protocols::simple_filters::SSElementMotifContactFilter Class Reference

#include <SSElementMotifContactFilter.hh>

Inheritance diagram for protocols::simple_filters::SSElementMotifContactFilter:

Public Types
typedef protocols::filters::Filter	Super
typedef protocols::filters::Filter	Filter
typedef protocols::filters::FilterOP	FilterOP
typedef core::Size	Size
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
	SSElementMotifContactFilter ()
	SSElementMotifContactFilter (SSElementMotifContactFilter const &rval)
	~SSElementMotifContactFilter () override
filters::FilterOP	clone () const override
filters::FilterOP	fresh_instance () const override
void	filtered_value (Real const &value)
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
protocols::loops::Loops	get_ss_elements (const Pose &pose) const
	get ss_elements More...
core::Size	which_ssElement (core::Size res, protocols::loops::Loops ssElements) const
core::Size	get_SSelements_in_contact (core::Size element, protocols::loops::Loops ssElements, const Pose &pose) const
core::Size	get_ssElements_in_contact_w_threshold (std::multiset< core::Size > ssElements_in_contact) const
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
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
Real	filtered_value_
core::Size	ignore_n_terminal_SS_
core::Size	ignore_c_terminal_SS_
bool	only_n_term_
bool	only_c_term_
Real	threshold_
core::Size	contacts_between_ssElement_threshold_
bool	report_avg_
bool	use_atomic_contact_filter_
core::scoring::motif::MotifHashManager *	mman_

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

Member Typedef Documentation

DataMap

typedef basic::datacache::DataMap protocols::simple_filters::SSElementMotifContactFilter::DataMap

Filter

typedef protocols::filters::Filter protocols::simple_filters::SSElementMotifContactFilter::Filter

FilterOP

typedef protocols::filters::FilterOP protocols::simple_filters::SSElementMotifContactFilter::FilterOP

Pose

typedef core::pose::Pose protocols::simple_filters::SSElementMotifContactFilter::Pose

Real

typedef core::Real protocols::simple_filters::SSElementMotifContactFilter::Real

Size

typedef core::Size protocols::simple_filters::SSElementMotifContactFilter::Size

String

typedef std::string protocols::simple_filters::SSElementMotifContactFilter::String

Super

typedef protocols::filters::Filter protocols::simple_filters::SSElementMotifContactFilter::Super

TagCOP

typedef utility::tag::TagCOP protocols::simple_filters::SSElementMotifContactFilter::TagCOP

Constructor & Destructor Documentation

SSElementMotifContactFilter() [1/2]

protocols::simple_filters::SSElementMotifContactFilter::SSElementMotifContactFilter

(

)

SSElementMotifContactFilter() [2/2]

protocols::simple_filters::SSElementMotifContactFilter::SSElementMotifContactFilter ( SSElementMotifContactFilter const &  rval )

default

~SSElementMotifContactFilter()

protocols::simple_filters::SSElementMotifContactFilter::~SSElementMotifContactFilter ( )

overridedefault

Member Function Documentation

apply()

bool protocols::simple_filters::SSElementMotifContactFilter::apply ( const Pose &  pose ) const

overridevirtual

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

Implements protocols::filters::Filter.

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

class_name()

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

static

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

clone()

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

inlineoverridevirtual

Implements protocols::filters::Filter.

compute()

Real protocols::simple_filters::SSElementMotifContactFilter::compute

(

const Pose &

pose

)

const

References get_ss_elements(), get_SSelements_in_contact(), ignore_c_terminal_SS_, ignore_n_terminal_SS_, only_c_term_, only_n_term_, report_avg_, protocols::filters::Filter::score(), protocols::loops::Loops::size(), and protocols::simple_filters::TR().

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

filtered_value()

void protocols::simple_filters::SSElementMotifContactFilter::filtered_value

(

Real const &

value

)

References filtered_value_.

fresh_instance()

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

inlineoverridevirtual

Implements protocols::filters::Filter.

get_ss_elements()

protocols::loops::Loops protocols::simple_filters::SSElementMotifContactFilter::get_ss_elements

(

const Pose &

pose

)

const

get ss_elements

References protocols::loops::Loops::add_loop(), protocols::simple_filters::dssp(), core::pose::symmetry::is_symmetric(), core::pose::Pose::size(), and core::pose::symmetry::symmetry_info().

Referenced by compute().

get_SSelements_in_contact()

Size protocols::simple_filters::SSElementMotifContactFilter::get_SSelements_in_contact	(	core::Size	element,
		protocols::loops::Loops	ssElements,
		const Pose &	pose
	)		const

References protocols::simple_filters::AtomicContactFilter::apply(), protocols::simple_filters::dssp(), core::pose::Pose::fold_tree(), core::pose::motif::get_backbone_reference_frame(), get_ssElements_in_contact_w_threshold(), core::scoring::motif::MotifHashManager::get_xform_score_BB_BB(), core::kinematics::FoldTree::is_jump_point(), core::pose::symmetry::is_symmetric(), mman_, core::conformation::Residue::name1(), core::pose::Pose::residue(), core::pose::Pose::size(), protocols::loops::start, core::pose::symmetry::symmetry_info(), use_atomic_contact_filter_, which_ssElement(), and core::conformation::Residue::xyz().

Referenced by compute().

get_ssElements_in_contact_w_threshold()

Size protocols::simple_filters::SSElementMotifContactFilter::get_ssElements_in_contact_w_threshold

(

std::multiset< core::Size >

ssElements_in_contact

)

const

References contacts_between_ssElement_threshold_.

Referenced by get_SSelements_in_contact().

name()

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

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

parse_my_tag()

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

overridevirtual

parse xml

Reimplemented from protocols::filters::Filter.

References contacts_between_ssElement_threshold_, ignore_c_terminal_SS_, ignore_n_terminal_SS_, mman_, only_c_term_, only_n_term_, report_avg_, threshold_, and use_atomic_contact_filter_.

provide_xml_schema()

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

static

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

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

report()

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

overridevirtual

Reimplemented from protocols::filters::Filter.

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

report_sm()

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

overridevirtual

used to report filter internals through a score or silent file

Reimplemented from protocols::filters::Filter.

References compute().

which_ssElement()

Size protocols::simple_filters::SSElementMotifContactFilter::which_ssElement	(	core::Size	res,
		protocols::loops::Loops	ssElements
	)		const

References protocols::loops::Loops::size(), protocols::loops::start, and protocols::loops::stop.

Referenced by get_SSelements_in_contact().

Member Data Documentation

contacts_between_ssElement_threshold_

core::Size protocols::simple_filters::SSElementMotifContactFilter::contacts_between_ssElement_threshold_

private

Referenced by get_ssElements_in_contact_w_threshold(), and parse_my_tag().

filtered_value_

Real protocols::simple_filters::SSElementMotifContactFilter::filtered_value_

private

Referenced by filtered_value().

ignore_c_terminal_SS_

core::Size protocols::simple_filters::SSElementMotifContactFilter::ignore_c_terminal_SS_

private

Referenced by compute(), and parse_my_tag().

ignore_n_terminal_SS_

core::Size protocols::simple_filters::SSElementMotifContactFilter::ignore_n_terminal_SS_

private

Referenced by compute(), and parse_my_tag().

mman_

core::scoring::motif::MotifHashManager* protocols::simple_filters::SSElementMotifContactFilter::mman_

private

Referenced by get_SSelements_in_contact(), and parse_my_tag().

only_c_term_

bool protocols::simple_filters::SSElementMotifContactFilter::only_c_term_

private

Referenced by compute(), and parse_my_tag().

only_n_term_

bool protocols::simple_filters::SSElementMotifContactFilter::only_n_term_

private

Referenced by compute(), and parse_my_tag().

report_avg_

bool protocols::simple_filters::SSElementMotifContactFilter::report_avg_

private

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

threshold_

Real protocols::simple_filters::SSElementMotifContactFilter::threshold_

private

Referenced by apply(), and parse_my_tag().

use_atomic_contact_filter_

bool protocols::simple_filters::SSElementMotifContactFilter::use_atomic_contact_filter_

private

Referenced by get_SSelements_in_contact(), and parse_my_tag().

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

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