protocols::simple_filters::LeastNativeLike9merFilter Class Reference

#include <LeastNativeLike9merFilter.hh>

Inheritance diagram for protocols::simple_filters::LeastNativeLike9merFilter:

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
	LeastNativeLike9merFilter ()
	~LeastNativeLike9merFilter () 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 (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 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::SSHashedFragmentStore *	SSHashedFragmentStore_
bool	ignore_terminal_res_
bool	only_helices_
bool	report_mean_median_
core::select::residue_selector::ResidueSelectorCOP	residue_selector_

Additional Inherited Members
Protected Attributes inherited from protocols::filters::Filter
std::string	scorename_

Member Typedef Documentation

typedef basic::datacache::DataMap protocols::simple_filters::LeastNativeLike9merFilter::DataMap

typedef protocols::filters::Filter protocols::simple_filters::LeastNativeLike9merFilter::Filter

typedef protocols::filters::FilterOP protocols::simple_filters::LeastNativeLike9merFilter::FilterOP

typedef core::pose::Pose protocols::simple_filters::LeastNativeLike9merFilter::Pose

typedef core::Real protocols::simple_filters::LeastNativeLike9merFilter::Real

typedef std::string protocols::simple_filters::LeastNativeLike9merFilter::String

typedef protocols::filters::Filter protocols::simple_filters::LeastNativeLike9merFilter::Super

typedef utility::tag::TagCOP protocols::simple_filters::LeastNativeLike9merFilter::TagCOP

Constructor & Destructor Documentation

protocols::simple_filters::LeastNativeLike9merFilter::LeastNativeLike9merFilter

(

)

Referenced by clone(), and fresh_instance().

protocols::simple_filters::LeastNativeLike9merFilter::~LeastNativeLike9merFilter ( )

overridedefault

Member Function Documentation

bool protocols::simple_filters::LeastNativeLike9merFilter::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().

std::string protocols::simple_filters::LeastNativeLike9merFilter::class_name ( )

static

Referenced by protocols::simple_filters::LeastNativeLike9merFilterCreator::keyname(), name(), and provide_xml_schema().

filters::FilterOP protocols::simple_filters::LeastNativeLike9merFilter::clone ( ) const

inlineoverridevirtual

Implements protocols::filters::Filter.

References LeastNativeLike9merFilter().

LeastNativeLike9merFilter::Real protocols::simple_filters::LeastNativeLike9merFilter::compute

(

const Pose &

pose

)

const

References core::pose::Pose::conformation(), protocols::simple_filters::dssp(), core::scoring::dssp::Dssp::dssp_reduced(), core::scoring::dssp::Dssp::get_dssp_secstruct(), protocols::indexed_structure_store::SSHashedFragmentStore::get_fragment_length(), ignore_terminal_res_, core::pose::symmetry::is_symmetric(), protocols::indexed_structure_store::SSHashedFragmentStore::lookback(), protocols::indexed_structure_store::SSHashedFragmentStore::lookback_account_for_dssp_inaccuracy(), protocols::mean_field::max(), core::simple_metrics::metrics::mean, only_helices_, report_mean_median_, residue_selector_, rmsd_lookup_thresh_, core::pose::Pose::size(), SSHashedFragmentStore_, protocols::simple_filters::TR(), and write_mean_median().

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

filters::FilterOP protocols::simple_filters::LeastNativeLike9merFilter::fresh_instance ( ) const

inlineoverridevirtual

Implements protocols::filters::Filter.

References LeastNativeLike9merFilter().

std::string protocols::simple_filters::LeastNativeLike9merFilter::name ( ) const

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

void protocols::simple_filters::LeastNativeLike9merFilter::parse_my_tag ( TagCOP  tag, basic::datacache::DataMap &  data  )

overridevirtual

parse xml

Reimplemented from protocols::filters::Filter.

References filtered_value_, ignore_terminal_res_, only_helices_, core::select::residue_selector::parse_residue_selector(), report_mean_median_, rmsd_lookup_thresh_, set_residue_selector(), protocols::indexed_structure_store::SSHashedFragmentStore::set_threshold_distance(), SSHashedFragmentStore_, and protocols::simple_filters::TR().

void protocols::simple_filters::LeastNativeLike9merFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd )

static

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

Referenced by protocols::simple_filters::LeastNativeLike9merFilterCreator::provide_xml_schema().

void protocols::simple_filters::LeastNativeLike9merFilter::report ( std::ostream &  out, const Pose &  pose  ) const

overridevirtual

Reimplemented from protocols::filters::Filter.

References compute().

Referenced by set_report_mean_median().

LeastNativeLike9merFilter::Real protocols::simple_filters::LeastNativeLike9merFilter::report_sm ( const Pose &  ) const

overridevirtual

used to report filter internals through a score or silent file

Reimplemented from protocols::filters::Filter.

References compute().

void protocols::simple_filters::LeastNativeLike9merFilter::set_report_mean_median ( bool  report )

inline

References report(), and report_mean_median_.

void protocols::simple_filters::LeastNativeLike9merFilter::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().

void protocols::simple_filters::LeastNativeLike9merFilter::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(), and protocols::simple_filters::TR().

Referenced by compute().

Member Data Documentation

Real protocols::simple_filters::LeastNativeLike9merFilter::filtered_value_

private

Referenced by apply(), and parse_my_tag().

bool protocols::simple_filters::LeastNativeLike9merFilter::ignore_terminal_res_

private

Referenced by compute(), and parse_my_tag().

bool protocols::simple_filters::LeastNativeLike9merFilter::only_helices_

private

Referenced by compute(), and parse_my_tag().

bool protocols::simple_filters::LeastNativeLike9merFilter::report_mean_median_

private

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

core::select::residue_selector::ResidueSelectorCOP protocols::simple_filters::LeastNativeLike9merFilter::residue_selector_

private

Referenced by compute(), and set_residue_selector().

Real protocols::simple_filters::LeastNativeLike9merFilter::rmsd_lookup_thresh_

private

Referenced by compute(), and parse_my_tag().

protocols::indexed_structure_store::SSHashedFragmentStore* protocols::simple_filters::LeastNativeLike9merFilter::SSHashedFragmentStore_

private

Referenced by compute(), and parse_my_tag().

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

• src/protocols/simple_filters/LeastNativeLike9merFilter.hh
• src/protocols/simple_filters/LeastNativeLike9merFilter.cc