Rosetta
Public Types | Public Member Functions | Static Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::simple_filters::Worst9merFilter Class Reference

#include <Worst9merFilter.hh>

Inheritance diagram for protocols::simple_filters::Worst9merFilter:
Inheritance graph
[legend]

Public Types

typedef protocols::filters::Filter Super
 
typedef protocols::filters::Filter Filter
 
typedef protocols::filters::FilterOP FilterOP
 
typedef core::Real Real
 
typedef core::pose::Pose Pose
 
typedef std::string String
 
typedef utility::tag::TagCOP TagCOP
 
typedef basic::datacache::DataMap DataMap
 

Public Member Functions

 Worst9merFilter ()
 
 ~Worst9merFilter () override
 
filters::FilterOP clone () const override
 
filters::FilterOP fresh_instance () const override
 
Real report_sm (const Pose &pose) const override
 used to report filter internals through a score or silent file More...
 
void report (std::ostream &out, const Pose &pose) const override
 
Real compute (const Pose &pose) const
 
bool apply (const Pose &pose) const override
 Returns true if the given pose passes the filter, false otherwise. More...
 
void parse_my_tag (TagCOP tag, basic::datacache::DataMap &) override
 parse xml More...
 
std::string name () const override
 
void set_report_mean_median (bool report)
 
void set_residue_selector (core::select::residue_selector::ResidueSelector const &selector)
 
- Public Member Functions inherited from protocols::filters::Filter
 Filter ()
 
 Filter (std::string 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 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 class_name ()
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 

Private Member Functions

void write_mean_median (Pose const &pose, core::Real mean, core::Real median) const
 

Private Attributes

Real filtered_value_
 
Real rmsd_lookup_thresh_
 
protocols::indexed_structure_store::SSHashedFragmentStoreOP SSHashedFragmentStoreOP_
 
bool ignore_terminal_res_
 
bool only_helices_
 
bool report_mean_median_
 
core::select::residue_selector::ResidueSelectorCOP residue_selector_
 
std::string fragment_store_path_
 
std::string fragment_store_format_
 
std::string fragment_store_compression_
 

Additional Inherited Members

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

Member Typedef Documentation

◆ DataMap

typedef basic::datacache::DataMap protocols::simple_filters::Worst9merFilter::DataMap

◆ Filter

typedef protocols::filters::Filter protocols::simple_filters::Worst9merFilter::Filter

◆ FilterOP

typedef protocols::filters::FilterOP protocols::simple_filters::Worst9merFilter::FilterOP

◆ Pose

typedef core::pose::Pose protocols::simple_filters::Worst9merFilter::Pose

◆ Real

typedef core::Real protocols::simple_filters::Worst9merFilter::Real

◆ String

typedef std::string protocols::simple_filters::Worst9merFilter::String

◆ Super

typedef protocols::filters::Filter protocols::simple_filters::Worst9merFilter::Super

◆ TagCOP

typedef utility::tag::TagCOP protocols::simple_filters::Worst9merFilter::TagCOP

Constructor & Destructor Documentation

◆ Worst9merFilter()

protocols::simple_filters::Worst9merFilter::Worst9merFilter ( )

Referenced by clone(), and fresh_instance().

◆ ~Worst9merFilter()

protocols::simple_filters::Worst9merFilter::~Worst9merFilter ( )
overridedefault

Member Function Documentation

◆ apply()

bool protocols::simple_filters::Worst9merFilter::apply ( const Pose &  pose) const
overridevirtual

Returns true if the given pose passes the filter, false otherwise.

Implements protocols::filters::Filter.

References compute(), filtered_value_, and protocols::simple_filters::TR().

◆ class_name()

std::string protocols::simple_filters::Worst9merFilter::class_name ( )
static

Referenced by protocols::simple_filters::Worst9merFilterCreator::keyname(), name(), and provide_xml_schema().

◆ clone()

filters::FilterOP protocols::simple_filters::Worst9merFilter::clone ( ) const
inlineoverridevirtual

Implements protocols::filters::Filter.

References Worst9merFilter().

◆ compute()

Worst9merFilter::Real protocols::simple_filters::Worst9merFilter::compute ( const Pose &  pose) const

References core::pose::Pose::conformation(), protocols::simple_filters::dssp(), ignore_terminal_res_, core::pose::symmetry::is_symmetric(), protocols::mean_field::max(), core::simple_metrics::metrics::mean, only_helices_, report_mean_median_, residue_selector_, rmsd_lookup_thresh_, core::pose::Pose::size(), SSHashedFragmentStoreOP_, protocols::simple_filters::TR(), and write_mean_median().

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

◆ fresh_instance()

filters::FilterOP protocols::simple_filters::Worst9merFilter::fresh_instance ( ) const
inlineoverridevirtual

Implements protocols::filters::Filter.

References Worst9merFilter().

◆ name()

std::string protocols::simple_filters::Worst9merFilter::name ( ) const
overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

◆ parse_my_tag()

void protocols::simple_filters::Worst9merFilter::parse_my_tag ( TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual

parse xml

Reimplemented from protocols::filters::Filter.

References filtered_value_, fragment_store_compression_, fragment_store_format_, fragment_store_path_, ignore_terminal_res_, only_helices_, core::select::residue_selector::parse_residue_selector(), report_mean_median_, rmsd_lookup_thresh_, set_residue_selector(), SSHashedFragmentStoreOP_, and protocols::simple_filters::TR().

◆ provide_xml_schema()

void protocols::simple_filters::Worst9merFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static

References class_name(), and protocols::filters::xsd_type_definition_w_attributes().

Referenced by protocols::simple_filters::Worst9merFilterCreator::provide_xml_schema().

◆ report()

void protocols::simple_filters::Worst9merFilter::report ( std::ostream &  out,
const Pose &  pose 
) const
overridevirtual

Reimplemented from protocols::filters::Filter.

References compute(), and core::conformation::membrane::out.

Referenced by set_report_mean_median().

◆ report_sm()

Worst9merFilter::Real protocols::simple_filters::Worst9merFilter::report_sm ( const Pose &  ) const
overridevirtual

used to report filter internals through a score or silent file

Reimplemented from protocols::filters::Filter.

References compute().

◆ set_report_mean_median()

void protocols::simple_filters::Worst9merFilter::set_report_mean_median ( bool  report)
inline

References report(), and report_mean_median_.

◆ set_residue_selector()

void protocols::simple_filters::Worst9merFilter::set_residue_selector ( core::select::residue_selector::ResidueSelector const &  selector)

References core::select::residue_selector::ResidueSelector::clone(), and residue_selector_.

Referenced by parse_my_tag().

◆ write_mean_median()

void protocols::simple_filters::Worst9merFilter::write_mean_median ( Pose const &  pose,
core::Real  mean,
core::Real  median 
) const
private

References protocols::jd2::add_string_real_pair_to_current_job(), protocols::filters::Filter::get_user_defined_name(), core::simple_metrics::metrics::mean, and protocols::simple_filters::TR().

Referenced by compute().

Member Data Documentation

◆ filtered_value_

Real protocols::simple_filters::Worst9merFilter::filtered_value_
private

Referenced by apply(), and parse_my_tag().

◆ fragment_store_compression_

std::string protocols::simple_filters::Worst9merFilter::fragment_store_compression_
private

Referenced by parse_my_tag().

◆ fragment_store_format_

std::string protocols::simple_filters::Worst9merFilter::fragment_store_format_
private

Referenced by parse_my_tag().

◆ fragment_store_path_

std::string protocols::simple_filters::Worst9merFilter::fragment_store_path_
private

Referenced by parse_my_tag().

◆ ignore_terminal_res_

bool protocols::simple_filters::Worst9merFilter::ignore_terminal_res_
private

Referenced by compute(), and parse_my_tag().

◆ only_helices_

bool protocols::simple_filters::Worst9merFilter::only_helices_
private

Referenced by compute(), and parse_my_tag().

◆ report_mean_median_

bool protocols::simple_filters::Worst9merFilter::report_mean_median_
private

Referenced by compute(), parse_my_tag(), and set_report_mean_median().

◆ residue_selector_

core::select::residue_selector::ResidueSelectorCOP protocols::simple_filters::Worst9merFilter::residue_selector_
private

Referenced by compute(), and set_residue_selector().

◆ rmsd_lookup_thresh_

Real protocols::simple_filters::Worst9merFilter::rmsd_lookup_thresh_
private

Referenced by compute(), and parse_my_tag().

◆ SSHashedFragmentStoreOP_

protocols::indexed_structure_store::SSHashedFragmentStoreOP protocols::simple_filters::Worst9merFilter::SSHashedFragmentStoreOP_
private

Referenced by compute(), and parse_my_tag().

The documentation for this class was generated from the following files:
Generated on Mon Sep 4 2023 11:02:40 for Rosetta by doxygen 1.9.1