#include <SSElementBisectddGFilter.hh>

Inheritance diagram for protocols::simple_ddg::SSElementBisectddGFilter:

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
	SSElementBisectddGFilter (core::scoring::ScoreFunctionOP scorefxn, Real threshold, bool report_avg, core::Size ignore_terminal_SS, bool only_n_term, bool only_c_term, bool skip_ss_element, bool report_sasa_instead, bool convert_charged_res_to_ala, protocols::moves::MoverOP relax_mover)

	SSElementBisectddGFilter ()

	SSElementBisectddGFilter (SSElementBisectddGFilter const &rval)

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

protocols::loops::Loops	get_ss_elements (const Pose &pose) const
	get ss_elements More...

Real	get_ddg_bisect_score (core::Size element, protocols::loops::Loops ssElements, const Pose &pose) const

Real	compute (const Pose &orig_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 &data) override
	parse xml 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 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)

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

Member Typedef Documentation

typedef basic::datacache::DataMap protocols::simple_ddg::SSElementBisectddGFilter::DataMap

typedef protocols::filters::Filter protocols::simple_ddg::SSElementBisectddGFilter::Filter

typedef protocols::filters::FilterOP protocols::simple_ddg::SSElementBisectddGFilter::FilterOP

typedef core::pose::Pose protocols::simple_ddg::SSElementBisectddGFilter::Pose

typedef core::Real protocols::simple_ddg::SSElementBisectddGFilter::Real

typedef std::string protocols::simple_ddg::SSElementBisectddGFilter::String

typedef protocols::filters::Filter protocols::simple_ddg::SSElementBisectddGFilter::Super

typedef utility::tag::TagCOP protocols::simple_ddg::SSElementBisectddGFilter::TagCOP

Constructor & Destructor Documentation

protocols::simple_ddg::SSElementBisectddGFilter::SSElementBisectddGFilter	(	core::scoring::ScoreFunctionOP	scorefxn,
		Real	threshold,
		bool	report_avg,
		core::Size	ignore_terminal_SS,
		bool	only_n_term,
		bool	only_c_term,
		bool	skip_ss_element,
		bool	report_sasa_instead,
		bool	convert_charged_res_to_ala,
		protocols::moves::MoverOP	relax_mover
	)

References convert_charged_res_to_ala_, ignore_terminal_SS_, only_c_term_, only_n_term_, relax_mover_, report_avg_, report_sasa_instead_, scorefxn_, skip_ss_element_, and threshold_.

protocols::simple_ddg::SSElementBisectddGFilter::SSElementBisectddGFilter ( )

protocols::simple_ddg::SSElementBisectddGFilter::SSElementBisectddGFilter ( SSElementBisectddGFilter const & rval )

Member Function Documentation

bool protocols::simple_ddg::SSElementBisectddGFilter::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 tr().

std::string protocols::simple_ddg::SSElementBisectddGFilter::class_name ( )

static

Referenced by protocols::simple_ddg::SSElementBisectddGFilterCreator::keyname(), name(), and provide_xml_schema().

filters::FilterOP protocols::simple_ddg::SSElementBisectddGFilter::clone ( ) const

inlineoverridevirtual

Implements protocols::filters::Filter.

Real protocols::simple_ddg::SSElementBisectddGFilter::compute ( const Pose & orig_pose ) const

References core::pose::Pose::clone(), convert_charged_res_to_ala_, get_ddg_bisect_score(), get_ss_elements(), ignore_terminal_SS_, only_c_term_, only_n_term_, report_avg_, protocols::filters::Filter::score(), protocols::loops::Loops::size(), and skip_ss_element_.

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

filters::FilterOP protocols::simple_ddg::SSElementBisectddGFilter::fresh_instance ( ) const

inlineoverridevirtual

Implements protocols::filters::Filter.

Real protocols::simple_ddg::SSElementBisectddGFilter::get_ddg_bisect_score	(	core::Size	element,
		protocols::loops::Loops	ssElements,
		const Pose &	pose
	)		const

References core::pose::append_pose_to_pose(), core::conformation::change_cys_state(), protocols::simple_filters::InterfaceSasaFilter::compute(), protocols::simple_ddg::DdgFilter::compute(), core::pose::get_resnums_for_chain_id(), core::pose::symmetry::is_symmetric(), core::pose::pdbslice(), protocols::simple_ddg::DdgFilter::relax_mover(), relax_mover_, report_sasa_instead_, scorefxn_, core::pose::Pose::size(), skip_ss_element_, protocols::loops::start, and core::pose::symmetry::symmetry_info().

Referenced by compute().

protocols::loops::Loops protocols::simple_ddg::SSElementBisectddGFilter::get_ss_elements ( const Pose & pose ) const

get ss_elements

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

Referenced by compute().

std::string protocols::simple_ddg::SSElementBisectddGFilter::name ( ) const

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

void protocols::simple_ddg::SSElementBisectddGFilter::parse_my_tag	(	TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

parse xml

Reimplemented from protocols::filters::Filter.

References convert_charged_res_to_ala_, ignore_terminal_SS_, only_c_term_, only_n_term_, protocols::rosetta_scripts::parse_mover(), core::scoring::parse_score_function(), relax_mover_, report_avg_, report_sasa_instead_, scorefxn_, skip_ss_element_, and threshold_.

void protocols::simple_ddg::SSElementBisectddGFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References core::scoring::attributes_for_parse_score_function(), class_name(), and protocols::filters::xsd_type_definition_w_attributes().

Referenced by protocols::simple_ddg::SSElementBisectddGFilterCreator::provide_xml_schema().

void protocols::simple_ddg::SSElementBisectddGFilter::report	(	std::ostream &	out,
		const Pose &	pose
	)		const

overridevirtual

Reimplemented from protocols::filters::Filter.

References compute(), and report_avg_.

SSElementBisectddGFilter::Real protocols::simple_ddg::SSElementBisectddGFilter::report_sm ( const Pose & ) const

overridevirtual

used to report filter internals through a score or silent file

Reimplemented from protocols::filters::Filter.

References compute().

Member Data Documentation

bool protocols::simple_ddg::SSElementBisectddGFilter::convert_charged_res_to_ala_

private

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

core::Size protocols::simple_ddg::SSElementBisectddGFilter::ignore_terminal_SS_

private

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

bool protocols::simple_ddg::SSElementBisectddGFilter::only_c_term_

private

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

bool protocols::simple_ddg::SSElementBisectddGFilter::only_n_term_

private

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

protocols::moves::MoverOP protocols::simple_ddg::SSElementBisectddGFilter::relax_mover_

private

Referenced by get_ddg_bisect_score(), parse_my_tag(), and SSElementBisectddGFilter().

bool protocols::simple_ddg::SSElementBisectddGFilter::report_avg_

private

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

bool protocols::simple_ddg::SSElementBisectddGFilter::report_sasa_instead_

private

Referenced by get_ddg_bisect_score(), parse_my_tag(), and SSElementBisectddGFilter().

core::scoring::ScoreFunctionOP protocols::simple_ddg::SSElementBisectddGFilter::scorefxn_

private

Referenced by get_ddg_bisect_score(), parse_my_tag(), and SSElementBisectddGFilter().

bool protocols::simple_ddg::SSElementBisectddGFilter::skip_ss_element_

private

Referenced by compute(), get_ddg_bisect_score(), parse_my_tag(), and SSElementBisectddGFilter().

Real protocols::simple_ddg::SSElementBisectddGFilter::threshold_

private

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

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

src/protocols/simple_ddg/SSElementBisectddGFilter.hh
src/protocols/simple_ddg/SSElementBisectddGFilter.cc

Private Attributes
core::scoring::ScoreFunctionOP	scorefxn_

core::Size	ignore_terminal_SS_

bool	only_n_term_

bool	only_c_term_

Real	threshold_

bool	report_avg_

bool	skip_ss_element_

bool	report_sasa_instead_

bool	convert_charged_res_to_ala_

protocols::moves::MoverOP	relax_mover_

Public Types

Public Member Functions

Static Public Member Functions

Private Attributes

Additional Inherited Members

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation