Run the set of SimpleMetrics. Add the data to the pose, which will be output int the score file. with the given prefix and suffix. (prefix+metric_name+suffix) More...

#include <RunSimpleMetricsMover.hh>

Inheritance diagram for protocols::analysis::simple_metrics::RunSimpleMetricsMover:

[legend]

Public Member Functions
	RunSimpleMetricsMover ()

	RunSimpleMetricsMover (utility::vector1< core::simple_metrics::SimpleMetricCOP > const &metrics)

	RunSimpleMetricsMover (RunSimpleMetricsMover const &src)

	~RunSimpleMetricsMover () override

void	add_simple_metric (const core::simple_metrics::SimpleMetricCOP &metric)
	Add a simple metric to run. More...

void	set_simple_metrics (const utility::vector1< core::simple_metrics::SimpleMetricCOP > &metrics)

void	apply (core::pose::Pose &pose, std::string const &prefix, std::string const &suffix, std::string const &metric_to_bfactor)
	Run the set of SimpleMetrics. Add the data to the pose, which will be output int the score file. with the given prefix and suffix. (prefix+metric_name+suffix) More...

void	apply (core::pose::Pose &pose) override
	Run the set of SimpleMetrics. Add the data to the Pose, which will be output in the score file. More...

void	set_prefix (std::string const &prefix)

void	set_suffix (std::string const &suffix)

void	set_bfactor (std::string const &metric_to_bfactor)

void	set_override (bool override_existing_data)
	Should we override existing data? Default False. More...

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
	parse XML tag (to use this Mover in Rosetta Scripts) More...

protocols::moves::MoverOP	fresh_instance () const override
	required in the context of the parser/scripting scheme More...

protocols::moves::MoverOP	clone () const override
	required in the context of the parser/scripting scheme More...

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...

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...

virtual core::pose::PoseOP	get_additional_output ()
	Mechanism by which a mover may return multiple output poses from a single input pose. 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...

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	set_metric_to_bfactor (core::pose::Pose &pose, core::simple_metrics::SimpleMetricCOP const &metric)

Private Attributes
utility::vector1< core::simple_metrics::SimpleMetricCOP >	metrics_

std::string	prefix_

std::string	suffix_

std::string	metric_to_bfactor_

bool	override_existing_data_ = false

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 std::list< std::string >	Strings

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

Run the set of SimpleMetrics. Add the data to the pose, which will be output int the score file. with the given prefix and suffix. (prefix+metric_name+suffix)

Constructor & Destructor Documentation

◆ RunSimpleMetricsMover() [1/3]

protocols::analysis::simple_metrics::RunSimpleMetricsMover::RunSimpleMetricsMover ( )

◆ RunSimpleMetricsMover() [2/3]

protocols::analysis::simple_metrics::RunSimpleMetricsMover::RunSimpleMetricsMover ( utility::vector1< core::simple_metrics::SimpleMetricCOP > const & metrics )

◆ RunSimpleMetricsMover() [3/3]

protocols::analysis::simple_metrics::RunSimpleMetricsMover::RunSimpleMetricsMover ( RunSimpleMetricsMover const & src )

References metrics_.

◆ ~RunSimpleMetricsMover()

protocols::analysis::simple_metrics::RunSimpleMetricsMover::~RunSimpleMetricsMover ( )

overridedefault

Member Function Documentation

◆ add_simple_metric()

void protocols::analysis::simple_metrics::RunSimpleMetricsMover::add_simple_metric ( const core::simple_metrics::SimpleMetricCOP & metric )

Add a simple metric to run.

References metrics_.

◆ apply() [1/2]

void protocols::analysis::simple_metrics::RunSimpleMetricsMover::apply ( core::pose::Pose & pose )

overridevirtual

Run the set of SimpleMetrics. Add the data to the Pose, which will be output in the score file.

Implements protocols::moves::Mover.

References metric_to_bfactor_, metrics_, override_existing_data_, prefix_, set_metric_to_bfactor(), suffix_, and protocols::TR().

◆ apply() [2/2]

void protocols::analysis::simple_metrics::RunSimpleMetricsMover::apply	(	core::pose::Pose &	pose,
		std::string const &	prefix,
		std::string const &	suffix,
		std::string const &	metric_to_bfactor
	)

Run the set of SimpleMetrics. Add the data to the pose, which will be output int the score file. with the given prefix and suffix. (prefix+metric_name+suffix)

References set_bfactor(), set_prefix(), and set_suffix().

Referenced by protocols::energy_based_clustering::EnergyBasedClusteringProtocol::pose_from_posedata().

◆ clone()

protocols::moves::MoverOP protocols::analysis::simple_metrics::RunSimpleMetricsMover::clone ( ) const

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

◆ fresh_instance()

protocols::moves::MoverOP protocols::analysis::simple_metrics::RunSimpleMetricsMover::fresh_instance ( ) const

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

◆ get_name()

std::string protocols::analysis::simple_metrics::RunSimpleMetricsMover::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

◆ mover_name()

std::string protocols::analysis::simple_metrics::RunSimpleMetricsMover::mover_name ( )

static

Referenced by get_name(), protocols::analysis::simple_metrics::RunSimpleMetricsMoverCreator::keyname(), provide_citation_info(), and provide_xml_schema().

◆ parse_my_tag()

void protocols::analysis::simple_metrics::RunSimpleMetricsMover::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

parse XML tag (to use this Mover in Rosetta Scripts)

Reimplemented from protocols::moves::Mover.

References core::simple_metrics::get_metrics_from_datamap_and_subtags(), metric_to_bfactor_, override_existing_data_, prefix_, set_override(), set_simple_metrics(), and suffix_.

◆ provide_citation_info()

void protocols::analysis::simple_metrics::RunSimpleMetricsMover::provide_citation_info ( basic::citation_manager::CitationCollectionList & citations ) const

overridevirtual

Provide the citation.

Reimplemented from protocols::moves::Mover.

References mover_name().

◆ provide_xml_schema()

void protocols::analysis::simple_metrics::RunSimpleMetricsMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References mover_name(), and protocols::moves::xsd_type_definition_w_attributes_and_repeatable_subelements().

Referenced by protocols::analysis::simple_metrics::RunSimpleMetricsMoverCreator::provide_xml_schema().

◆ set_bfactor()

void protocols::analysis::simple_metrics::RunSimpleMetricsMover::set_bfactor ( std::string const & metric_to_bfactor )

References metric_to_bfactor_.

Referenced by apply().

◆ set_metric_to_bfactor()

void protocols::analysis::simple_metrics::RunSimpleMetricsMover::set_metric_to_bfactor	(	core::pose::Pose &	pose,
		core::simple_metrics::SimpleMetricCOP const &	metric
	)

private

References core::simple_metrics::get_sm_data(), metric_to_bfactor_, core::pose::Pose::pdb_info(), prefix_, core::pose::Pose::residue(), suffix_, and protocols::TR().

Referenced by apply().

◆ set_override()

void protocols::analysis::simple_metrics::RunSimpleMetricsMover::set_override ( bool override_existing_data )

Should we override existing data? Default False.

If existing data is found and this option is false, we will throw an exception.

References override_existing_data_.

Referenced by parse_my_tag().

◆ set_prefix()

void protocols::analysis::simple_metrics::RunSimpleMetricsMover::set_prefix ( std::string const & prefix )

References prefix_.

Referenced by apply().

◆ set_simple_metrics()

void protocols::analysis::simple_metrics::RunSimpleMetricsMover::set_simple_metrics ( const utility::vector1< core::simple_metrics::SimpleMetricCOP > & metrics )

References metrics_.

Referenced by parse_my_tag().

◆ set_suffix()

void protocols::analysis::simple_metrics::RunSimpleMetricsMover::set_suffix ( std::string const & suffix )

References suffix_.

Referenced by apply().

Member Data Documentation

◆ metric_to_bfactor_

std::string protocols::analysis::simple_metrics::RunSimpleMetricsMover::metric_to_bfactor_

private

Referenced by apply(), parse_my_tag(), set_bfactor(), and set_metric_to_bfactor().

◆ metrics_

utility::vector1< core::simple_metrics::SimpleMetricCOP > protocols::analysis::simple_metrics::RunSimpleMetricsMover::metrics_

private

Referenced by add_simple_metric(), apply(), RunSimpleMetricsMover(), and set_simple_metrics().

◆ override_existing_data_

bool protocols::analysis::simple_metrics::RunSimpleMetricsMover::override_existing_data_ = false

private

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

◆ prefix_

std::string protocols::analysis::simple_metrics::RunSimpleMetricsMover::prefix_

private

Referenced by apply(), parse_my_tag(), set_metric_to_bfactor(), and set_prefix().

◆ suffix_

std::string protocols::analysis::simple_metrics::RunSimpleMetricsMover::suffix_

private

Referenced by apply(), parse_my_tag(), set_metric_to_bfactor(), and set_suffix().

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

src/protocols/analysis/simple_metrics/RunSimpleMetricsMover.hh
src/protocols/analysis/simple_metrics/RunSimpleMetricsMover.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ RunSimpleMetricsMover() [1/3]

◆ RunSimpleMetricsMover() [2/3]

◆ RunSimpleMetricsMover() [3/3]

◆ ~RunSimpleMetricsMover()

Member Function Documentation

◆ add_simple_metric()

◆ apply() [1/2]

◆ apply() [2/2]

◆ clone()

◆ fresh_instance()

◆ get_name()

◆ mover_name()

◆ parse_my_tag()

◆ provide_citation_info()

◆ provide_xml_schema()

◆ set_bfactor()

◆ set_metric_to_bfactor()

◆ set_override()

◆ set_prefix()

◆ set_simple_metrics()

◆ set_suffix()

Member Data Documentation

◆ metric_to_bfactor_

◆ metrics_

◆ override_existing_data_

◆ prefix_

◆ suffix_