A string metric that generates a string of PyMol commands to colour a structure's polar groups based on burial. More...

#include <PolarGroupBurialPyMolStringMetric.hh>

Inheritance diagram for protocols::analysis::burial_metrics::PolarGroupBurialPyMolStringMetric:

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Public Member Functions
	PolarGroupBurialPyMolStringMetric ()
	Constructors ///. More...

	PolarGroupBurialPyMolStringMetric (PolarGroupBurialPyMolStringMetric const &src)
	Copy constructor (not needed unless you need deep copies) More...

	~PolarGroupBurialPyMolStringMetric () override
	Destructor (important for properly forward-declaring smart-pointer members) More...

std::string	calculate (core::pose::Pose const &original_pose) const override
	Metric Methods ///. More...

std::string	name () const override
	Name of the class. More...

std::string	metric () const override
	Name (descriptive) of the metric. More...

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
	Given an XML tag, configure an instance of this class. More...

core::simple_metrics::SimpleMetricOP	clone () const override

void	set_scorefxn (core::scoring::ScoreFunctionCOP sfxn_in)
	Set the scorefunction. More...

void	set_verbose (bool const setting)
	Set whether this metric should also output to tracer when evaluated. More...

Public Member Functions inherited from core::simple_metrics::StringMetric
	StringMetric ()

	~StringMetric () override

	StringMetric (StringMetric const &other)

void	apply (std::string const &out_label, pose::Pose &pose, bool override_existing_data=false) const override
	Calculate the metric and add it to the pose as a score. labeled as out_label. More...

std::string	cached_calculate (pose::Pose const &pose, bool use_cache, std::string prefix="", std::string suffix="", bool fail_on_missing_cache=true) const
	Grab the data from the pose if it exists or calculate the metric. More...

utility::vector1< std::string >	get_metric_names () const override
	Get the metric name that this Metric will calculate. More...

virtual void	apply (std::string const &out_label, pose::Pose &pose, bool override_existing_data=false) const=0
	Calculate the metric and add it to the Score, which is output into a scorefile - labeled as `label` Must be implemented by derived classes. More...

void	apply (pose::Pose &pose, std::string const &prefix="", std::string const &suffix="", bool override_existing_data=false) const
	Calculate the metric and add it to the Score, which is output into a scorefile - labeled as prefix+metric+suffix. More...

Public Member Functions inherited from core::simple_metrics::SimpleMetric
	SimpleMetric (std::string const &simple_metric_type)

	~SimpleMetric () override

	SimpleMetric (SimpleMetric const &other)

SimpleMetric &	operator= (SimpleMetric const &)

void	apply (pose::Pose &pose, std::string const &prefix="", std::string const &suffix="", bool override_existing_data=false) const
	Calculate the metric and add it to the Score, which is output into a scorefile - labeled as prefix+metric+suffix. More...

void	set_custom_type (std::string const &custom_type)

std::string	get_custom_type () const
	Additional setting to prefix/suffix. More...

virtual void	parse_base_tag (utility::tag::TagCOP tag)
	Parse the base class tag. Keep required interface for parse_my_tag. More...

std::string	simple_metric_type () const

std::string	get_final_sm_type () const
	Get the final name of this metric including its simple_metric_type_ name and any set custom type. More...

virtual void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

Static Public Member Functions
static std::string	name_static ()
	Name of the class for creator. More...

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

Static Public Member Functions inherited from core::simple_metrics::SimpleMetric
static utility::tag::XMLSchemaComplexTypeGeneratorOP	complex_type_generator_for_simple_metric (utility::tag::XMLSchemaDefinition &)

Private Attributes
core::scoring::ScoreFunctionCOP	sfxn_
	A scorefunction, from which configurations will be copied. More...

bool	verbose_
	Should this metric also output to tracer when evaluated? Default false. More...

Detailed Description

A string metric that generates a string of PyMol commands to colour a structure's polar groups based on burial.

Constructor & Destructor Documentation

◆ PolarGroupBurialPyMolStringMetric() [1/2]

protocols::analysis::burial_metrics::PolarGroupBurialPyMolStringMetric::PolarGroupBurialPyMolStringMetric ( )

Constructors ///.

Default constructor

Initializes ScoreFunction to nullptr.

◆ PolarGroupBurialPyMolStringMetric() [2/2]

protocols::analysis::burial_metrics::PolarGroupBurialPyMolStringMetric::PolarGroupBurialPyMolStringMetric ( PolarGroupBurialPyMolStringMetric const & src )

Copy constructor (not needed unless you need deep copies)

Copy constructor.

Copies, but does not clone, input scorefunction.

◆ ~PolarGroupBurialPyMolStringMetric()

protocols::analysis::burial_metrics::PolarGroupBurialPyMolStringMetric::~PolarGroupBurialPyMolStringMetric ( )

override

Destructor (important for properly forward-declaring smart-pointer members)

Member Function Documentation

◆ calculate()

std::string protocols::analysis::burial_metrics::PolarGroupBurialPyMolStringMetric::calculate ( core::pose::Pose const & original_pose ) const

overridevirtual

Metric Methods ///.

Defined in RealMetric:

Calculate the metric and add it to the pose as a score. labeled as prefix+metric+suffix.

Score is added through setExtraScorePose and is output into the score tables/file at pose output.

Calculate the metric.

Implements core::simple_metrics::StringMetric.

References core::scoring::EnergiesCacheableDataType::BURIED_UNSAT_HBOND_GRAPH, core::scoring::buried_unsatisfied_penalty, core::pack::create_packer_graph(), core::scoring::Energies::data(), core::pose::Pose::energies(), core::conformation::symmetry::is_symmetric(), core::pose::symmetry::is_symmetric(), core::pack::make_new_symmetric_PackerTask_by_requested_method(), core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::provide_pymol_commands_to_show_groups(), core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::set_prevent_pruning(), core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::set_up_residuearrayannealableenergy_for_packing(), sfxn_, core::pose::Pose::total_residue(), protocols::TR(), and verbose_.

◆ clone()

core::simple_metrics::SimpleMetricOP protocols::analysis::burial_metrics::PolarGroupBurialPyMolStringMetric::clone ( ) const

overridevirtual

Implements core::simple_metrics::StringMetric.

◆ metric()

std::string protocols::analysis::burial_metrics::PolarGroupBurialPyMolStringMetric::metric ( ) const

overridevirtual

Name (descriptive) of the metric.

Implements core::simple_metrics::StringMetric.

◆ name()

std::string protocols::analysis::burial_metrics::PolarGroupBurialPyMolStringMetric::name ( ) const

overridevirtual

Name of the class.

Calls name_static().

Implements core::simple_metrics::StringMetric.

References name_static().

◆ name_static()

std::string protocols::analysis::burial_metrics::PolarGroupBurialPyMolStringMetric::name_static ( )

static

Name of the class for creator.

Referenced by protocols::analysis::burial_metrics::PolarGroupBurialPyMolStringMetricCreator::keyname(), name(), and provide_xml_schema().

◆ parse_my_tag()

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

overridevirtual

Given an XML tag, configure an instance of this class.

Implements core::simple_metrics::StringMetric.

References core::scoring::parse_score_function(), set_scorefxn(), and set_verbose().

◆ provide_xml_schema()

void protocols::analysis::burial_metrics::PolarGroupBurialPyMolStringMetric::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References core::scoring::attributes_for_parse_score_function_w_description_when_required(), name_static(), and core::simple_metrics::xsd_simple_metric_type_definition_w_attributes().

Referenced by protocols::analysis::burial_metrics::PolarGroupBurialPyMolStringMetricCreator::provide_xml_schema().

◆ set_scorefxn()

void protocols::analysis::burial_metrics::PolarGroupBurialPyMolStringMetric::set_scorefxn ( core::scoring::ScoreFunctionCOP sfxn_in )

Set the scorefunction.

Used for definition of burial. Input pointer is copied without cloning.

References sfxn_.

Referenced by parse_my_tag().

◆ set_verbose()

void protocols::analysis::burial_metrics::PolarGroupBurialPyMolStringMetric::set_verbose ( bool const setting )

Set whether this metric should also output to tracer when evaluated.

References verbose_.

Referenced by parse_my_tag().

Member Data Documentation

◆ sfxn_

core::scoring::ScoreFunctionCOP protocols::analysis::burial_metrics::PolarGroupBurialPyMolStringMetric::sfxn_

private

A scorefunction, from which configurations will be copied.

Referenced by calculate(), and set_scorefxn().

◆ verbose_

bool protocols::analysis::burial_metrics::PolarGroupBurialPyMolStringMetric::verbose_

private

Should this metric also output to tracer when evaluated? Default false.

Referenced by calculate(), and set_verbose().

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

src/protocols/analysis/burial_metrics/PolarGroupBurialPyMolStringMetric.hh
src/protocols/analysis/burial_metrics/PolarGroupBurialPyMolStringMetric.cc

Public Member Functions

Static Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ PolarGroupBurialPyMolStringMetric() [1/2]

◆ PolarGroupBurialPyMolStringMetric() [2/2]

◆ ~PolarGroupBurialPyMolStringMetric()

Member Function Documentation

◆ calculate()

◆ clone()

◆ metric()

◆ name()

◆ name_static()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ set_scorefxn()

◆ set_verbose()

Member Data Documentation

◆ sfxn_

◆ verbose_