#include <ParallelBetaPairingPreferenceFilter.hh>

Inheritance diagram for protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter:

Public Types
typedef protocols::filters::Filter	Super

typedef core::Size	Size

typedef core::Real	Real

typedef core::chemical::AA	AA

typedef protocols::filters::Filter	Filter

typedef std::string	String

typedef protocols::filters::FilterOP	FilterOP

typedef core::pose::Pose	Pose

typedef utility::tag::TagCOP	TagCOP

typedef basic::datacache::DataMap	DataMap

Public Member Functions
	ParallelBetaPairingPreferenceFilter ()

	ParallelBetaPairingPreferenceFilter (ParallelBetaPairingPreferenceFilter const &rval)

	~ParallelBetaPairingPreferenceFilter () override

FilterOP	clone () const override

FilterOP	fresh_instance () const override

void	filter_value (Real const value)

Real	compute (Pose const &pose) const
	compute number of contacts More...

Real	score_pairmatrix (AA aa1, AA aa2) const
	refer score of residue pair More...

Real	report_sm (Pose const &pose) const override
	used to report score More...

void	report (std::ostream &out, Pose const &pose) const override
	used to report score More...

bool	apply (Pose const &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 (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 Attributes
Real	filter_value_

utility::vector1 < utility::vector1< Real > >	score_pairmatrix_

bool	verbose_

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

Member Typedef Documentation

typedef core::chemical::AA protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter::AA

typedef basic::datacache::DataMap protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter::DataMap

typedef protocols::filters::Filter protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter::Filter

typedef protocols::filters::FilterOP protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter::FilterOP

typedef core::pose::Pose protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter::Pose

typedef core::Real protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter::Real

typedef core::Size protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter::Size

typedef std::string protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter::String

typedef protocols::filters::Filter protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter::Super

typedef utility::tag::TagCOP protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter::TagCOP

Constructor & Destructor Documentation

protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter::ParallelBetaPairingPreferenceFilter ( )

References protocols::cluster::calibur::aa, core::chemical::aa_from_oneletter_code(), core::chemical::aa_pro, and score_pairmatrix_.

protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter::ParallelBetaPairingPreferenceFilter ( ParallelBetaPairingPreferenceFilter const & rval )

default

protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter::~ParallelBetaPairingPreferenceFilter ( )

inlineoverride

Member Function Documentation

bool protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter::apply ( Pose const & pose ) const

overridevirtual

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

Implements protocols::filters::Filter.

References compute(), filter_value_, and protocols::filters::Filter::score().

std::string protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter::class_name ( )

static

Referenced by protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilterCreator::keyname(), name(), and provide_xml_schema().

FilterOP protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter::clone ( ) const

inlineoverridevirtual

Implements protocols::filters::Filter.

ParallelBetaPairingPreferenceFilter::Real protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter::compute ( Pose const & pose ) const

compute number of contacts

References core::pose::Pose::aa(), protocols::fldsgn::topology::calc_strand_pairing_set(), protocols::simple_filters::dssp(), core::chemical::oneletter_code_from_aa(), protocols::filters::Filter::score(), score_pairmatrix(), core::pose::Pose::size(), protocols::fldsgn::TR(), and verbose_.

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

void protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter::filter_value ( Real const value )

References filter_value_.

Referenced by parse_my_tag().

FilterOP protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter::fresh_instance ( ) const

inlineoverridevirtual

Implements protocols::filters::Filter.

std::string protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter::name ( ) const

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

void protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter::parse_my_tag	(	TagCOP	tag,
		basic::datacache::DataMap &
	)

overridevirtual

parse xml

Reimplemented from protocols::filters::Filter.

References filter_value(), and verbose_.

void protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

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

Referenced by protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilterCreator::provide_xml_schema().

void protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter::report	(	std::ostream &	out,
		Pose const &	pose
	)		const

overridevirtual

used to report score

report filter results

Reimplemented from protocols::filters::Filter.

References compute().

ParallelBetaPairingPreferenceFilter::Real protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter::report_sm ( Pose const & pose ) const

overridevirtual

used to report score

return filter value

Reimplemented from protocols::filters::Filter.

References compute().

ParallelBetaPairingPreferenceFilter::Real protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter::score_pairmatrix	(	AA	aa1,
		AA	aa2
	)		const

refer score of residue pair

References score_pairmatrix_.

Referenced by compute().

Member Data Documentation

Real protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter::filter_value_

private

Referenced by apply(), and filter_value().

utility::vector1< utility::vector1< Real > > protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter::score_pairmatrix_

private

Referenced by ParallelBetaPairingPreferenceFilter(), and score_pairmatrix().

bool protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter::verbose_

private

Referenced by compute(), and parse_my_tag().

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

src/protocols/fldsgn/filters/ParallelBetaPairingPreferenceFilter.hh
src/protocols/fldsgn/filters/ParallelBetaPairingPreferenceFilter.cc

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