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

#include <TotalSasaFilter.hh>

Inheritance diagram for protocols::simple_filters::TotalSasaFilter:
Inheritance graph

Public Member Functions

 TotalSasaFilter ()
 TotalSasaFilter (core::Real const lower_threshold, bool const hydrophobic=false, bool const polar=false, core::Real const upper_threshold=100000000.0, bool report_per_residue_sasa=false)
bool apply (core::pose::Pose const &pose) const override
 Returns true if the given pose passes the filter, false otherwise. More...
void report (std::ostream &out, core::pose::Pose const &pose) const override
core::Real report_sm (core::pose::Pose const &pose) const override
 used to report filter internals through a score or silent file More...
core::Real compute (core::pose::Pose const &pose) const
core::pack::task::TaskFactoryOP task_factory ()
void task_factory (core::pack::task::TaskFactoryOP task_factory)
 Set the task factory to limit SASA calculation to packable residues. More...
filters::FilterOP clone () const override
filters::FilterOP fresh_instance () const override
 ~TotalSasaFilter () override
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &) override
 Called by FilterFactory when constructing new Filter. Takes care of the specific mover's parsing. 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 bool filter_provides_citation_info () const
 Does this filter provide information about how to cite it? More...
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
virtual bool filter_is_unpublished () const
 Does this filter indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. More...

Static Public Member Functions

static std::string class_name ()
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

Private Attributes

core::Real lower_threshold_
core::Real upper_threshold_
core::pack::task::TaskFactoryOP taskfactory_
bool hydrophobic_
 Residue subset definition. Only the surface area from packable residues. More...
bool polar_
bool report_per_residue_sasa_
 count only hydrophobics? polars? More...

Additional Inherited Members

- Protected Attributes inherited from protocols::filters::Filter
std::string scorename_

Constructor & Destructor Documentation

protocols::simple_filters::TotalSasaFilter::TotalSasaFilter ( )
protocols::simple_filters::TotalSasaFilter::TotalSasaFilter ( core::Real const  lower_threshold,
bool const  hydrophobic = false,
bool const  polar = false,
core::Real const  upper_threshold = 100000000.0,
bool  report_per_residue_sasa = false 
protocols::simple_filters::TotalSasaFilter::~TotalSasaFilter ( )

Member Function Documentation

bool protocols::simple_filters::TotalSasaFilter::apply ( core::pose::Pose const &  pose) const

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

Implements protocols::filters::Filter.

References compute(), lower_threshold_, protocols::simple_filters::TR(), and upper_threshold_.

std::string protocols::simple_filters::TotalSasaFilter::class_name ( )
filters::FilterOP protocols::simple_filters::TotalSasaFilter::clone ( ) const
core::Real protocols::simple_filters::TotalSasaFilter::compute ( core::pose::Pose const &  pose) const
filters::FilterOP protocols::simple_filters::TotalSasaFilter::fresh_instance ( ) const
std::string protocols::simple_filters::TotalSasaFilter::name ( ) const

Reimplemented from protocols::filters::Filter.

References class_name().

void protocols::simple_filters::TotalSasaFilter::parse_my_tag ( utility::tag::TagCOP  ,
basic::datacache::DataMap &   

Called by FilterFactory when constructing new Filter. Takes care of the specific mover's parsing.

Reimplemented from protocols::filters::Filter.

References hydrophobic_, lower_threshold_, core::pack::task::parse_task_operations(), polar_, report_per_residue_sasa_, task_factory(), protocols::simple_filters::TR(), and upper_threshold_.

void protocols::simple_filters::TotalSasaFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
void protocols::simple_filters::TotalSasaFilter::report ( std::ostream &  out,
core::pose::Pose const &  pose 
) const
core::Real protocols::simple_filters::TotalSasaFilter::report_sm ( core::pose::Pose const &  ) const

used to report filter internals through a score or silent file

Reimplemented from protocols::filters::Filter.

References compute().

core::pack::task::TaskFactoryOP protocols::simple_filters::TotalSasaFilter::task_factory ( )

References taskfactory_.

Referenced by parse_my_tag(), and task_factory().

void protocols::simple_filters::TotalSasaFilter::task_factory ( core::pack::task::TaskFactoryOP  task_factory)

Set the task factory to limit SASA calculation to packable residues.

References task_factory(), and taskfactory_.

Member Data Documentation

bool protocols::simple_filters::TotalSasaFilter::hydrophobic_

Residue subset definition. Only the surface area from packable residues.

Referenced by compute(), and parse_my_tag().

core::Real protocols::simple_filters::TotalSasaFilter::lower_threshold_

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

bool protocols::simple_filters::TotalSasaFilter::polar_

Referenced by compute(), and parse_my_tag().

bool protocols::simple_filters::TotalSasaFilter::report_per_residue_sasa_

count only hydrophobics? polars?

Referenced by compute(), parse_my_tag(), and report().

core::pack::task::TaskFactoryOP protocols::simple_filters::TotalSasaFilter::taskfactory_

Referenced by compute(), and task_factory().

core::Real protocols::simple_filters::TotalSasaFilter::upper_threshold_

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

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