Public Types | Public Member Functions | Static Public Member Functions | Private Attributes | List of all members
protocols::matdes::OligomericAverageDegreeFilter Class Reference

#include <OligomericAverageDegreeFilter.hh>

Inheritance diagram for protocols::matdes::OligomericAverageDegreeFilter:
Inheritance graph

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 () 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

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

◆ DataMap

◆ Filter

◆ FilterOP

◆ Pose

◆ Real

◆ Super

◆ TagCOP

Constructor & Destructor Documentation

◆ OligomericAverageDegreeFilter() [1/3]

protocols::matdes::OligomericAverageDegreeFilter::OligomericAverageDegreeFilter ( )

◆ OligomericAverageDegreeFilter() [2/3]

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 

◆ OligomericAverageDegreeFilter() [3/3]

protocols::matdes::OligomericAverageDegreeFilter::OligomericAverageDegreeFilter ( OligomericAverageDegreeFilter const &  rval)

◆ ~OligomericAverageDegreeFilter()

protocols::matdes::OligomericAverageDegreeFilter::~OligomericAverageDegreeFilter ( )

Member Function Documentation

◆ apply()

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

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

Implements protocols::filters::Filter.

References compute(), and threshold().

◆ class_name()

std::string protocols::matdes::OligomericAverageDegreeFilter::class_name ( )

◆ clone()

protocols::filters::FilterOP protocols::matdes::OligomericAverageDegreeFilter::clone ( ) const

◆ compute()

core::Real protocols::matdes::OligomericAverageDegreeFilter::compute ( core::pose::Pose const &  pose,
bool const &  verbose,
bool const &  write 
) const

◆ distance_threshold() [1/2]

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

References distance_threshold_.

Referenced by compute(), and parse_my_tag().

◆ distance_threshold() [2/2]

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

References distance_threshold_.

◆ fresh_instance()

protocols::filters::FilterOP protocols::matdes::OligomericAverageDegreeFilter::fresh_instance ( ) const

◆ jump_id() [1/2]

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

References jump_id_.

Referenced by parse_my_tag().

◆ jump_id() [2/2]

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

References jump_id_.

◆ jump_set() [1/2]

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

References jump_set_.

Referenced by jump_set(), and parse_my_tag().

◆ jump_set() [2/2]

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

References jump_set(), and jump_set_.

◆ multicomp() [1/2]

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

References multicomp_.

Referenced by compute(), and parse_my_tag().

◆ multicomp() [2/2]

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

References multicomp_.

◆ name()

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

Reimplemented from protocols::filters::Filter.

References class_name().

Referenced by write_to_pdb().

◆ parse_my_tag()

void protocols::matdes::OligomericAverageDegreeFilter::parse_my_tag ( TagCOP  tag,
basic::datacache::DataMap data 

◆ provide_xml_schema()

void protocols::matdes::OligomericAverageDegreeFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)

◆ report()

void protocols::matdes::OligomericAverageDegreeFilter::report ( std::ostream &  out,
core::pose::Pose const &  pose 
) const

◆ report_sm()

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

◆ sym_dof_names() [1/2]

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

References sym_dof_names_.

Referenced by parse_my_tag().

◆ sym_dof_names() [2/2]

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

References sym_dof_names_.

◆ task_factory() [1/2]

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

References task_factory_.

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

◆ task_factory() [2/2]

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

References task_factory(), and task_factory_.

◆ threshold() [1/2]

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

References threshold_.

Referenced by apply(), and parse_my_tag().

◆ threshold() [2/2]

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

◆ verbose() [1/2]

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

References verbose_.

Referenced by compute(), and parse_my_tag().

◆ verbose() [2/2]

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

References verbose_.

◆ write2pdb() [1/2]

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

References write2pdb_.

Referenced by parse_my_tag().

◆ write2pdb() [2/2]

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

References write2pdb_.

◆ write_to_pdb()

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

◆ distance_threshold_

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

Referenced by distance_threshold().

◆ jump_id_

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

Referenced by compute(), and jump_id().

◆ jump_set_

bool protocols::matdes::OligomericAverageDegreeFilter::jump_set_

Referenced by compute(), and jump_set().

◆ multicomp_

bool protocols::matdes::OligomericAverageDegreeFilter::multicomp_

Referenced by compute(), and multicomp().

◆ sym_dof_names_

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

Referenced by compute(), and sym_dof_names().

◆ task_factory_

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

Referenced by task_factory().

◆ threshold_

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

Referenced by threshold().

◆ verbose_

bool protocols::matdes::OligomericAverageDegreeFilter::verbose_

Referenced by report(), and verbose().

◆ write2pdb_

bool protocols::matdes::OligomericAverageDegreeFilter::write2pdb_

Referenced by report(), and write2pdb().

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