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protocols::protein_interface_design::filters::SequenceRecoveryFilter Class Reference

#include <SequenceRecoveryFilter.hh>

Inheritance diagram for protocols::protein_interface_design::filters::SequenceRecoveryFilter:
Inheritance graph
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Public Member Functions

 SequenceRecoveryFilter ()
 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 (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...
 
 ~SequenceRecoveryFilter () 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 write2pdb () const
 
void write2pdb (bool const write)
 
void scorefxn (core::scoring::ScoreFunctionCOP sfx)
 
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::scoring::ScoreFunctionOP scorefxn_
 
core::Real rate_threshold_
 
core::Size mutation_threshold_
 
bool mutations_
 
bool verbose_
 
bool write2pdb_
 

Additional Inherited Members

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

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::protein_interface_design::filters::SequenceRecoveryFilter::SequenceRecoveryFilter ( )

default ctor

protocols::protein_interface_design::filters::SequenceRecoveryFilter::~SequenceRecoveryFilter ( )
overridedefault

Member Function Documentation

bool protocols::protein_interface_design::filters::SequenceRecoveryFilter::apply ( core::pose::Pose const &  pose) const
overridevirtual
std::string protocols::protein_interface_design::filters::SequenceRecoveryFilter::class_name ( )
static
protocols::filters::FilterOP protocols::protein_interface_design::filters::SequenceRecoveryFilter::clone ( ) const
overridevirtual
core::Real protocols::protein_interface_design::filters::SequenceRecoveryFilter::compute ( core::pose::Pose const &  pose,
bool const &  write 
) const
protocols::filters::FilterOP protocols::protein_interface_design::filters::SequenceRecoveryFilter::fresh_instance ( ) const
overridevirtual
core::Size protocols::protein_interface_design::filters::SequenceRecoveryFilter::mutation_threshold ( ) const

References mutation_threshold_.

Referenced by parse_my_tag().

void protocols::protein_interface_design::filters::SequenceRecoveryFilter::mutation_threshold ( core::Size const  mut)

References mutation_threshold_.

bool protocols::protein_interface_design::filters::SequenceRecoveryFilter::mutations ( ) const

References mutations_.

Referenced by parse_my_tag().

void protocols::protein_interface_design::filters::SequenceRecoveryFilter::mutations ( bool const  muts)

References mutations_.

std::string protocols::protein_interface_design::filters::SequenceRecoveryFilter::name ( ) const
overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

void protocols::protein_interface_design::filters::SequenceRecoveryFilter::parse_my_tag ( utility::tag::TagCOP  ,
basic::datacache::DataMap &   
)
overridevirtual
void protocols::protein_interface_design::filters::SequenceRecoveryFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
core::Real protocols::protein_interface_design::filters::SequenceRecoveryFilter::rate_threshold ( ) const

References rate_threshold_.

Referenced by parse_my_tag().

void protocols::protein_interface_design::filters::SequenceRecoveryFilter::rate_threshold ( core::Real const  rate)

References rate_threshold_.

core::pose::PoseCOP protocols::protein_interface_design::filters::SequenceRecoveryFilter::reference_pose ( ) const

References reference_pose_.

Referenced by compute(), and parse_my_tag().

void protocols::protein_interface_design::filters::SequenceRecoveryFilter::reference_pose ( core::pose::PoseCOP  reference_pose)

References reference_pose_.

void protocols::protein_interface_design::filters::SequenceRecoveryFilter::reference_pose ( core::pose::Pose const &  pose)

References reference_pose_.

void protocols::protein_interface_design::filters::SequenceRecoveryFilter::report ( std::ostream &  out,
core::pose::Pose const &  pose 
) const
overridevirtual

Reimplemented from protocols::filters::Filter.

References compute().

core::Real protocols::protein_interface_design::filters::SequenceRecoveryFilter::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(), and write2pdb().

void protocols::protein_interface_design::filters::SequenceRecoveryFilter::scorefxn ( core::scoring::ScoreFunctionCOP  sfx)

References scorefxn_.

Referenced by parse_my_tag().

core::pack::task::TaskFactoryOP protocols::protein_interface_design::filters::SequenceRecoveryFilter::task_factory ( ) const

References task_factory_.

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

void protocols::protein_interface_design::filters::SequenceRecoveryFilter::task_factory ( core::pack::task::TaskFactoryOP  task_factory)

References task_factory(), and task_factory_.

bool protocols::protein_interface_design::filters::SequenceRecoveryFilter::verbose ( ) const

References verbose_.

Referenced by parse_my_tag().

void protocols::protein_interface_design::filters::SequenceRecoveryFilter::verbose ( bool const  verb)

References verbose_.

bool protocols::protein_interface_design::filters::SequenceRecoveryFilter::write2pdb ( ) const

References write2pdb_.

Referenced by parse_my_tag(), and report_sm().

void protocols::protein_interface_design::filters::SequenceRecoveryFilter::write2pdb ( bool const  write)

References write2pdb_.

void protocols::protein_interface_design::filters::SequenceRecoveryFilter::write_to_pdb ( 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.

References protocols::jd2::add_string_to_current_job(), and protocols::filters::Filter::get_user_defined_name().

Referenced by compute().

Member Data Documentation

core::Size protocols::protein_interface_design::filters::SequenceRecoveryFilter::mutation_threshold_
private

Referenced by apply(), and mutation_threshold().

bool protocols::protein_interface_design::filters::SequenceRecoveryFilter::mutations_
private

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

core::Real protocols::protein_interface_design::filters::SequenceRecoveryFilter::rate_threshold_
private

Referenced by apply(), and rate_threshold().

core::pose::PoseCOP protocols::protein_interface_design::filters::SequenceRecoveryFilter::reference_pose_
private

Referenced by reference_pose().

core::scoring::ScoreFunctionOP protocols::protein_interface_design::filters::SequenceRecoveryFilter::scorefxn_
private

Referenced by compute(), and scorefxn().

core::pack::task::TaskFactoryOP protocols::protein_interface_design::filters::SequenceRecoveryFilter::task_factory_
private

Referenced by compute(), and task_factory().

bool protocols::protein_interface_design::filters::SequenceRecoveryFilter::verbose_
private

Referenced by compute(), and verbose().

bool protocols::protein_interface_design::filters::SequenceRecoveryFilter::write2pdb_
private

Referenced by write2pdb().


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