Calculate sequence recovery statistics on a protein, relative to a reference. More...

#include <SequenceRecoveryMetric.hh>

Inheritance diagram for protocols::analysis::simple_metrics::SequenceRecoveryMetric:

[legend]

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

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

	~SequenceRecoveryMetric () 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. More...

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

void	set_residue_selector_ref (core::select::residue_selector::ResidueSelectorCOP residue_selector)
	Set a residue selector (for the reference) to calculate the recovery from a subset of residues This needs to select the same number of residues as the set_residue_selector If not set (or nullptr), will use the same list as the selector passed to set_residue_selector() More...

void	load_pssm (std::string const &pssm_filename)
	Load the PSSM for reference from the given file. More...

void	set_use_ave_pssm (bool setting)
	Set if we want to use a average PSSM value metric, or the pass/fail setting. 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)

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...

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::SimpleMetric
static utility::tag::XMLSchemaComplexTypeGeneratorOP	complex_type_generator_for_simple_metric (utility::tag::XMLSchemaDefinition &)

Private Attributes
core::select::residue_selector::ResidueSelectorCOP	res_select_
	The subsection of residues to use for sequence recovery. More...

core::pose::PoseCOP	ref_pose_
	The reference pose to use for sequence recovery purposes. More...

core::select::residue_selector::ResidueSelectorCOP	res_select_ref_
	The subsection of residues to use for sequence recovery on the reference side If not set, use the same residues as in the passed pose. More...

core::sequence::SequenceProfileOP	ref_profile_
	If set, do pssm recovery,. More...

bool	use_ave_pssm_ = false
	If true, do an averaged PSSM value, rather than a pass/fail one. More...

Detailed Description

Calculate sequence recovery statistics on a protein, relative to a reference.

There's several options for how the sequence recovery is calculated, depending on what parameters are set. Each metric is only calculated over the set of residues specified by the residue selector.

Standard - Used when PSSM isn't set but reference pose is This is a strict match/no-match fraction.
Pass/Fail PSSM - Used when PSSM is set and use_ave_pssm is not (does not use reference pose) This is the PSSM recovery metric from DeLuca, Dorr & Meiler 2011 Biochem 50(40):8521 Residue identities with positive (or zero) values in the PSSM count as a match, those with negative vales as no-match.
Ave PSSM - Used when PSSM is set, use_ave_pssm is true, and no reference PDB is given This value is the average of the values in the PSSM matrix for the residue identities.
Delta PSSM - Used when PSSM is set, use_ave_pssm is true, and a reference PDB is provided. This value is the average of the change in value of the PSSM matrix (mut - ref)

For PSSM metrics, it's assumed that the Pose numbering of both the main and reference structure matches the numbering of the PSSM.

Constructor & Destructor Documentation

◆ SequenceRecoveryMetric() [1/2]

protocols::analysis::simple_metrics::SequenceRecoveryMetric::SequenceRecoveryMetric ( )

Constructors ///.

Default constructor

◆ SequenceRecoveryMetric() [2/2]

protocols::analysis::simple_metrics::SequenceRecoveryMetric::SequenceRecoveryMetric ( SequenceRecoveryMetric const & src )

default

Copy constructor (not needed unless you need deep copies)

Copy constructor.

◆ ~SequenceRecoveryMetric()

protocols::analysis::simple_metrics::SequenceRecoveryMetric::~SequenceRecoveryMetric ( )

override

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

Member Function Documentation

◆ calculate()

core::Real protocols::analysis::simple_metrics::SequenceRecoveryMetric::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.

Implements core::simple_metrics::RealMetric.

References core::pose::Pose::aa(), protocols::cluster::calibur::aa, core::chemical::aa_unk, core::select::get_residues_from_subset(), core::conformation::Residue::name1(), ref_pose_, ref_profile_, res_select_, res_select_ref_, core::pose::Pose::residue(), core::id::to_string(), protocols::TR(), and use_ave_pssm_.

◆ clone()

core::simple_metrics::SimpleMetricOP protocols::analysis::simple_metrics::SequenceRecoveryMetric::clone ( ) const

overridevirtual

Implements core::simple_metrics::RealMetric.

◆ load_pssm()

void protocols::analysis::simple_metrics::SequenceRecoveryMetric::load_pssm ( std::string const & pssm_filename )

Load the PSSM for reference from the given file.

References ref_profile_.

Referenced by parse_my_tag().

◆ metric()

std::string protocols::analysis::simple_metrics::SequenceRecoveryMetric::metric ( ) const

overridevirtual

Name of the metric.

Implements core::simple_metrics::RealMetric.

◆ name()

std::string protocols::analysis::simple_metrics::SequenceRecoveryMetric::name ( ) const

overridevirtual

Name of the class.

Implements core::simple_metrics::RealMetric.

References name_static().

◆ name_static()

std::string protocols::analysis::simple_metrics::SequenceRecoveryMetric::name_static ( )

static

Name of the class for creator.

Referenced by protocols::analysis::simple_metrics::SequenceRecoveryMetricCreator::keyname(), name(), and provide_xml_schema().

◆ parse_my_tag()

void protocols::analysis::simple_metrics::SequenceRecoveryMetric::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 load_pssm(), core::simple_metrics::SimpleMetric::parse_base_tag(), core::select::residue_selector::parse_residue_selector(), core::pack::task::parse_task_operations(), ref_pose_, core::pose::saved_native_pose(), core::pose::saved_reference_pose(), set_residue_selector(), set_residue_selector_ref(), set_use_ave_pssm(), and protocols::TR().

◆ provide_xml_schema()

void protocols::analysis::simple_metrics::SequenceRecoveryMetric::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

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

Referenced by protocols::analysis::simple_metrics::SequenceRecoveryMetricCreator::provide_xml_schema().

◆ set_comparison_pose()

void protocols::analysis::simple_metrics::SequenceRecoveryMetric::set_comparison_pose ( core::pose::PoseCOP pose )

Set a reference pose.

References ref_pose_.

◆ set_residue_selector()

void protocols::analysis::simple_metrics::SequenceRecoveryMetric::set_residue_selector ( core::select::residue_selector::ResidueSelectorCOP residue_selector )

Set a residue selector to calculate the recovery from a subset of residues.

References res_select_.

Referenced by parse_my_tag().

◆ set_residue_selector_ref()

void protocols::analysis::simple_metrics::SequenceRecoveryMetric::set_residue_selector_ref ( core::select::residue_selector::ResidueSelectorCOP residue_selector )

Set a residue selector (for the reference) to calculate the recovery from a subset of residues This needs to select the same number of residues as the set_residue_selector If not set (or nullptr), will use the same list as the selector passed to set_residue_selector()

References res_select_ref_.

Referenced by parse_my_tag().

◆ set_use_ave_pssm()

void protocols::analysis::simple_metrics::SequenceRecoveryMetric::set_use_ave_pssm ( bool setting )

inline

Set if we want to use a average PSSM value metric, or the pass/fail setting.

References use_ave_pssm_.

Referenced by parse_my_tag().

Member Data Documentation

◆ ref_pose_

core::pose::PoseCOP protocols::analysis::simple_metrics::SequenceRecoveryMetric::ref_pose_

private

The reference pose to use for sequence recovery purposes.

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

◆ ref_profile_

core::sequence::SequenceProfileOP protocols::analysis::simple_metrics::SequenceRecoveryMetric::ref_profile_

private

If set, do pssm recovery,.

Referenced by calculate(), and load_pssm().

◆ res_select_

core::select::residue_selector::ResidueSelectorCOP protocols::analysis::simple_metrics::SequenceRecoveryMetric::res_select_

private

The subsection of residues to use for sequence recovery.

Referenced by calculate(), and set_residue_selector().

◆ res_select_ref_

core::select::residue_selector::ResidueSelectorCOP protocols::analysis::simple_metrics::SequenceRecoveryMetric::res_select_ref_

private

The subsection of residues to use for sequence recovery on the reference side If not set, use the same residues as in the passed pose.

Referenced by calculate(), and set_residue_selector_ref().

◆ use_ave_pssm_

bool protocols::analysis::simple_metrics::SequenceRecoveryMetric::use_ave_pssm_ = false

private

If true, do an averaged PSSM value, rather than a pass/fail one.

Referenced by calculate(), and set_use_ave_pssm().

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

src/protocols/analysis/simple_metrics/SequenceRecoveryMetric.hh
src/protocols/analysis/simple_metrics/SequenceRecoveryMetric.cc

Public Member Functions

Static Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ SequenceRecoveryMetric() [1/2]

◆ SequenceRecoveryMetric() [2/2]

◆ ~SequenceRecoveryMetric()

Member Function Documentation

◆ calculate()

◆ clone()

◆ load_pssm()

◆ metric()

◆ name()

◆ name_static()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ set_comparison_pose()

◆ set_residue_selector()

◆ set_residue_selector_ref()

◆ set_use_ave_pssm()

Member Data Documentation

◆ ref_pose_

◆ ref_profile_

◆ res_select_

◆ res_select_ref_

◆ use_ave_pssm_