Classes | Public Types | Public Member Functions | Static Public Member Functions | Private Attributes | List of all members
protocols::simple_filters::SecretionPredictionFilter Class Reference

#include <SecretionPredictionFilter.hh>

Inheritance diagram for protocols::simple_filters::SecretionPredictionFilter:
Inheritance graph


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 () 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_regionfind_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 () 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

◆ DataMap

◆ Filter

◆ FilterOP

◆ Pose

◆ Real

◆ String

◆ Super

◆ TagCOP

Constructor & Destructor Documentation

◆ SecretionPredictionFilter()

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

◆ ~SecretionPredictionFilter()

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

Member Function Documentation

◆ apply()

bool protocols::simple_filters::SecretionPredictionFilter::apply ( const Pose pose) const

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

Implements protocols::filters::Filter.

References compute(), threshold_, and protocols::simple_filters::tr().

◆ class_name()

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

◆ clone()

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

◆ compute()

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

◆ dG_ins_for_window()

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

References get_coeff().

Referenced by find_tm_regions().

◆ find_tm_regions()

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

◆ fresh_instance()

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

◆ get_coeff()

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

Referenced by dG_ins_for_window().

◆ get_window_at_index()

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

◆ name()

std::string protocols::simple_filters::SecretionPredictionFilter::name ( ) const

Reimplemented from protocols::filters::Filter.

References class_name().

◆ parse_my_tag()

void protocols::simple_filters::SecretionPredictionFilter::parse_my_tag ( TagCOP  tag,

parse xml

Reimplemented from protocols::filters::Filter.

References threshold_, and window_size_.

◆ provide_xml_schema()

void protocols::simple_filters::SecretionPredictionFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)

◆ report()

void protocols::simple_filters::SecretionPredictionFilter::report ( std::ostream &  out,
const Pose pose 
) const

◆ report_sm()

SecretionPredictionFilter::Real protocols::simple_filters::SecretionPredictionFilter::report_sm ( const Pose ) const

used to report filter internals through a score or silent file

Reimplemented from protocols::filters::Filter.

References compute().

Member Data Documentation

◆ dG_ins_threshold_

Real protocols::simple_filters::SecretionPredictionFilter::dG_ins_threshold_

◆ keep_

std::string protocols::simple_filters::SecretionPredictionFilter::keep_

◆ threshold_

Real protocols::simple_filters::SecretionPredictionFilter::threshold_

Referenced by apply(), and parse_my_tag().

◆ window_size_

core::Size protocols::simple_filters::SecretionPredictionFilter::window_size_

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