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core::simple_metrics::metrics::DihedralDistanceMetric Class Reference

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:
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Public Member Functions

 DihedralDistanceMetric ()
 Constructors ///. More...
 
 DihedralDistanceMetric (core::select::residue_selector::ResidueSelectorCOP selector)
 
 DihedralDistanceMetric (DihedralDistanceMetric const &src)
 Copy constructor (not needed unless you need deep copies) More...
 
 ~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
 
utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const override
 This simple metric is unpublished, but can provide citation information for the residue selector that it uses. More...
 
bool simple_metric_is_unpublished () const override
 This simple metric is unpublished (returns true). More...
 
utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const override
 This simple metric is unpublished. It returns Jared Adolf-Bryfogle. More...
 
- Public Member Functions inherited from core::simple_metrics::RealMetric
 RealMetric ()
 
 ~RealMetric () override
 
 RealMetric (RealMetric 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...
 
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...
 
- 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...
 

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::Sizeres_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

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

Constructors ///.

Default constructor

core::simple_metrics::metrics::DihedralDistanceMetric::DihedralDistanceMetric ( core::select::residue_selector::ResidueSelectorCOP  selector)
core::simple_metrics::metrics::DihedralDistanceMetric::DihedralDistanceMetric ( DihedralDistanceMetric const &  src)

Copy constructor (not needed unless you need deep copies)

Copy constructor.

References ref_pose_, residue_selector_, and residue_selector_ref_.

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

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

Member Function Documentation

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().

core::simple_metrics::SimpleMetricOP core::simple_metrics::metrics::DihedralDistanceMetric::clone ( ) const
overridevirtual
std::string core::simple_metrics::metrics::DihedralDistanceMetric::metric ( ) const
overridevirtual

Name of the metric.

Implements core::simple_metrics::RealMetric.

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_authorship_info_for_unpublished().

std::string core::simple_metrics::metrics::DihedralDistanceMetric::name_static ( )
static
void core::simple_metrics::metrics::DihedralDistanceMetric::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual
utility::vector1< basic::citation_manager::UnpublishedModuleInfoCOP > core::simple_metrics::metrics::DihedralDistanceMetric::provide_authorship_info_for_unpublished ( ) const
overridevirtual

This simple metric is unpublished. It returns Jared Adolf-Bryfogle.

Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org)

Reimplemented from core::simple_metrics::SimpleMetric.

References name(), residue_selector_, and residue_selector_ref_.

utility::vector1< basic::citation_manager::CitationCollectionCOP > core::simple_metrics::metrics::DihedralDistanceMetric::provide_citation_info ( ) const
overridevirtual

This simple metric is unpublished, but can provide citation information for the residue selector that it uses.

Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org)

Reimplemented from core::simple_metrics::SimpleMetric.

References residue_selector_, and residue_selector_ref_.

void core::simple_metrics::metrics::DihedralDistanceMetric::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void core::simple_metrics::metrics::DihedralDistanceMetric::set_comparison_pose ( core::pose::PoseCOP  pose)

Set a reference pose to calculate rmsd.

References ref_pose_.

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().

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_.

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().

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().

bool core::simple_metrics::metrics::DihedralDistanceMetric::simple_metric_is_unpublished ( ) const
overridevirtual

This simple metric is unpublished (returns true).

Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org)

Reimplemented from core::simple_metrics::SimpleMetric.

Member Data Documentation

bool core::simple_metrics::metrics::DihedralDistanceMetric::include_protein_omega_ = false
private
core::pose::PoseCOP core::simple_metrics::metrics::DihedralDistanceMetric::ref_pose_ = nullptr
private
std::map< core::Size, core::Size > core::simple_metrics::metrics::DihedralDistanceMetric::res_map_
private

Referenced by calculate(), and set_residue_mapping().

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

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