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

#include <MutationsFilter.hh>

Inheritance diagram for protocols::simple_filters::MutationsFilter:
Inheritance graph

Public Member Functions

 MutationsFilter ()
 default ctor More...
bool apply (core::pose::Pose const &pose) const override
 Constructor with a single target residue. 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...
protocols::filters::FilterOP clone () const override
protocols::filters::FilterOP fresh_instance () const override
core::Real compute (core::pose::Pose const &pose, bool const &write) const
void write_to_pdb (core::pose::Pose const &pose, std::map< core::Size, std::string > const &res_names1, std::map< core::Size, std::string > const &res_names2) const
 Add each mutation to the output pdb if desired. More...
 ~MutationsFilter () override
core::pack::task::TaskFactoryOP task_factory () const
void task_factory (core::pack::task::TaskFactoryOP task_factory)
core::Real rate_threshold () const
void rate_threshold (core::Real const rate)
core::Size mutation_threshold () const
void mutation_threshold (core::Size const mut)
bool mutations () const
void mutations (bool const muts)
bool verbose () const
void verbose (bool const verb)
bool packable () const
void packable (bool const pack)
bool write2pdb () const
void write2pdb (bool const write)
core::pose::PoseCOP reference_pose () const
void reference_pose (core::pose::PoseCOP reference_pose)
void reference_pose (core::pose::Pose const &pose)
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 Types

typedef protocols::filters::Filter parent

Private Attributes

core::pack::task::TaskFactoryOP task_factory_
core::pose::PoseCOP reference_pose_
core::Real rate_threshold_
core::Size mutation_threshold_
bool mutations_
bool verbose_
bool packable_
bool write2pdb_

Additional Inherited Members

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

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::simple_filters::MutationsFilter::MutationsFilter ( )

default ctor

protocols::simple_filters::MutationsFilter::~MutationsFilter ( )

Member Function Documentation

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

Constructor with a single target residue.

Implements protocols::filters::Filter.

References compute(), mutation_threshold_, mutations_, rate_threshold_, and protocols::simple_filters::TR().

std::string protocols::simple_filters::MutationsFilter::class_name ( )
protocols::filters::FilterOP protocols::simple_filters::MutationsFilter::clone ( ) const
core::Real protocols::simple_filters::MutationsFilter::compute ( core::pose::Pose const &  pose,
bool const &  write 
) const
protocols::filters::FilterOP protocols::simple_filters::MutationsFilter::fresh_instance ( ) const
core::Size protocols::simple_filters::MutationsFilter::mutation_threshold ( ) const

References mutation_threshold_.

Referenced by parse_my_tag().

void protocols::simple_filters::MutationsFilter::mutation_threshold ( core::Size const  mut)

References mutation_threshold_.

bool protocols::simple_filters::MutationsFilter::mutations ( ) const

References mutations_.

Referenced by parse_my_tag().

void protocols::simple_filters::MutationsFilter::mutations ( bool const  muts)

References mutations_.

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

Reimplemented from protocols::filters::Filter.

References class_name().

bool protocols::simple_filters::MutationsFilter::packable ( ) const

References packable_.

Referenced by parse_my_tag().

void protocols::simple_filters::MutationsFilter::packable ( bool const  pack)

References packable_.

void protocols::simple_filters::MutationsFilter::parse_my_tag ( utility::tag::TagCOP  ,
basic::datacache::DataMap &   
void protocols::simple_filters::MutationsFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
core::Real protocols::simple_filters::MutationsFilter::rate_threshold ( ) const

References rate_threshold_.

Referenced by parse_my_tag().

void protocols::simple_filters::MutationsFilter::rate_threshold ( core::Real const  rate)

References rate_threshold_.

core::pose::PoseCOP protocols::simple_filters::MutationsFilter::reference_pose ( ) const

References reference_pose_.

Referenced by compute(), and parse_my_tag().

void protocols::simple_filters::MutationsFilter::reference_pose ( core::pose::PoseCOP  reference_pose)

References reference_pose_.

void protocols::simple_filters::MutationsFilter::reference_pose ( core::pose::Pose const &  pose)

References reference_pose_.

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

Reimplemented from protocols::filters::Filter.

References compute(), and write2pdb().

core::Real protocols::simple_filters::MutationsFilter::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::MutationsFilter::task_factory ( ) const

References task_factory_.

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

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

References task_factory(), and task_factory_.

bool protocols::simple_filters::MutationsFilter::verbose ( ) const

References verbose_.

Referenced by parse_my_tag().

void protocols::simple_filters::MutationsFilter::verbose ( bool const  verb)

References verbose_.

bool protocols::simple_filters::MutationsFilter::write2pdb ( ) const

References write2pdb_.

Referenced by parse_my_tag(), and report().

void protocols::simple_filters::MutationsFilter::write2pdb ( bool const  write)

References write2pdb_.

void protocols::simple_filters::MutationsFilter::write_to_pdb ( core::pose::Pose const &  pose,
std::map< core::Size, std::string > const &  res_names1,
std::map< core::Size, std::string > const &  res_names2 
) const

Member Data Documentation

core::Size protocols::simple_filters::MutationsFilter::mutation_threshold_

Referenced by apply(), and mutation_threshold().

bool protocols::simple_filters::MutationsFilter::mutations_

Referenced by apply(), compute(), and mutations().

bool protocols::simple_filters::MutationsFilter::packable_

Referenced by compute(), and packable().

core::Real protocols::simple_filters::MutationsFilter::rate_threshold_

Referenced by apply(), and rate_threshold().

core::pose::PoseCOP protocols::simple_filters::MutationsFilter::reference_pose_

Referenced by reference_pose().

core::pack::task::TaskFactoryOP protocols::simple_filters::MutationsFilter::task_factory_

Referenced by compute(), and task_factory().

bool protocols::simple_filters::MutationsFilter::verbose_

Referenced by compute(), and verbose().

bool protocols::simple_filters::MutationsFilter::write2pdb_

Referenced by write2pdb().

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