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

#include <ParallelBetaPairingPreferenceFilter.hh>

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 protocols::filters::Filters_map	Filters_map
typedef basic::datacache::DataMap	DataMap
typedef protocols::moves::Movers_map	Movers_map

Public Member Functions
	ParallelBetaPairingPreferenceFilter ()
	ParallelBetaPairingPreferenceFilter (ParallelBetaPairingPreferenceFilter const &rval)
virtual	~ParallelBetaPairingPreferenceFilter ()
virtual FilterOP	clone () const
virtual FilterOP	fresh_instance () const
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...
virtual Real	report_sm (Pose const &pose) const
	used to report score More...
virtual void	report (std::ostream &out, Pose const &pose) const
	used to report score More...
virtual bool	apply (Pose const &pose) const
	Returns true if the given pose passes the filter, false otherwise. More...
virtual void	parse_my_tag (TagCOP tag, basic::datacache::DataMap &, Filters_map const &, Movers_map const &, Pose const &)
	parse xml More...
Public Member Functions inherited from protocols::filters::Filter
	Filter ()
	Filter (std::string const &)
	Filter (Filter const &)
virtual	~Filter ()
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 void	apply (core::io::serialization::PipeMap &pmap)
virtual void	score (core::io::serialization::PipeMap &pmap)
virtual core::Real	score (core::pose::Pose &pose)
virtual void	parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks)
virtual std::string	name () const

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

typedef protocols::moves::Movers_map protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter::Movers_map

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 core::chemical::aa_from_oneletter_code(), core::chemical::aa_pro, getline(), basic::database::open(), runtime_assert, score_pairmatrix_, and utility::string_split().

Referenced by clone(), and fresh_instance().

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

(

ParallelBetaPairingPreferenceFilter const &

rval

)

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

inlinevirtual

Member Function Documentation

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

virtual

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

Implements protocols::filters::Filter.

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

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

inlinevirtual

Implements protocols::filters::Filter.

References ParallelBetaPairingPreferenceFilter().

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(), sc, protocols::filters::Filter::score(), score_pairmatrix(), core::pose::Pose::total_residue(), 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().

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

inlinevirtual

Implements protocols::filters::Filter.

References ParallelBetaPairingPreferenceFilter().

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

virtual

parse xml

Reimplemented from protocols::filters::Filter.

References filter_value(), and verbose_.

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

virtual

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

virtual

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().

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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