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protocols::helical_bundle::BundleReporterFilter Class Reference

#include <BundleReporterFilter.hh>

Inheritance diagram for protocols::helical_bundle::BundleReporterFilter:
Inheritance graph
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Public Member Functions

 BundleReporterFilter ()
 Constructor. More...
 
 BundleReporterFilter (BundleReporterFilter const &src)
 Copy constructor. More...
 
 ~BundleReporterFilter () override
 Destructor. More...
 
filters::FilterOP clone () const override
 Returns an owning pointer to a new instance of this filter, with copied variables (a copy of this filter). More...
 
filters::FilterOP fresh_instance () const override
 Returns an owning pointer to a new instance of this filter, with default initialization (NOT a copy). More...
 
void set_score_type_threshold (core::Real const &val)
 Set the score threshold. More...
 
core::Real score_type_threshold () const
 Get the score threshold. More...
 
void set_score_type (core::scoring::ScoreType const &type)
 Set the score type. More...
 
core::scoring::ScoreType score_type () const
 Get the score type. More...
 
void set_scorefxn (core::scoring::ScoreFunctionOP scorefxn_in)
 Set the scorefunction. More...
 
core::scoring::ScoreFunctionOP scorefxn ()
 Get the scorefunction (by owning pointer). More...
 
void set_filter_behaviour (std::string const &behaviour_string)
 Set the behaviour by string. More...
 
void set_filter_behaviour (BundleReporterFilterBehaviour const behaviour_in)
 Set the behaviour by enum. More...
 
BundleReporterFilterBehaviour filter_behaviour () const
 Get the filter behaviour. More...
 
bool apply (core::pose::Pose const &pose) const override
 Actually apply the filter to a pose. More...
 
void report (std::ostream &out, core::pose::Pose const &pose) const override
 Allows reporting of filter values to a stream. More...
 
core::Real report_sm (core::pose::Pose const &pose) const override
 Allows reporting of the filter value to a float. More...
 
std::string generate_full_tracer_report (core::Size const jobno, core::Real const &score, core::pose::Pose const &pose) const
 Generates the text of the full report that the filter writes out to the REPORT tracer. More...
 
core::Real compute (core::pose::Pose const &pose) const
 Computes the energy of the pose. More...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &) override
 Parse XML (RosettaScripts) setup. More...
 
void set_report_sequence (bool const val=true)
 Set whether we report sequences. More...
 
void set_use_threeletter (bool const val=true)
 Set whether we report three-letter codes. More...
 
bool report_sequence () const
 Get whether we report sequences. More...
 
bool use_threeletter () const
 Get whether we report three-letter codes. More...
 
std::string name () const override
 
- Public Member Functions inherited from protocols::filters::Filter
 Filter ()
 
 Filter (std::string const &)
 
 Filter (Filter const &)
 
 ~Filter () override
 
virtual std::string get_type () const
 
std::string get_user_defined_name () const
 
void set_user_defined_name (std::string const &name)
 
virtual void clear ()
 used to clear internal variables if needed. Using fresh_instance is preferred since it's a pure virtual More...
 
virtual core::Real score (core::pose::Pose &pose)
 
virtual bool filter_provides_citation_info () const
 Does this filter 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 filter_is_unpublished () const
 Does this filter 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 class_name ()
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 

Private Attributes

core::Real score_type_threshold_
 If the score is used to filter, what's the cutoff threshold above which the filter returns false? More...
 
core::scoring::ScoreType score_type_
 What score term should be reported/used to filter? More...
 
core::scoring::ScoreFunctionOP scorefxn_
 What scorefunction should be reported/used to filter? More...
 
BundleReporterFilterBehaviour behaviour_
 The behaviour of this filter. More...
 
bool report_sequence_
 Report sequence? False by default. More...
 
bool report_three_letter_codes_
 Report one- or three-letter codes? False (one-letter codes) by default. More...
 

Additional Inherited Members

- Protected Attributes inherited from protocols::filters::Filter
std::string scorename_
 

Constructor & Destructor Documentation

protocols::helical_bundle::BundleReporterFilter::BundleReporterFilter ( )

Constructor.

protocols::helical_bundle::BundleReporterFilter::BundleReporterFilter ( BundleReporterFilter const &  src)

Copy constructor.

protocols::helical_bundle::BundleReporterFilter::~BundleReporterFilter ( )
overridedefault

Destructor.

Member Function Documentation

bool protocols::helical_bundle::BundleReporterFilter::apply ( core::pose::Pose const &  pose) const
overridevirtual

Actually apply the filter to a pose.

This scores the pose with the scorefunction, writes out the energy and the bundle parameters (if any) to the REPORT tracer, then applies the selected behaviour of the filter (always true, always false, or actually filtering by score).

Implements protocols::filters::Filter.

References protocols::helical_bundle::brf_always_false, protocols::helical_bundle::brf_always_true, protocols::helical_bundle::brf_filter_by_energy, compute(), protocols::jd2::current_nstruct_index(), filter_behaviour(), generate_full_tracer_report(), protocols::filters::Filter::score(), score_type_threshold(), protocols::helical_bundle::TR(), and protocols::helical_bundle::TRReport().

std::string protocols::helical_bundle::BundleReporterFilter::class_name ( )
static
filters::FilterOP protocols::helical_bundle::BundleReporterFilter::clone ( ) const
inlineoverridevirtual

Returns an owning pointer to a new instance of this filter, with copied variables (a copy of this filter).

Implements protocols::filters::Filter.

Referenced by parse_my_tag().

core::Real protocols::helical_bundle::BundleReporterFilter::compute ( core::pose::Pose const &  pose) const

Computes the energy of the pose.

the energy function must be suitable for residue type set of the pose, and must be symmetric if this is a symmetric pose.

References protocols::filters::Filter::score(), score_type_, scorefxn_, and core::scoring::total_score.

Referenced by apply(), report(), and report_sm().

BundleReporterFilterBehaviour protocols::helical_bundle::BundleReporterFilter::filter_behaviour ( ) const
inline

Get the filter behaviour.

References behaviour_.

Referenced by apply(), and parse_my_tag().

filters::FilterOP protocols::helical_bundle::BundleReporterFilter::fresh_instance ( ) const
inlineoverridevirtual

Returns an owning pointer to a new instance of this filter, with default initialization (NOT a copy).

Implements protocols::filters::Filter.

std::string protocols::helical_bundle::BundleReporterFilter::generate_full_tracer_report ( core::Size const  jobno,
core::Real const &  score,
core::pose::Pose const &  pose 
) const

Generates the text of the full report that the filter writes out to the REPORT tracer.

Called by the APPLY function. Jobno is the RosettaScripts job number; ignored if set to 0.

Called by the APPLY function.

References core::pose::Pose::conformation(), core::conformation::Conformation::n_parameters_sets(), core::conformation::Residue::name3(), core::conformation::Conformation::parameters_set(), report_sequence(), core::pose::Pose::residue(), core::pose::Pose::sequence(), core::pose::Pose::size(), and use_threeletter().

Referenced by apply().

std::string protocols::helical_bundle::BundleReporterFilter::name ( ) const
overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

void protocols::helical_bundle::BundleReporterFilter::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual
void protocols::helical_bundle::BundleReporterFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::helical_bundle::BundleReporterFilter::report ( std::ostream &  out,
core::pose::Pose const &  pose 
) const
overridevirtual

Allows reporting of filter values to a stream.

Reimplemented from protocols::filters::Filter.

References compute(), core::scoring::ScoreTypeManager::name_from_score_type(), and score_type_.

bool protocols::helical_bundle::BundleReporterFilter::report_sequence ( ) const
inline

Get whether we report sequences.

References report_sequence_.

Referenced by generate_full_tracer_report(), and parse_my_tag().

core::Real protocols::helical_bundle::BundleReporterFilter::report_sm ( core::pose::Pose const &  pose) const
overridevirtual

Allows reporting of the filter value to a float.

Reimplemented from protocols::filters::Filter.

References compute().

core::scoring::ScoreType protocols::helical_bundle::BundleReporterFilter::score_type ( ) const
inline

Get the score type.

References score_type_.

core::Real protocols::helical_bundle::BundleReporterFilter::score_type_threshold ( ) const
inline

Get the score threshold.

References score_type_threshold_.

Referenced by apply().

core::scoring::ScoreFunctionOP protocols::helical_bundle::BundleReporterFilter::scorefxn ( )
inline

Get the scorefunction (by owning pointer).

Non-const access.

References scorefxn_.

void protocols::helical_bundle::BundleReporterFilter::set_filter_behaviour ( std::string const &  behaviour_string)

Set the behaviour by string.

Options are "ALWAYS_TRUE", "ALWAYS_FALSE", or "FILTER".

References protocols::helical_bundle::brf_always_false, protocols::helical_bundle::brf_always_true, protocols::helical_bundle::brf_filter_by_energy, and protocols::helical_bundle::brf_undefined.

Referenced by parse_my_tag().

void protocols::helical_bundle::BundleReporterFilter::set_filter_behaviour ( BundleReporterFilterBehaviour const  behaviour_in)
inline

Set the behaviour by enum.

Options are brf_always_true, brf_always_false, or brf_filter_by_energy.

References behaviour_, and protocols::helical_bundle::brf_undefined.

void protocols::helical_bundle::BundleReporterFilter::set_report_sequence ( bool const  val = true)
inline

Set whether we report sequences.

References report_sequence_, and protocols::hybridization::val.

Referenced by parse_my_tag().

void protocols::helical_bundle::BundleReporterFilter::set_score_type ( core::scoring::ScoreType const &  type)
inline

Set the score type.

References score_type_.

Referenced by parse_my_tag().

void protocols::helical_bundle::BundleReporterFilter::set_score_type_threshold ( core::Real const &  val)
inline

Set the score threshold.

References score_type_threshold_, and protocols::hybridization::val.

Referenced by parse_my_tag().

void protocols::helical_bundle::BundleReporterFilter::set_scorefxn ( core::scoring::ScoreFunctionOP  scorefxn_in)
inline

Set the scorefunction.

References scorefxn_.

Referenced by parse_my_tag().

void protocols::helical_bundle::BundleReporterFilter::set_use_threeletter ( bool const  val = true)
inline

Set whether we report three-letter codes.

References report_three_letter_codes_, and protocols::hybridization::val.

Referenced by parse_my_tag().

bool protocols::helical_bundle::BundleReporterFilter::use_threeletter ( ) const
inline

Get whether we report three-letter codes.

References report_three_letter_codes_.

Referenced by generate_full_tracer_report(), and parse_my_tag().

Member Data Documentation

BundleReporterFilterBehaviour protocols::helical_bundle::BundleReporterFilter::behaviour_
private

The behaviour of this filter.

Defaults to always returning true, but can be set to always return false or to filter by energy.

Referenced by filter_behaviour(), and set_filter_behaviour().

bool protocols::helical_bundle::BundleReporterFilter::report_sequence_
private

Report sequence? False by default.

Referenced by report_sequence(), and set_report_sequence().

bool protocols::helical_bundle::BundleReporterFilter::report_three_letter_codes_
private

Report one- or three-letter codes? False (one-letter codes) by default.

Referenced by set_use_threeletter(), and use_threeletter().

core::scoring::ScoreType protocols::helical_bundle::BundleReporterFilter::score_type_
private

What score term should be reported/used to filter?

Set to total_score by default.

Referenced by compute(), report(), score_type(), and set_score_type().

core::Real protocols::helical_bundle::BundleReporterFilter::score_type_threshold_
private

If the score is used to filter, what's the cutoff threshold above which the filter returns false?

0.0 by default.

Referenced by score_type_threshold(), and set_score_type_threshold().

core::scoring::ScoreFunctionOP protocols::helical_bundle::BundleReporterFilter::scorefxn_
private

What scorefunction should be reported/used to filter?

Must be specified by the user or in the code prior to invoking the filter; defaults to a null pointer.

Referenced by compute(), scorefxn(), and set_scorefxn().


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