protocols::pose_sewing::filters::CoreScorer Class Reference

a filter that evaluates pairwise MotifScores More...

#include <CoreScorer.hh>

Inheritance diagram for protocols::pose_sewing::filters::CoreScorer:

Public Member Functions
	CoreScorer ()
	~CoreScorer () override
bool	apply (core::pose::Pose const &pose) const override
	returns true if the structure passes the filter, false otherwise More...
core::Real	report_sm (core::pose::Pose const &pose) const override
	required for reporting score values More...
void	report (std::ostream &os, core::pose::Pose const &pose) const override
	allows printing data to a stream More...
std::string	name () const override
void	set_selector (core::select::residue_selector::ResidueSelectorCOP selector)
void	set_score_cutoff (core::Real score_cutoff)
void	set_distance_cutoff (core::Real distance_cutoff)
void	set_window_width (core::Size window_width)
void	set_link_cutoff (core::Size link_cutoff)
void	set_sum (bool sum)
void	set_distance_mode (bool distance_mode)
void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
	parse XML tag (to use this Filter in Rosetta Scripts) More...
protocols::filters::FilterOP	fresh_instance () const override
	required in the context of the parser/scripting scheme More...
protocols::filters::FilterOP	clone () const override
	required in the context of the parser/scripting scheme More...
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 Attributes
core::Real	score_cutoff_
core::Real	distance_cutoff_
core::Size	link_cutoff_ = 3
core::Size	window_width_
core::select::residue_selector::ResidueSelectorCOP	selector_
std::map< char, CSSettings >	ss_settings_
bool	sum_ = false
bool	distance_mode_ = false

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

Detailed Description

a filter that evaluates pairwise MotifScores

Constructor & Destructor Documentation

CoreScorer()

protocols::pose_sewing::filters::CoreScorer::CoreScorer

(

)

Referenced by clone().

~CoreScorer()

protocols::pose_sewing::filters::CoreScorer::~CoreScorer ( )

override

Member Function Documentation

apply()

bool protocols::pose_sewing::filters::CoreScorer::apply ( core::pose::Pose const &  pose ) const

overridevirtual

returns true if the structure passes the filter, false otherwise

Implements protocols::filters::Filter.

References link_cutoff_, and report_sm().

class_name()

std::string protocols::pose_sewing::filters::CoreScorer::class_name ( )

static

Referenced by protocols::pose_sewing::filters::CoreScorerCreator::keyname(), name(), and provide_xml_schema().

clone()

protocols::filters::FilterOP protocols::pose_sewing::filters::CoreScorer::clone ( ) const

overridevirtual

required in the context of the parser/scripting scheme

Implements protocols::filters::Filter.

References CoreScorer().

fresh_instance()

protocols::filters::FilterOP protocols::pose_sewing::filters::CoreScorer::fresh_instance ( ) const

overridevirtual

required in the context of the parser/scripting scheme

Implements protocols::filters::Filter.

name()

std::string protocols::pose_sewing::filters::CoreScorer::name ( ) const

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

parse_my_tag()

void protocols::pose_sewing::filters::CoreScorer::parse_my_tag ( utility::tag::TagCOP  tag, basic::datacache::DataMap &  data  )

overridevirtual

parse XML tag (to use this Filter in Rosetta Scripts)

Reimplemented from protocols::filters::Filter.

References distance_cutoff_, distance_mode_, core::select::residue_selector::get_residue_selector(), link_cutoff_, score_cutoff_, selector_, sum_, and window_width_.

provide_xml_schema()

void protocols::pose_sewing::filters::CoreScorer::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd )

static

References core::select::residue_selector::attributes_for_parse_residue_selector(), class_name(), and protocols::filters::xsd_type_definition_w_attributes().

Referenced by protocols::pose_sewing::filters::CoreScorerCreator::provide_xml_schema().

report()

void protocols::pose_sewing::filters::CoreScorer::report ( std::ostream &  os, core::pose::Pose const &  pose  ) const

overridevirtual

allows printing data to a stream

Reimplemented from protocols::filters::Filter.

References report_sm(), and protocols::TR().

report_sm()

core::Real protocols::pose_sewing::filters::CoreScorer::report_sm ( core::pose::Pose const &  pose ) const

overridevirtual

required for reporting score values

Reimplemented from protocols::filters::Filter.

References core::conformation::Residue::atoms(), protocols::pose_sewing::calculate_blocks_from_subset(), core::kinematics::distance(), distance_cutoff_, distance_mode_, core::pose::motif::get_backbone_reference_frame(), protocols::sewing::scoring::MotifScorer::get_score(), core::conformation::Residue::is_virtual_residue(), core::conformation::Residue::name1(), core::pose::Pose::residue(), score_cutoff_, core::pose::Pose::secstruct(), selector_, core::pose::Pose::size(), sum_, protocols::analysis::total, protocols::TR(), window_width_, and protocols::kinmatch::xyz().

Referenced by apply(), and report().

set_distance_cutoff()

void protocols::pose_sewing::filters::CoreScorer::set_distance_cutoff

(

core::Real

distance_cutoff

)

References distance_cutoff_.

set_distance_mode()

void protocols::pose_sewing::filters::CoreScorer::set_distance_mode

(

bool

distance_mode

)

References distance_mode_.

set_link_cutoff()

void protocols::pose_sewing::filters::CoreScorer::set_link_cutoff

(

core::Size

link_cutoff

)

References link_cutoff_.

set_score_cutoff()

void protocols::pose_sewing::filters::CoreScorer::set_score_cutoff

(

core::Real

score_cutoff

)

References score_cutoff_.

set_selector()

void protocols::pose_sewing::filters::CoreScorer::set_selector

(

core::select::residue_selector::ResidueSelectorCOP

selector

)

References selector_.

set_sum()

void protocols::pose_sewing::filters::CoreScorer::set_sum

(

bool

sum

)

References core::simple_metrics::metrics::sum, and sum_.

set_window_width()

void protocols::pose_sewing::filters::CoreScorer::set_window_width

(

core::Size

window_width

)

References window_width_.

Member Data Documentation

distance_cutoff_

core::Real protocols::pose_sewing::filters::CoreScorer::distance_cutoff_

private

Referenced by parse_my_tag(), report_sm(), and set_distance_cutoff().

distance_mode_

bool protocols::pose_sewing::filters::CoreScorer::distance_mode_ = false

private

Referenced by parse_my_tag(), report_sm(), and set_distance_mode().

link_cutoff_

core::Size protocols::pose_sewing::filters::CoreScorer::link_cutoff_ = 3

private

Referenced by apply(), parse_my_tag(), and set_link_cutoff().

score_cutoff_

core::Real protocols::pose_sewing::filters::CoreScorer::score_cutoff_

private

Referenced by parse_my_tag(), report_sm(), and set_score_cutoff().

selector_

core::select::residue_selector::ResidueSelectorCOP protocols::pose_sewing::filters::CoreScorer::selector_

private

Referenced by parse_my_tag(), report_sm(), and set_selector().

ss_settings_

std::map< char, CSSettings > protocols::pose_sewing::filters::CoreScorer::ss_settings_

private

sum_

bool protocols::pose_sewing::filters::CoreScorer::sum_ = false

private

Referenced by parse_my_tag(), report_sm(), and set_sum().

window_width_

core::Size protocols::pose_sewing::filters::CoreScorer::window_width_

private

Referenced by parse_my_tag(), report_sm(), and set_window_width().

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

• src/protocols/pose_sewing/filters/CoreScorer.hh
• src/protocols/pose_sewing/filters/CoreScorer.cc