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

#include <ResidueBurialFilter.hh>

Inheritance diagram for protocols::simple_filters::ResidueBurialFilter:
Inheritance graph
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Public Member Functions

 ResidueBurialFilter ()
 
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::Size compute (core::pose::Pose const &pose) const
 
filters::FilterOP clone () const override
 
filters::FilterOP fresh_instance () const override
 
core::pack::task::TaskFactoryOP task_factory () const
 
void task_factory (core::pack::task::TaskFactoryOP tf)
 
 ~ResidueBurialFilter () 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...
 
core::Real residue_fraction_buried () const
 
void residue_fraction_buried (core::Real const r)
 
std::string residue () const
 
void residue (std::string const &s)
 
core::Size neighbors () const
 
void neighbors (core::Size const n)
 
core::Real distance_threshold () const
 
void distance_threshold (core::Real const r)
 
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 Does this filter indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)?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

std::string residue_
 
core::Size neighbors_
 
core::Real distance_threshold_
 
core::pack::task::TaskFactoryOP task_factory_
 
core::Real residue_fraction_buried_
 used to determine which residues to check for burial dynamically. All designable residues will be checked, and if any of them is buried, returns true More...
 

Additional Inherited Members

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

Constructor & Destructor Documentation

protocols::simple_filters::ResidueBurialFilter::ResidueBurialFilter ( )
protocols::simple_filters::ResidueBurialFilter::~ResidueBurialFilter ( )
overridedefault

Member Function Documentation

bool protocols::simple_filters::ResidueBurialFilter::apply ( core::pose::Pose const &  pose) const
overridevirtual
std::string protocols::simple_filters::ResidueBurialFilter::class_name ( )
static
filters::FilterOP protocols::simple_filters::ResidueBurialFilter::clone ( ) const
overridevirtual
core::Size protocols::simple_filters::ResidueBurialFilter::compute ( core::pose::Pose const &  pose) const
core::Real protocols::simple_filters::ResidueBurialFilter::distance_threshold ( ) const
inline

References distance_threshold_.

Referenced by apply().

void protocols::simple_filters::ResidueBurialFilter::distance_threshold ( core::Real const  r)
inline

References distance_threshold_.

filters::FilterOP protocols::simple_filters::ResidueBurialFilter::fresh_instance ( ) const
overridevirtual
std::string protocols::simple_filters::ResidueBurialFilter::name ( ) const
overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

core::Size protocols::simple_filters::ResidueBurialFilter::neighbors ( ) const
inline

References neighbors_.

Referenced by apply().

void protocols::simple_filters::ResidueBurialFilter::neighbors ( core::Size const  n)
inline

References neighbors_.

void protocols::simple_filters::ResidueBurialFilter::parse_my_tag ( utility::tag::TagCOP  ,
basic::datacache::DataMap &   
)
overridevirtual

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

Reimplemented from protocols::filters::Filter.

References distance_threshold_, neighbors_, core::pack::task::parse_task_operations(), residue(), protocols::simple_filters::residue_burial_filter_tracer(), residue_fraction_buried(), and task_factory().

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

used to report filter internals through a score or silent file

Reimplemented from protocols::filters::Filter.

References compute(), protocols::ligand_docking::ga_ligand_dock::count_neighbors(), and task_factory().

std::string protocols::simple_filters::ResidueBurialFilter::residue ( ) const
inline

References residue_.

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

void protocols::simple_filters::ResidueBurialFilter::residue ( std::string const &  s)
inline

References residue_.

core::Real protocols::simple_filters::ResidueBurialFilter::residue_fraction_buried ( ) const
inline

References residue_fraction_buried_.

Referenced by apply(), and parse_my_tag().

void protocols::simple_filters::ResidueBurialFilter::residue_fraction_buried ( core::Real const  r)
inline
core::pack::task::TaskFactoryOP protocols::simple_filters::ResidueBurialFilter::task_factory ( ) const

References task_factory_.

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

void protocols::simple_filters::ResidueBurialFilter::task_factory ( core::pack::task::TaskFactoryOP  tf)

References task_factory_.

Member Data Documentation

core::Real protocols::simple_filters::ResidueBurialFilter::distance_threshold_
private
core::Size protocols::simple_filters::ResidueBurialFilter::neighbors_
private

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

std::string protocols::simple_filters::ResidueBurialFilter::residue_
private

Referenced by residue().

core::Real protocols::simple_filters::ResidueBurialFilter::residue_fraction_buried_
private

used to determine which residues to check for burial dynamically. All designable residues will be checked, and if any of them is buried, returns true

Referenced by residue_fraction_buried().

core::pack::task::TaskFactoryOP protocols::simple_filters::ResidueBurialFilter::task_factory_
private

Referenced by task_factory().


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