protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter Class Reference

#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 () 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	initialize_filter () const
	Initialize this filter. More...

Private Attributes
Real	filter_value_
utility::vector1< utility::vector1< Real > >	score_pairmatrix_
bool	verbose_
bool	initialized_ = false
	Has this been initialized? More...

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

Member Typedef Documentation

AA

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

DataMap

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

Filter

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

FilterOP

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

Pose

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

Real

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

Size

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

String

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

Super

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

TagCOP

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

Constructor & Destructor Documentation

ParallelBetaPairingPreferenceFilter() [1/2]

protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter::ParallelBetaPairingPreferenceFilter

(

)

ParallelBetaPairingPreferenceFilter() [2/2]

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

default

~ParallelBetaPairingPreferenceFilter()

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

inlineoverride

Member Function Documentation

apply()

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().

class_name()

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

static

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

clone()

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

inlineoverridevirtual

Implements protocols::filters::Filter.

compute()

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(), initialize_filter(), 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().

filter_value()

void protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter::filter_value

(

Real const

value

)

References filter_value_.

Referenced by parse_my_tag().

fresh_instance()

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

inlineoverridevirtual

Implements protocols::filters::Filter.

initialize_filter()

void protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter::initialize_filter ( ) const

private

Initialize this filter.

Does nothing if already initialized.

Author

Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).

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

Referenced by compute().

name()

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

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

parse_my_tag()

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_.

provide_xml_schema()

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().

report()

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(), and core::conformation::membrane::out.

report_sm()

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().

score_pairmatrix()

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

filter_value_

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

private

Referenced by apply(), and filter_value().

initialized_

bool protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter::initialized_ = false

mutableprivate

Has this been initialized?

Referenced by initialize_filter().

score_pairmatrix_

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

mutableprivate

Referenced by initialize_filter(), and score_pairmatrix().

verbose_

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

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