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core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric Class Reference

A per-residue metric thtat will calculate the RMSD for each residue given in a residue selector to a reference pose. More...

#include <PerResidueRMSDMetric.hh>

Inheritance diagram for core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric:
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Public Member Functions

 PerResidueRMSDMetric ()
 Constructors ///. More...
 
 PerResidueRMSDMetric (core::pose::PoseCOP ref_pose)
 Default constructor. More...
 
 PerResidueRMSDMetric (PerResidueRMSDMetric const &src)
 Copy constructor (not needed unless you need deep copies) More...
 
 ~PerResidueRMSDMetric () override
 Destructor (important for properly forward-declaring smart-pointer members) More...
 
std::map< core::Size, core::Realcalculate (core::pose::Pose const &pose) const override
 Metric Methods ///. More...
 
void set_comparison_pose (core::pose::PoseCOP ref_pose)
 Set a reference pose to calculate rmsd. More...
 
void set_residue_selector_reference (core::select::residue_selector::ResidueSelectorCOP residue_selector)
 
void set_residue_selector_super (core::select::residue_selector::ResidueSelectorCOP residue_selector)
 Optional - Set a residue selector specifically for superposition. More...
 
void set_residue_selector_super_reference (core::select::residue_selector::ResidueSelectorCOP residue_selector)
 
void set_residue_mapping (std::map< core::Size, core::Size > const &rmsd_map)
 Set a map to compute the RMSD on input->reference residue numbers. More...
 
void set_run_superimpose (bool super)
 Run a superimpose on the residues selected in the residue selector (or all) default False. More...
 
void set_rmsd_type (scoring::rmsd_atoms rmsd_type)
 Set what we will be calculating the RMSD on. More...
 
void set_corresponding_atoms_robust (bool robust)
 Set whether we are robust to atom mismatches for selected residues. More...
 
void set_desymmetrize_residue_selector (bool desym)
 Should we de-symmetrize the residue selector(s) where we only consider the master subunit? Default True. More...
 
std::map< core::id::AtomID,
core::id::AtomID
create_atom_id_map (core::pose::Pose const &pose, bool desymmetrize_res_selector=true) const
 Create an AtomID map according to options set in this class. If desymmetrize_res_selector is true, we only consider the master subunit. More...
 
std::map< core::id::AtomID,
core::id::AtomID
create_atom_id_map (core::pose::Pose const &pose, std::map< core::Size, core::Size > const &residue_map) const
 Create an AtomID map according to residue_map. 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::Realcached_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 &)
 

Private Member Functions

void setup_name_mapping ()
 Setup Str to rmsd_atom map. More...
 

Private Attributes

core::select::residue_selector::ResidueSelectorCOP residue_selector_ref_ = nullptr
 
core::select::residue_selector::ResidueSelectorCOP residue_selector_super_ = nullptr
 
core::select::residue_selector::ResidueSelectorCOP residue_selector_super_ref_ = nullptr
 
std::map< core::Size, core::Sizermsd_map_
 
core::pose::PoseCOP ref_pose_ = nullptr
 
scoring::rmsd_atoms rmsd_type_ = scoring::rmsd_all_heavy
 
utility::vector1< std::string > override_atom_names_
 
std::map< scoring::rmsd_atoms,
utility::vector1< std::string > > 
rmsd_atom_names_
 
bool robust_ = true
 
std::map< std::string,
scoring::rmsd_atoms
name_mapping_
 
bool superimpose_ = false
 
bool desymmetrize_res_selector_ = true
 

Detailed Description

A per-residue metric thtat will calculate the RMSD for each residue given in a residue selector to a reference pose.

Constructor & Destructor Documentation

core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::PerResidueRMSDMetric ( )

Constructors ///.

Default constructor

References setup_name_mapping().

core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::PerResidueRMSDMetric ( core::pose::PoseCOP  ref_pose)

Default constructor.

References setup_name_mapping().

core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::PerResidueRMSDMetric ( PerResidueRMSDMetric const &  src)
default

Copy constructor (not needed unless you need deep copies)

Copy constructor.

core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::~PerResidueRMSDMetric ( )
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::PerResidueRMSDMetric::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 create_atom_id_map(), desymmetrize_res_selector_, core::pose::symmetry::extract_asymmetric_unit(), core::select::get_master_subunit_selection(), core::select::residue_selector::get_residue_mapping_from_selectors(), core::simple_metrics::PerResidueRealMetric::get_selector(), core::pose::symmetry::is_symmetric(), core::conformation::symmetry::is_symmetric(), core::scoring::per_res_rms_at_corresponding_atoms_no_super(), ref_pose_, residue_selector_super_, residue_selector_super_ref_, superimpose_, core::scoring::superimpose_pose(), and TR().

core::simple_metrics::SimpleMetricOP core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::clone ( ) const
overridevirtual
std::map< id::AtomID, id::AtomID > core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::create_atom_id_map ( core::pose::Pose const &  pose,
bool  desymmetrize_res_selector = true 
) const

Create an AtomID map according to options set in this class. If desymmetrize_res_selector is true, we only consider the master subunit.

References core::select::residue_selector::get_residue_mapping_from_selectors(), core::simple_metrics::PerResidueRealMetric::get_selector(), ref_pose_, residue_selector_ref_, and rmsd_map_.

Referenced by calculate().

std::map< id::AtomID, id::AtomID > core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::create_atom_id_map ( core::pose::Pose const &  pose,
std::map< core::Size, core::Size > const &  residue_map 
) const
std::string core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::metric ( ) const
overridevirtual

Name of the metric.

Implements core::simple_metrics::PerResidueRealMetric.

std::string core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::name ( ) const
overridevirtual

Name of the class.

Implements core::simple_metrics::PerResidueRealMetric.

References name_static().

std::string core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::name_static ( )
static
void core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual
void core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::set_comparison_pose ( core::pose::PoseCOP  ref_pose)

Set a reference pose to calculate rmsd.

References ref_pose_.

void core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::set_corresponding_atoms_robust ( bool  robust)

Set whether we are robust to atom mismatches for selected residues.

Set this to false to fail instead.

References robust_.

Referenced by parse_my_tag().

void core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::set_desymmetrize_residue_selector ( bool  desym)

Should we de-symmetrize the residue selector(s) where we only consider the master subunit? Default True.

References desymmetrize_res_selector_.

Referenced by parse_my_tag().

void core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::set_residue_mapping ( std::map< core::Size, core::Size > const &  rmsd_map)

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

References rmsd_map_.

void core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::set_residue_selector_reference ( core::select::residue_selector::ResidueSelectorCOP  residue_selector)

Set a reference residue selector. Both selectors should return the same number of residues. If not set, will use the main residue selector.

References residue_selector_ref_.

Referenced by parse_my_tag().

void core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::set_residue_selector_super ( core::select::residue_selector::ResidueSelectorCOP  residue_selector)

Optional - Set a residue selector specifically for superposition.

References residue_selector_super_.

Referenced by parse_my_tag().

void core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::set_residue_selector_super_reference ( core::select::residue_selector::ResidueSelectorCOP  residue_selector)

Set a reference residue selector for superposition. Both selectors should return the same number of residues. If not set, but super selector is set, will use that.

References residue_selector_super_ref_.

Referenced by parse_my_tag().

void core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::set_rmsd_type ( scoring::rmsd_atoms  rmsd_type)

Set what we will be calculating the RMSD on.

References rmsd_type_.

Referenced by parse_my_tag().

void core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::set_run_superimpose ( bool  super)

Run a superimpose on the residues selected in the residue selector (or all) default False.

References superimpose_.

Referenced by parse_my_tag().

void core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::setup_name_mapping ( )
private

Member Data Documentation

bool core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::desymmetrize_res_selector_ = true
private
std::map< std::string, scoring::rmsd_atoms > core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::name_mapping_
private

Referenced by parse_my_tag(), and setup_name_mapping().

utility::vector1< std::string> core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::override_atom_names_
private

Referenced by create_atom_id_map().

core::pose::PoseCOP core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::ref_pose_ = nullptr
private
core::select::residue_selector::ResidueSelectorCOP core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::residue_selector_ref_ = nullptr
private
core::select::residue_selector::ResidueSelectorCOP core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::residue_selector_super_ = nullptr
private
core::select::residue_selector::ResidueSelectorCOP core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::residue_selector_super_ref_ = nullptr
private
std::map< scoring::rmsd_atoms, utility::vector1< std::string > > core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::rmsd_atom_names_
private
std::map< core::Size, core::Size > core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::rmsd_map_
private
scoring::rmsd_atoms core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::rmsd_type_ = scoring::rmsd_all_heavy
private
bool core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::robust_ = true
private
bool core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::superimpose_ = false
private

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