A metric to calculate the dihedral distance between two poses. Can set a subset of residues to calculate via ResidueSelector. More...

#include <DihedralDistanceMetric.hh>

Inheritance diagram for core::simple_metrics::metrics::DihedralDistanceMetric:

[legend]

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

	DihedralDistanceMetric (core::select::residue_selector::ResidueSelectorCOP selector)

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

core::Real	calculate (core::pose::Pose const &pose) const override
	Metric Methods ///. More...

void	set_comparison_pose (core::pose::PoseCOP pose)
	Set a reference pose to calculate rmsd. More...

void	set_residue_selector (core::select::residue_selector::ResidueSelectorCOP residue_selector)
	Set a residue selector to calculate total energy of a subset of residues. More...

void	set_residue_selector_reference (core::select::residue_selector::ResidueSelectorCOP residue_selector_ref)
	Set a residue selector for the comparison pose. More...

void	set_residue_mapping (std::map< core::Size, core::Size > const &res_map)
	Set a map to compute the Dihedral distance on input->reference residue numbers. More...

void	set_include_protein_omega (bool include_omega)
	Set the boolean to include protein omega. Default false. 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

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

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

	~RealMetric () override

	RealMetric (RealMetric const &other)

RealMetric &	operator= (RealMetric const &)

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...

core::Real	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(s) 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...

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::select::residue_selector::ResidueSelectorCOP	residue_selector_ = nullptr

core::select::residue_selector::ResidueSelectorCOP	residue_selector_ref_ = nullptr

core::pose::PoseCOP	ref_pose_ = nullptr

bool	include_protein_omega_ = false

std::map< core::Size, core::Size >	res_map_

Detailed Description

A metric to calculate the dihedral distance between two poses. Can set a subset of residues to calculate via ResidueSelector.

This is the normalized metric in degrees

Metric described in: North B, Lehmann A, Dunbrack RL. A new clustering of antibody CDR loop conformations. J Mol Biol 2011; 406:228-256.

NOTE: Only works for Protein and Carbohydrate residues as dihedral definitions in Rosetta are still aweful. Metric is computed on the protein and carbohydrate backbone.

Constructor & Destructor Documentation

◆ DihedralDistanceMetric() [1/2]

core::simple_metrics::metrics::DihedralDistanceMetric::DihedralDistanceMetric ( )

Constructors ///.

Default constructor

◆ DihedralDistanceMetric() [2/2]

core::simple_metrics::metrics::DihedralDistanceMetric::DihedralDistanceMetric ( core::select::residue_selector::ResidueSelectorCOP selector )

References set_residue_selector().

◆ ~DihedralDistanceMetric()

core::simple_metrics::metrics::DihedralDistanceMetric::~DihedralDistanceMetric ( )

override

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

Member Function Documentation

◆ calculate()

core::Real core::simple_metrics::metrics::DihedralDistanceMetric::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.

Calculate DihedralDistance metric. This is the normalized metric in degrees

Metric described in: North B, Lehmann A, Dunbrack RL. A new clustering of antibody CDR loop conformations. J Mol Biol 2011; 406:228-256.

Implements core::simple_metrics::RealMetric.

References core::conformation::carbohydrates::get_glycosidic_torsion(), core::conformation::carbohydrates::get_n_glycosidic_torsions_in_res(), core::select::residue_selector::get_residue_mapping_from_selectors(), include_protein_omega_, core::chemical::ResidueType::is_carbohydrate(), core::chemical::ResidueTypeBase::is_protein(), core::pose::Pose::omega(), core::pose::Pose::phi(), PI, core::pose::Pose::psi(), ref_pose_, res_map_, residue_selector_, residue_selector_ref_, core::pose::Pose::residue_type(), core::id::to_string(), and TR().

◆ clone()

core::simple_metrics::SimpleMetricOP core::simple_metrics::metrics::DihedralDistanceMetric::clone ( ) const

overridevirtual

Implements core::simple_metrics::RealMetric.

◆ metric()

std::string core::simple_metrics::metrics::DihedralDistanceMetric::metric ( ) const

overridevirtual

Name of the metric.

Implements core::simple_metrics::RealMetric.

◆ name()

std::string core::simple_metrics::metrics::DihedralDistanceMetric::name ( ) const

overridevirtual

Name of the class.

Implements core::simple_metrics::RealMetric.

References name_static().

Referenced by provide_citation_info().

◆ name_static()

std::string core::simple_metrics::metrics::DihedralDistanceMetric::name_static ( )

static

Name of the class for creator.

Referenced by core::simple_metrics::metrics::DihedralDistanceMetricCreator::keyname(), name(), and provide_xml_schema().

◆ parse_my_tag()

void core::simple_metrics::metrics::DihedralDistanceMetric::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::RealMetric.

References include_protein_omega_, core::simple_metrics::SimpleMetric::parse_base_tag(), core::select::residue_selector::parse_residue_selector(), ref_pose_, core::pose::saved_native_pose(), core::pose::saved_reference_pose(), set_include_protein_omega(), set_residue_selector(), set_residue_selector_reference(), and TR().

◆ provide_citation_info()

void core::simple_metrics::metrics::DihedralDistanceMetric::provide_citation_info ( basic::citation_manager::CitationCollectionList & citations ) const

overridevirtual

Provide the citation.

Reimplemented from core::simple_metrics::SimpleMetric.

References name(), residue_selector_, and residue_selector_ref_.

◆ provide_xml_schema()

void core::simple_metrics::metrics::DihedralDistanceMetric::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References core::select::residue_selector::attributes_for_parse_residue_selector(), core::pose::attributes_for_saved_reference_pose(), name_static(), and core::simple_metrics::xsd_simple_metric_type_definition_w_attributes().

Referenced by core::simple_metrics::metrics::DihedralDistanceMetricCreator::provide_xml_schema().

◆ set_comparison_pose()

void core::simple_metrics::metrics::DihedralDistanceMetric::set_comparison_pose ( core::pose::PoseCOP pose )

Set a reference pose to calculate rmsd.

References ref_pose_.

◆ set_include_protein_omega()

void core::simple_metrics::metrics::DihedralDistanceMetric::set_include_protein_omega ( bool include_omega )

Set the boolean to include protein omega. Default false.

References include_protein_omega_.

Referenced by parse_my_tag().

◆ set_residue_mapping()

void core::simple_metrics::metrics::DihedralDistanceMetric::set_residue_mapping ( std::map< core::Size, core::Size > const & res_map )

Set a map to compute the Dihedral distance on input->reference residue numbers.

References res_map_.

◆ set_residue_selector()

void core::simple_metrics::metrics::DihedralDistanceMetric::set_residue_selector ( core::select::residue_selector::ResidueSelectorCOP residue_selector )

Set a residue selector to calculate total energy of a subset of residues.

References residue_selector_.

Referenced by DihedralDistanceMetric(), and parse_my_tag().

◆ set_residue_selector_reference()

void core::simple_metrics::metrics::DihedralDistanceMetric::set_residue_selector_reference ( core::select::residue_selector::ResidueSelectorCOP residue_selector_ref )

Set a residue selector for the comparison pose.

References residue_selector_ref_.

Referenced by parse_my_tag().

Member Data Documentation

◆ include_protein_omega_

bool core::simple_metrics::metrics::DihedralDistanceMetric::include_protein_omega_ = false

private

Referenced by calculate(), parse_my_tag(), and set_include_protein_omega().

◆ ref_pose_

core::pose::PoseCOP core::simple_metrics::metrics::DihedralDistanceMetric::ref_pose_ = nullptr

private

Referenced by calculate(), parse_my_tag(), and set_comparison_pose().

◆ res_map_

std::map< core::Size, core::Size > core::simple_metrics::metrics::DihedralDistanceMetric::res_map_

private

Referenced by calculate(), and set_residue_mapping().

◆ residue_selector_

core::select::residue_selector::ResidueSelectorCOP core::simple_metrics::metrics::DihedralDistanceMetric::residue_selector_ = nullptr

private

Referenced by calculate(), provide_citation_info(), and set_residue_selector().

◆ residue_selector_ref_

core::select::residue_selector::ResidueSelectorCOP core::simple_metrics::metrics::DihedralDistanceMetric::residue_selector_ref_ = nullptr

private

Referenced by calculate(), provide_citation_info(), and set_residue_selector_reference().

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

src/core/simple_metrics/metrics/DihedralDistanceMetric.hh
src/core/simple_metrics/metrics/DihedralDistanceMetric.cc

Public Member Functions

Static Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ DihedralDistanceMetric() [1/2]

◆ DihedralDistanceMetric() [2/2]

◆ ~DihedralDistanceMetric()

Member Function Documentation

◆ calculate()

◆ clone()

◆ metric()

◆ name()

◆ name_static()

◆ parse_my_tag()

◆ provide_citation_info()

◆ provide_xml_schema()

◆ set_comparison_pose()

◆ set_include_protein_omega()

◆ set_residue_mapping()

◆ set_residue_selector()

◆ set_residue_selector_reference()

Member Data Documentation

◆ include_protein_omega_

◆ ref_pose_

◆ res_map_

◆ residue_selector_

◆ residue_selector_ref_