A metric that outputs the layer of the glycan tree as measured by the residue distance to the root. More...

#include <PerResidueGlycanLayerMetric.hh>

Inheritance diagram for core::simple_metrics::per_residue_metrics::PerResidueGlycanLayerMetric:

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

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

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

std::map< core::Size, core::Real >	calculate (core::pose::Pose const &pose) const override
	Metric Methods ///. More...

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

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

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
	called by parse_my_tag – should not be used directly More...

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

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

	~PerResidueRealMetric () override

	PerResidueRealMetric (PerResidueRealMetric const &other)

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

void	set_residue_selector (select::residue_selector::ResidueSelectorCOP selector)
	Set a ResidueSelector for which we will calculate values over. More...

void	set_output_as_pdb_nums (bool output_as_pdb_nums)
	Set to output in PDB numbering instead of Rosetta during the Apply function, which adds the data to pose as extra scores. More...

std::map< core::Size, core::Real >	cached_calculate (pose::Pose const &pose, bool use_cache, std::string prefix="", std::string suffix="", bool fail_on_missing_cache=true, bool use_ref_pose_for_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 submetric names that this Metric will calculate. More...

select::residue_selector::ResidueSelectorCOP	get_selector () const
	Get the set residue selector of this class. More...

virtual void	parse_per_residue_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data)
	Parse the base class tag. Keep required interface for parse_my_tag. More...

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

	~SimpleMetric () override

	SimpleMetric (SimpleMetric const &other)

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 bool	simple_metric_provides_citation_info () const
	Does this simple metric provide information about how to cite it? More...

virtual utility::vector1 < basic::citation_manager::CitationCollectionCOP >	provide_citation_info () const
	Provide the citation. More...

virtual bool	simple_metric_is_unpublished () const
	Does this simple metric indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...

virtual utility::vector1 < basic::citation_manager::UnpublishedModuleInfoCOP >	provide_authorship_info_for_unpublished () const
	Provide a list of authors and their e-mail addresses, as strings. 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::PerResidueRealMetric
static void	add_schema (utility::tag::XMLSchemaComplexTypeGeneratorOP complex_schema)
	Add options to the schema from this base class. More...

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

Detailed Description

A metric that outputs the layer of the glycan tree as measured by the residue distance to the root.

Constructor & Destructor Documentation

core::simple_metrics::per_residue_metrics::PerResidueGlycanLayerMetric::PerResidueGlycanLayerMetric ( )

Constructors ///.

Default constructor

core::simple_metrics::per_residue_metrics::PerResidueGlycanLayerMetric::PerResidueGlycanLayerMetric ( PerResidueGlycanLayerMetric const & src )

default

Copy constructor (not needed unless you need deep copies)

Copy constructor.

core::simple_metrics::per_residue_metrics::PerResidueGlycanLayerMetric::~PerResidueGlycanLayerMetric ( )

override

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

Member Function Documentation

std::map< core::Size, core::Real > core::simple_metrics::per_residue_metrics::PerResidueGlycanLayerMetric::calculate ( core::pose::Pose const & 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. Defined in PerResidueRealMetric Calculate the metric. This map is Rosetta Resnum->value and includes only those residues selected.

Return by value as this function can not STORE the result, it only calculates. Store the result in the pose by using the apply method, which calls this method and stores the result in the pose as ExtraScoreValues.

Implements core::simple_metrics::PerResidueRealMetric.

References core::simple_metrics::PerResidueRealMetric::get_selector(), core::pose::Pose::glycan_tree_set(), core::chemical::ResidueType::is_carbohydrate(), core::pose::Pose::residue_type(), and core::pose::Pose::size().

core::simple_metrics::SimpleMetricOP core::simple_metrics::per_residue_metrics::PerResidueGlycanLayerMetric::clone ( ) const

overridevirtual

Implements core::simple_metrics::PerResidueRealMetric.

std::string core::simple_metrics::per_residue_metrics::PerResidueGlycanLayerMetric::metric ( ) const

overridevirtual

Name of the metric.

Implements core::simple_metrics::PerResidueRealMetric.

std::string core::simple_metrics::per_residue_metrics::PerResidueGlycanLayerMetric::name ( ) const

overridevirtual

Name of the class.

Implements core::simple_metrics::PerResidueRealMetric.

References name_static().

std::string core::simple_metrics::per_residue_metrics::PerResidueGlycanLayerMetric::name_static ( )

static

Name of the class for creator.

Referenced by core::simple_metrics::per_residue_metrics::PerResidueGlycanLayerMetricCreator::keyname(), name(), and provide_xml_schema().

void core::simple_metrics::per_residue_metrics::PerResidueGlycanLayerMetric::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

called by parse_my_tag – should not be used directly

Implements core::simple_metrics::PerResidueRealMetric.

References core::simple_metrics::SimpleMetric::parse_base_tag(), and core::simple_metrics::PerResidueRealMetric::parse_per_residue_tag().

void core::simple_metrics::per_residue_metrics::PerResidueGlycanLayerMetric::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References name_static(), and core::simple_metrics::xsd_per_residue_real_metric_type_definition_w_attributes().

Referenced by core::simple_metrics::per_residue_metrics::PerResidueGlycanLayerMetricCreator::provide_xml_schema().

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

src/core/simple_metrics/per_residue_metrics/PerResidueGlycanLayerMetric.hh
src/core/simple_metrics/per_residue_metrics/PerResidueGlycanLayerMetric.cc

Public Member Functions

Static Public Member Functions

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation