover()

bool protocols::rosetta_scripts::ParsedProtocol::apply_mover	(	Pose &	pose,
		ParsedProtocolStep const &	step
	)

private

apply the mover of the step

References end(), protocols::moves::Mover::get_native_pose(), protocols::moves::Mover::info(), last_mover_, protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep::mover, mover_name(), protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep::mover_user_name, protocols::moves::MS_SUCCESS, protocols::moves::Mover::set_last_move_status(), and protocols::rosetta_scripts::TR().

Referenced by apply_step().

◆ apply_probability() [1/2]

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

References apply_probability_, and core::simple_metrics::metrics::sum.

Referenced by parse_my_tag(), and random_single_protocol().

◆ apply_probability() [2/2]

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

References core::pose::motif::a(), apply_probability_, steps_, and core::simple_metrics::metrics::sum.

◆ apply_step()

bool protocols::rosetta_scripts::ParsedProtocol::apply_step	(	Pose &	pose,
		ParsedProtocolStep const &	step,
		bool	skip_mover = `false`
	)

private

apply the components of the step

Returns false on failure

References apply_filter(), apply_metrics(), apply_mover(), and n_steps_passed_in_previous_run_.

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

◆ begin() [1/2]

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

References steps_.

◆ begin() [2/2]

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

References steps_.

◆ call_order()

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

inline

References call_order_.

◆ clear()

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

inline

References steps_.

◆ clone()

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

overridevirtual

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.

◆ end() [1/2]

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

References steps_.

Referenced by apply_mover().

◆ end() [2/2]

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

References steps_.

◆ final_score()

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

References final_scorefxn().

Referenced by apply(), and get_additional_output().

◆ final_scorefxn() [1/2]

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

References final_scorefxn_.

Referenced by final_score().

◆ final_scorefxn() [2/2]

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

References final_scorefxn_.

◆ finish_protocol()

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

private

References protocols::jd2::current_output_name(), protocols::jd2::jd2_used(), protocols::moves::MS_SUCCESS, report_all(), report_call_order(), report_filters_to_pose(), protocols::moves::Mover::set_last_move_status(), steps_, protocols::rosetta_scripts::TR(), protocols::rosetta_scripts::TR_call_order(), and protocols::rosetta_scripts::TR_report().

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

◆ fresh_instance()

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

inlineoverridevirtual

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.

◆ get_additional_output()

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

overridevirtual

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.

References apply_step(), final_score(), mode_, protocols::moves::MS_SUCCESS, report_all(), report_filters_to_pose(), resume_support_, protocols::moves::Mover::set_last_move_status(), steps_, protocols::rosetta_scripts::TR(), and protocols::rosetta_scripts::TR_report().

◆ get_filter_status()

bool protocols::rosetta_scripts::ParsedProtocol::get_filter_status ( ) const

inline

Get the status of any filters after running.

References filter_status_.

◆ get_mover()

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

inline

References steps_.

◆ get_name()

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

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

◆ get_step()

ParsedProtocolStep protocols::rosetta_scripts::ParsedProtocol::get_step ( core::Size const step_number ) const

inline

References steps_.

◆ last_attempted_mover_idx() [1/2]

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

inline

References last_attempted_mover_idx_.

Referenced by random_single_protocol().

◆ last_attempted_mover_idx() [2/2]

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

inline

References last_attempted_mover_idx_.

◆ mode()

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

inline

References mode_.

◆ mover_name()

std::string protocols::rosetta_scripts::ParsedProtocol::mover_name ( )

static

Referenced by add_step(), apply(), apply_mover(), get_name(), protocols::rosetta_scripts::ParsedProtocolCreator::keyname(), protocols::rosetta_scripts::parse_mover_subtag(), parse_my_tag(), provide_xml_schema(), and protocols::rosetta_scripts::RosettaScriptsSchemaValidator::write_ROSETTASCRIPTS_complex_type().

◆ n_steps_passed_in_previous_run()

core::Size protocols::rosetta_scripts::ParsedProtocol::n_steps_passed_in_previous_run ( ) const

inline

References n_steps_passed_in_previous_run_.

◆ parse_my_tag()

void protocols::rosetta_scripts::ParsedProtocol::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

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 force people to reimplement this method. However, we should be chatty about the fact that someone is using a RosettaScripts interface to a mover which didn't define parse_my_tag()

Reimplemented from protocols::moves::Mover.

References AFTER_APPLY, apply_probability(), AT_END, core::simple_metrics::get_metrics_from_datamap_and_subtags(), protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep::metric_labels, protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep::metrics, mode_, mover_name(), NONE, protocols::rosetta_scripts::parse_filter_or_null(), protocols::rosetta_scripts::parse_mover_subtag(), report_call_order(), resume_support_, steps_, and protocols::rosetta_scripts::TR().