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protocols::analysis::simple_metrics::SequenceRecoveryMetric Class Reference

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

#include <SequenceRecoveryMetric.hh>

Inheritance diagram for protocols::analysis::simple_metrics::SequenceRecoveryMetric:
Inheritance graph
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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)
 
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...
 
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::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.

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

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

Constructors ///.

Default constructor

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

Copy constructor (not needed unless you need deep copies)

Copy constructor.

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

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

Member Function Documentation

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 protocols::cluster::calibur::aa, core::pose::Pose::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_.

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

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

Name of the metric.

Implements core::simple_metrics::RealMetric.

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

Name of the class.

Implements core::simple_metrics::RealMetric.

References name_static().

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

Set a reference pose.

References ref_pose_.

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().

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().

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

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().

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

If set, do pssm recovery,.

Referenced by calculate(), and load_pssm().

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().

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().

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: