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

#include <RMSDMetric.hh>

Inheritance diagram for core::simple_metrics::metrics::RMSDMetric:

[legend]

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

	RMSDMetric (core::pose::PoseCOP ref_pose)

	RMSDMetric (core::pose::PoseCOP ref_pose, core::select::residue_selector::ResidueSelectorCOP selector)

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

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

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

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	This simple metric is unpublished, but can provide citation information for the residue selector that it uses.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	This simple metric is unpublished (returns true).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	This simple metric is unpublished.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

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)

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...

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::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 Member Functions
void	setup_name_mapping ()
	Setup Str to rmsd_atom map. More...

Private Attributes
core::select::residue_selector::ResidueSelectorCOP	residue_selector_ = nullptr

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_

bool	robust_ = true

std::map< std::string, scoring::rmsd_atoms >	name_mapping_

bool	superimpose_ =false

Detailed Description

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

Default is all_heavy

We match all corresponding atoms and do not fail if a residue does not match up.

Constructor & Destructor Documentation

core::simple_metrics::metrics::RMSDMetric::RMSDMetric ( )

Constructors ///.

Default constructor

References setup_name_mapping().

core::simple_metrics::metrics::RMSDMetric::RMSDMetric ( core::pose::PoseCOP ref_pose )

References set_comparison_pose(), and setup_name_mapping().

core::simple_metrics::metrics::RMSDMetric::RMSDMetric	(	core::pose::PoseCOP	ref_pose,
		core::select::residue_selector::ResidueSelectorCOP	selector
	)

References set_comparison_pose(), set_residue_selector(), and setup_name_mapping().

core::simple_metrics::metrics::RMSDMetric::RMSDMetric ( RMSDMetric 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::RMSDMetric::~RMSDMetric ( )

override

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

Member Function Documentation

core::Real core::simple_metrics::metrics::RMSDMetric::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 the metric. This is the RMSD between the input and the set comparison pose. Deafult is to calculate all_heavy atoms - but this can be set.

Make sure that reference pose and set pose are the same length or set a map to compare specific residues. We match all corresponding atoms for each residue to match.

Implements core::simple_metrics::RealMetric.

References core::pose::symmetry::extract_asymmetric_unit(), core::conformation::symmetry::is_symmetric(), ref_pose_, residue_selector_, residue_selector_ref_, residue_selector_super_, residue_selector_super_ref_, core::scoring::rms, core::scoring::rms_at_corresponding_atoms_no_super(), rmsd_map_, rmsd_type_, robust_, superimpose_, and core::scoring::superimpose_pose().

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

overridevirtual

Implements core::simple_metrics::RealMetric.

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

overridevirtual

Name of the metric.

Implements core::simple_metrics::RealMetric.

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

static

Name of the class for creator.

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

void core::simple_metrics::metrics::RMSDMetric::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 name_mapping_, core::simple_metrics::SimpleMetric::parse_base_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_residue_selector(), set_residue_selector_reference(), set_residue_selector_super(), set_residue_selector_super_reference(), set_rmsd_type(), set_run_superimpose(), superimpose_, and TR().

utility::vector1< basic::citation_manager::UnpublishedModuleInfoCOP > core::simple_metrics::metrics::RMSDMetric::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_, residue_selector_ref_, residue_selector_super_, and residue_selector_super_ref_.

utility::vector1< basic::citation_manager::CitationCollectionCOP > core::simple_metrics::metrics::RMSDMetric::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_, residue_selector_ref_, residue_selector_super_, and residue_selector_super_ref_.

void core::simple_metrics::metrics::RMSDMetric::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(), core::scoring::get_rmsd_type_names(), name_static(), core::id::to_string(), and core::simple_metrics::xsd_simple_metric_type_definition_w_attributes().

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

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

Set a reference pose to calculate rmsd.

References ref_pose_.

Referenced by RMSDMetric().

void core::simple_metrics::metrics::RMSDMetric::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::metrics::RMSDMetric::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::metrics::RMSDMetric::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 parse_my_tag(), and RMSDMetric().

void core::simple_metrics::metrics::RMSDMetric::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::metrics::RMSDMetric::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::metrics::RMSDMetric::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::metrics::RMSDMetric::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::metrics::RMSDMetric::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::metrics::RMSDMetric::setup_name_mapping ( )

private

Setup Str to rmsd_atom map.

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

Referenced by RMSDMetric().

bool core::simple_metrics::metrics::RMSDMetric::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

std::map< std::string, scoring::rmsd_atoms > core::simple_metrics::metrics::RMSDMetric::name_mapping_

private

Referenced by parse_my_tag(), and setup_name_mapping().

utility::vector1< std::string> core::simple_metrics::metrics::RMSDMetric::override_atom_names_

private

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

private

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

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

private

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

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

private

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

core::select::residue_selector::ResidueSelectorCOP core::simple_metrics::metrics::RMSDMetric::residue_selector_super_ = nullptr

private

Referenced by calculate(), provide_authorship_info_for_unpublished(), provide_citation_info(), and set_residue_selector_super().

core::select::residue_selector::ResidueSelectorCOP core::simple_metrics::metrics::RMSDMetric::residue_selector_super_ref_ = nullptr

private

Referenced by calculate(), provide_authorship_info_for_unpublished(), provide_citation_info(), and set_residue_selector_super_reference().

std::map< core::Size, core::Size > core::simple_metrics::metrics::RMSDMetric::rmsd_map_

private

Referenced by calculate(), and set_residue_mapping().

scoring::rmsd_atoms core::simple_metrics::metrics::RMSDMetric::rmsd_type_ = scoring::rmsd_all_heavy

private

Referenced by calculate(), and set_rmsd_type().

bool core::simple_metrics::metrics::RMSDMetric::robust_ = true

private

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

bool core::simple_metrics::metrics::RMSDMetric::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/metrics/RMSDMetric.hh
src/core/simple_metrics/metrics/RMSDMetric.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation