#include <SecretionPredictionFilter.hh>

Inheritance diagram for protocols::simple_filters::SecretionPredictionFilter:

Classes
struct	mutt

struct	tm_region

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
	SecretionPredictionFilter ()

	SecretionPredictionFilter (SecretionPredictionFilter const &rval)

	~SecretionPredictionFilter () override

filters::FilterOP	clone () const override

filters::FilterOP	fresh_instance () const override

double	get_coeff (const std::string &str1, const std::string &str2) const

core::Real	dG_ins_for_window (const std::string &window) const

std::string	get_window_at_index (const Pose &pose, const core::Size &wlen, const core::Size &start) const

utility::vector1 < SecretionPredictionFilter::tm_region >	find_tm_regions (std::ostream &out, const Pose &pose) const

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

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 (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	threshold_

core::Size	window_size_

Real	dG_ins_threshold_

std::string	keep_

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

Member Typedef Documentation

typedef basic::datacache::DataMap protocols::simple_filters::SecretionPredictionFilter::DataMap

typedef protocols::filters::Filter protocols::simple_filters::SecretionPredictionFilter::Filter

typedef protocols::filters::FilterOP protocols::simple_filters::SecretionPredictionFilter::FilterOP

typedef core::pose::Pose protocols::simple_filters::SecretionPredictionFilter::Pose

typedef core::Real protocols::simple_filters::SecretionPredictionFilter::Real

typedef std::string protocols::simple_filters::SecretionPredictionFilter::String

typedef protocols::filters::Filter protocols::simple_filters::SecretionPredictionFilter::Super

typedef utility::tag::TagCOP protocols::simple_filters::SecretionPredictionFilter::TagCOP

Constructor & Destructor Documentation

protocols::simple_filters::SecretionPredictionFilter::SecretionPredictionFilter ( )

References dG_ins_threshold_, keep_, and window_size_.

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

protocols::simple_filters::SecretionPredictionFilter::~SecretionPredictionFilter ( )

overridedefault

Member Function Documentation

bool protocols::simple_filters::SecretionPredictionFilter::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().

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

static

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

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

inlineoverridevirtual

Implements protocols::filters::Filter.

Real protocols::simple_filters::SecretionPredictionFilter::compute ( const Pose & pose ) const

References find_tm_regions(), and protocols::simple_filters::tr().

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

core::Real protocols::simple_filters::SecretionPredictionFilter::dG_ins_for_window ( const std::string & window ) const

References get_coeff().

Referenced by find_tm_regions().

vector1< SecretionPredictionFilter::tm_region > protocols::simple_filters::SecretionPredictionFilter::find_tm_regions	(	std::ostream &	out,
		const Pose &	pose
	)		const

References core::pose::Pose::chain_sequence(), protocols::simple_filters::SecretionPredictionFilter::tm_region::dG_ins, dG_ins_for_window(), dG_ins_threshold_, core::pose::get_chain_id_from_chain(), get_window_at_index(), protocols::simple_filters::SecretionPredictionFilter::tm_region::index, keep_, protocols::simple_filters::SecretionPredictionFilter::tm_region::possible_mutants, core::chemical::rings::q, protocols::simple_filters::SecretionPredictionFilter::tm_region::sequence, and window_size_.

Referenced by compute().

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

inlineoverridevirtual

Implements protocols::filters::Filter.

double protocols::simple_filters::SecretionPredictionFilter::get_coeff	(	const std::string &	str1,
		const std::string &	str2
	)		const

Referenced by dG_ins_for_window().

std::string protocols::simple_filters::SecretionPredictionFilter::get_window_at_index	(	const Pose &	pose,
		const core::Size &	wlen,
		const core::Size &	start
	)		const