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protocols::matdes::OligomericAverageDegreeFilter Class Reference

#include <OligomericAverageDegreeFilter.hh>

Inheritance diagram for protocols::matdes::OligomericAverageDegreeFilter:
Inheritance graph
[legend]

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 utility::tag::TagCOP TagCOP
 
typedef basic::datacache::DataMap DataMap
 

Public Member Functions

 OligomericAverageDegreeFilter ()
 
 OligomericAverageDegreeFilter (core::pack::task::TaskFactoryOP task_factory, core::Real const t, core::Real const d, bool jump_set, core::Size jump, std::string const &dof_names, bool mcomp)
 
 OligomericAverageDegreeFilter (OligomericAverageDegreeFilter const &rval)
 
 ~OligomericAverageDegreeFilter () override
 
protocols::filters::FilterOP clone () const override
 
protocols::filters::FilterOP fresh_instance () const override
 
void task_factory (core::pack::task::TaskFactoryOP task_factory)
 
void threshold (core::Real const t)
 
void distance_threshold (core::Real const d)
 
void jump_set (bool const jump_set)
 
void jump_id (core::Size const jump)
 
void sym_dof_names (std::string const &dof_names)
 
void write2pdb (bool const write)
 
void verbose (bool const verb)
 
void multicomp (bool const multicomp)
 
core::pack::task::TaskFactoryOP task_factory () const
 
core::Real threshold () const
 
core::Real distance_threshold () const
 
bool jump_set () const
 
core::Size jump_id () const
 
std::string sym_dof_names () const
 
bool write2pdb () const
 
bool verbose () const
 
bool multicomp () const
 
void parse_my_tag (TagCOP tag, basic::datacache::DataMap &) override
 parse xml More...
 
bool apply (core::pose::Pose const &pose) const override
 Returns true if the given pose passes the filter, false otherwise. More...
 
core::Real report_sm (core::pose::Pose const &pose) const override
 used to report filter internals through a score or silent file More...
 
void report (std::ostream &out, core::pose::Pose const &pose) const override
 
core::Real compute (core::pose::Pose const &pose, bool const &verbose, bool const &write) const
 calc oligomeric AverageDegree More...
 
void write_to_pdb (core::pose::Pose const &pose, core::Size const residue, std::string const &residue_name, core::Size const neighbors) const
 
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::pack::task::TaskFactoryOP task_factory_
 
core::Real threshold_
 
core::Real distance_threshold_
 
bool jump_set_
 
core::Size jump_id_
 
std::string sym_dof_names_
 
bool write2pdb_
 
bool verbose_
 
bool multicomp_
 

Additional Inherited Members

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

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::matdes::OligomericAverageDegreeFilter::OligomericAverageDegreeFilter ( )
protocols::matdes::OligomericAverageDegreeFilter::OligomericAverageDegreeFilter ( core::pack::task::TaskFactoryOP  task_factory,
core::Real const  t,
core::Real const  d,
bool  jump_set,
core::Size  jump,
std::string const &  dof_names,
bool  mcomp 
)
protocols::matdes::OligomericAverageDegreeFilter::OligomericAverageDegreeFilter ( OligomericAverageDegreeFilter const &  rval)
protocols::matdes::OligomericAverageDegreeFilter::~OligomericAverageDegreeFilter ( )
overridedefault

Member Function Documentation

bool protocols::matdes::OligomericAverageDegreeFilter::apply ( core::pose::Pose const &  pose) const
overridevirtual

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

Implements protocols::filters::Filter.

References compute(), and threshold().

std::string protocols::matdes::OligomericAverageDegreeFilter::class_name ( )
static
protocols::filters::FilterOP protocols::matdes::OligomericAverageDegreeFilter::clone ( ) const
overridevirtual
core::Real protocols::matdes::OligomericAverageDegreeFilter::compute ( core::pose::Pose const &  pose,
bool const &  verbose,
bool const &  write 
) const
void protocols::matdes::OligomericAverageDegreeFilter::distance_threshold ( core::Real const  d)

References distance_threshold_.

core::Real protocols::matdes::OligomericAverageDegreeFilter::distance_threshold ( ) const

References distance_threshold_.

Referenced by compute(), and parse_my_tag().

protocols::filters::FilterOP protocols::matdes::OligomericAverageDegreeFilter::fresh_instance ( ) const
overridevirtual
void protocols::matdes::OligomericAverageDegreeFilter::jump_id ( core::Size const  jump)

References jump_id_.

core::Size protocols::matdes::OligomericAverageDegreeFilter::jump_id ( ) const

References jump_id_.

Referenced by parse_my_tag().

void protocols::matdes::OligomericAverageDegreeFilter::jump_set ( bool const  jump_set)

References jump_set(), and jump_set_.

bool protocols::matdes::OligomericAverageDegreeFilter::jump_set ( ) const

References jump_set_.

Referenced by jump_set(), and parse_my_tag().

void protocols::matdes::OligomericAverageDegreeFilter::multicomp ( bool const  multicomp)

References multicomp_.

bool protocols::matdes::OligomericAverageDegreeFilter::multicomp ( ) const

References multicomp_.

Referenced by compute(), and parse_my_tag().

std::string protocols::matdes::OligomericAverageDegreeFilter::name ( ) const
overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

Referenced by write_to_pdb().

void protocols::matdes::OligomericAverageDegreeFilter::parse_my_tag ( TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual
void protocols::matdes::OligomericAverageDegreeFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::matdes::OligomericAverageDegreeFilter::report ( std::ostream &  out,
core::pose::Pose const &  pose 
) const
overridevirtual

Reimplemented from protocols::filters::Filter.

References compute(), verbose_, and write2pdb_.

core::Real protocols::matdes::OligomericAverageDegreeFilter::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().

void protocols::matdes::OligomericAverageDegreeFilter::sym_dof_names ( std::string const &  dof_names)

References sym_dof_names_.

std::string protocols::matdes::OligomericAverageDegreeFilter::sym_dof_names ( ) const

References sym_dof_names_.

Referenced by parse_my_tag().

void protocols::matdes::OligomericAverageDegreeFilter::task_factory ( core::pack::task::TaskFactoryOP  task_factory)

References task_factory(), and task_factory_.

core::pack::task::TaskFactoryOP protocols::matdes::OligomericAverageDegreeFilter::task_factory ( ) const

References task_factory_.

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

void protocols::matdes::OligomericAverageDegreeFilter::threshold ( core::Real const  t)
core::Real protocols::matdes::OligomericAverageDegreeFilter::threshold ( ) const

References threshold_.

Referenced by apply(), and parse_my_tag().

void protocols::matdes::OligomericAverageDegreeFilter::verbose ( bool const  verb)

References verbose_.

bool protocols::matdes::OligomericAverageDegreeFilter::verbose ( ) const

References verbose_.

Referenced by parse_my_tag().

void protocols::matdes::OligomericAverageDegreeFilter::write2pdb ( bool const  write)

References write2pdb_.

bool protocols::matdes::OligomericAverageDegreeFilter::write2pdb ( ) const

References write2pdb_.

Referenced by parse_my_tag().

void protocols::matdes::OligomericAverageDegreeFilter::write_to_pdb ( core::pose::Pose const &  pose,
core::Size const  residue,
std::string const &  residue_name,
core::Size const  neighbors 
) const

Member Data Documentation

core::Real protocols::matdes::OligomericAverageDegreeFilter::distance_threshold_
private

Referenced by distance_threshold().

core::Size protocols::matdes::OligomericAverageDegreeFilter::jump_id_
private

Referenced by compute(), and jump_id().

bool protocols::matdes::OligomericAverageDegreeFilter::jump_set_
private

Referenced by compute(), and jump_set().

bool protocols::matdes::OligomericAverageDegreeFilter::multicomp_
private

Referenced by compute(), and multicomp().

std::string protocols::matdes::OligomericAverageDegreeFilter::sym_dof_names_
private

Referenced by compute(), and sym_dof_names().

core::pack::task::TaskFactoryOP protocols::matdes::OligomericAverageDegreeFilter::task_factory_
private

Referenced by task_factory().

core::Real protocols::matdes::OligomericAverageDegreeFilter::threshold_
private

Referenced by threshold().

bool protocols::matdes::OligomericAverageDegreeFilter::verbose_
private

Referenced by report(), and verbose().

bool protocols::matdes::OligomericAverageDegreeFilter::write2pdb_
private

Referenced by report(), and write2pdb().


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