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::Real >	calculate (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)

PerResidueRealMetric &	operator= (PerResidueRealMetric 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...

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)

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::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::Size >	rmsd_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

Implements core::simple_metrics::PerResidueRealMetric.

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(), and core::simple_metrics::metrics::RMSDMetric::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

Create an AtomID map according to residue_map.

References core::chemical::ResidueType::atom_index(), core::chemical::ResidueType::atom_is_sidechain(), core::chemical::ResidueType::atom_name(), core::chemical::ResidueType::has(), core::chemical::ResidueType::is_virtual(), core::chemical::ResidueType::natoms(), core::chemical::ResidueType::nheavyatoms(), override_atom_names_, ref_pose_, core::pose::Pose::residue_type(), core::scoring::rmsd_all_heavy, rmsd_atom_names_, core::scoring::rmsd_sc, core::scoring::rmsd_sc_heavy, rmsd_type_, robust_, and core::id::to_string().

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

Name of the class for creator.

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

void core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::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 name_mapping_, core::simple_metrics::SimpleMetric::parse_base_tag(), core::simple_metrics::PerResidueRealMetric::parse_per_residue_tag(), core::select::residue_selector::parse_residue_selector(), ref_pose_, robust_, core::pose::saved_native_pose(), core::pose::saved_reference_pose(), set_corresponding_atoms_robust(), set_desymmetrize_residue_selector(), set_residue_selector_reference(), set_residue_selector_super(), set_residue_selector_super_reference(), set_rmsd_type(), set_run_superimpose(), superimpose_, and TR().

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

static

References core::select::residue_selector::attributes_for_parse_residue_selector(), core::scoring::get_rmsd_type_names(), name_static(), core::id::to_string(), and core::simple_metrics::xsd_per_residue_real_metric_type_definition_w_attributes().

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

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_.

Referenced by core::simple_metrics::metrics::RMSDMetric::calculate().

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 core::simple_metrics::metrics::RMSDMetric::calculate(), and 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_.

Referenced by core::simple_metrics::metrics::RMSDMetric::calculate().

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 core::simple_metrics::metrics::RMSDMetric::calculate(), and 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 core::simple_metrics::metrics::RMSDMetric::calculate(), and 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

Setup Str to rmsd_atom map.

References core::scoring::get_rmsd_type_name_map(), name_mapping_, rmsd_atom_names_, and core::scoring::setup_rmsd_atom_names().

Referenced by PerResidueRMSDMetric().

Member Data Documentation

bool core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::desymmetrize_res_selector_ = true

private

Referenced by calculate(), and set_desymmetrize_residue_selector().

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

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

core::select::residue_selector::ResidueSelectorCOP core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::residue_selector_ref_ = nullptr

private

Referenced by create_atom_id_map(), and set_residue_selector_reference().

core::select::residue_selector::ResidueSelectorCOP core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::residue_selector_super_ = nullptr

private

Referenced by calculate(), and set_residue_selector_super().

core::select::residue_selector::ResidueSelectorCOP core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::residue_selector_super_ref_ = nullptr

private

Referenced by calculate(), and set_residue_selector_super_reference().

std::map< scoring::rmsd_atoms, utility::vector1< std::string > > core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::rmsd_atom_names_

private

Referenced by create_atom_id_map(), and setup_name_mapping().

std::map< core::Size, core::Size > core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::rmsd_map_

private

Referenced by create_atom_id_map(), and set_residue_mapping().

scoring::rmsd_atoms core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::rmsd_type_ = scoring::rmsd_all_heavy

private

Referenced by create_atom_id_map(), and set_rmsd_type().

bool core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::robust_ = true

private

Referenced by create_atom_id_map(), parse_my_tag(), and set_corresponding_atoms_robust().

bool core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::superimpose_ = false

private

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

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

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

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation