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protocols::protein_interface_design::filters::FilterScanFilter Class Reference

#include <FilterScan.hh>

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

 FilterScanFilter ()
 default ctor More...
 
 ~FilterScanFilter () override
 
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::pack::task::TaskFactoryOP task_factory () const
 Undefined, commenting out to fix PyRosetta build core::Real compute( core::pose::Pose const & pose ) const;. More...
 
void task_factory (core::pack::task::TaskFactoryOP task_factory)
 
void resfile_name (std::string const &resfile_name)
 
void score_log_file (std::string const &score_log_file)
 
std::string resfile_name () const
 
std::string score_log_file () const
 
protocols::filters::FilterOP triage_filter () const
 
void triage_filter (protocols::filters::FilterOP filter)
 
protocols::filters::FilterOP filter () const
 
void filter (protocols::filters::FilterOP filter)
 
std::string resfile_general_property () const
 
void resfile_general_property (std::string const &)
 
void relax_mover (protocols::moves::MoverOP mover)
 
protocols::moves::MoverOP relax_mover () const
 
core::scoring::ScoreFunctionOP scorefxn () const
 
void scorefxn (core::scoring::ScoreFunctionOP scorefxn)
 
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...
 
bool unbound () const
 
void unbound (bool const u)
 
core::Size jump () const
 
void jump (core::Size const j)
 
bool delta () const
 
void delta (bool const d)
 
bool report_all () const
 
void report_all (bool const ra)
 
void dump_pdb (bool const d)
 
bool dump_pdb () const
 
bool rtmin () const
 
void rtmin (bool const r)
 
void single_substitution (core::pose::Pose &pose, core::Size const resi, core::chemical::AA const target_aa) const
 introduces a single-point subsitution and then performs the repack, rtmin, and relax moves that are requested. More...
 
utility::vector1
< protocols::simple_filters::DeltaFilterOP
delta_filters () const
 
void delta_filters (utility::vector1< protocols::simple_filters::DeltaFilterOP > const &d)
 
std::string dump_pdb_name () const
 
void dump_pdb_name (std::string const &s)
 
bool keep_native () const
 
void keep_native (bool const k)
 
utility::vector1< core::Realdelta_filter_thresholds () const
 
void delta_filter_thresholds (utility::vector1< core::Real > 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 Types

typedef protocols::filters::Filter parent
 

Private Member Functions

void unbind (core::pose::Pose &) const
 

Private Attributes

core::pack::task::TaskFactoryOP task_factory_
 
protocols::filters::FilterOP triage_filter_
 
protocols::filters::FilterOP filter_
 
std::string score_log_file_
 
std::string resfile_name_
 
std::string resfile_general_property_
 
protocols::moves::MoverOP relax_mover_
 
core::scoring::ScoreFunctionOP scorefxn_
 
bool delta_
 
bool unbound_
 
bool report_all_
 
core::Size jump_
 
bool dump_pdb_
 
bool rtmin_
 
utility::vector1
< protocols::simple_filters::DeltaFilterOP
delta_filters_
 
std::string dump_pdb_name_
 
bool keep_native_
 
utility::vector1< core::Realdelta_filter_thresholds_
 

Additional Inherited Members

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

Member Typedef Documentation

Constructor & Destructor Documentation

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

Member Function Documentation

bool protocols::protein_interface_design::filters::FilterScanFilter::apply ( core::pose::Pose const &  pose) const
overridevirtual
std::string protocols::protein_interface_design::filters::FilterScanFilter::class_name ( )
static
protocols::filters::FilterOP protocols::protein_interface_design::filters::FilterScanFilter::clone ( ) const
overridevirtual
bool protocols::protein_interface_design::filters::FilterScanFilter::delta ( ) const

References delta_.

Referenced by apply(), and parse_my_tag().

void protocols::protein_interface_design::filters::FilterScanFilter::delta ( bool const  d)

References delta_.

utility::vector1< core::Real > protocols::protein_interface_design::filters::FilterScanFilter::delta_filter_thresholds ( ) const
void protocols::protein_interface_design::filters::FilterScanFilter::delta_filter_thresholds ( utility::vector1< core::Real > const &  v)
utility::vector1< protocols::simple_filters::DeltaFilterOP > protocols::protein_interface_design::filters::FilterScanFilter::delta_filters ( ) const

References delta_filters_.

void protocols::protein_interface_design::filters::FilterScanFilter::delta_filters ( utility::vector1< protocols::simple_filters::DeltaFilterOP > const &  d)

References delta_filters_.

void protocols::protein_interface_design::filters::FilterScanFilter::dump_pdb ( bool const  d)

References dump_pdb_.

bool protocols::protein_interface_design::filters::FilterScanFilter::dump_pdb ( ) const

References dump_pdb_.

Referenced by apply(), and parse_my_tag().

std::string protocols::protein_interface_design::filters::FilterScanFilter::dump_pdb_name ( ) const
inline

References dump_pdb_name_.

Referenced by apply(), and parse_my_tag().

void protocols::protein_interface_design::filters::FilterScanFilter::dump_pdb_name ( std::string const &  s)
inline

References dump_pdb_name_.

protocols::filters::FilterOP protocols::protein_interface_design::filters::FilterScanFilter::filter ( ) const

References filter_.

Referenced by apply(), filter(), parse_my_tag(), and triage_filter().

void protocols::protein_interface_design::filters::FilterScanFilter::filter ( protocols::filters::FilterOP  filter)

References filter(), and filter_.

protocols::filters::FilterOP protocols::protein_interface_design::filters::FilterScanFilter::fresh_instance ( ) const
overridevirtual
core::Size protocols::protein_interface_design::filters::FilterScanFilter::jump ( ) const

References jump_.

Referenced by parse_my_tag(), and unbind().

void protocols::protein_interface_design::filters::FilterScanFilter::jump ( core::Size const  j)

References jump_.

bool protocols::protein_interface_design::filters::FilterScanFilter::keep_native ( ) const
inline

References keep_native_.

Referenced by apply(), and parse_my_tag().

void protocols::protein_interface_design::filters::FilterScanFilter::keep_native ( bool const  k)
inline

References keep_native_.

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

Reimplemented from protocols::filters::Filter.

References class_name().

void protocols::protein_interface_design::filters::FilterScanFilter::parse_my_tag ( utility::tag::TagCOP  ,
basic::datacache::DataMap &   
)
overridevirtual
void protocols::protein_interface_design::filters::FilterScanFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::protein_interface_design::filters::FilterScanFilter::relax_mover ( protocols::moves::MoverOP  mover)

References relax_mover_.

protocols::moves::MoverOP protocols::protein_interface_design::filters::FilterScanFilter::relax_mover ( ) const

References relax_mover_.

Referenced by parse_my_tag(), and single_substitution().

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

Reimplemented from protocols::filters::Filter.

bool protocols::protein_interface_design::filters::FilterScanFilter::report_all ( ) const

References report_all_.

Referenced by parse_my_tag().

void protocols::protein_interface_design::filters::FilterScanFilter::report_all ( bool const  ra)

References report_all_.

core::Real protocols::protein_interface_design::filters::FilterScanFilter::report_sm ( core::pose::Pose const &  ) const
overridevirtual

used to report filter internals through a score or silent file

Reimplemented from protocols::filters::Filter.

std::string protocols::protein_interface_design::filters::FilterScanFilter::resfile_general_property ( ) const
void protocols::protein_interface_design::filters::FilterScanFilter::resfile_general_property ( std::string const &  resfile_general_property)
void protocols::protein_interface_design::filters::FilterScanFilter::resfile_name ( std::string const &  resfile_name)

References resfile_name(), and resfile_name_.

std::string protocols::protein_interface_design::filters::FilterScanFilter::resfile_name ( ) const
bool protocols::protein_interface_design::filters::FilterScanFilter::rtmin ( ) const
inline

References rtmin_.

Referenced by parse_my_tag(), and single_substitution().

void protocols::protein_interface_design::filters::FilterScanFilter::rtmin ( bool const  r)
inline

References rtmin_.

void protocols::protein_interface_design::filters::FilterScanFilter::score_log_file ( std::string const &  score_log_file)
std::string protocols::protein_interface_design::filters::FilterScanFilter::score_log_file ( ) const

References score_log_file_.

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

core::scoring::ScoreFunctionOP protocols::protein_interface_design::filters::FilterScanFilter::scorefxn ( ) const
void protocols::protein_interface_design::filters::FilterScanFilter::scorefxn ( core::scoring::ScoreFunctionOP  scorefxn)

References scorefxn(), and scorefxn_.

void protocols::protein_interface_design::filters::FilterScanFilter::single_substitution ( core::pose::Pose pose,
core::Size const  resi,
core::chemical::AA const  target_aa 
) const
core::pack::task::TaskFactoryOP protocols::protein_interface_design::filters::FilterScanFilter::task_factory ( ) const

Undefined, commenting out to fix PyRosetta build core::Real compute( core::pose::Pose const & pose ) const;.

References task_factory_.

Referenced by apply(), parse_my_tag(), single_substitution(), and task_factory().

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

References task_factory(), and task_factory_.

protocols::filters::FilterOP protocols::protein_interface_design::filters::FilterScanFilter::triage_filter ( ) const

References triage_filter_.

Referenced by apply(), and parse_my_tag().

void protocols::protein_interface_design::filters::FilterScanFilter::triage_filter ( protocols::filters::FilterOP  filter)

References filter(), and triage_filter_.

void protocols::protein_interface_design::filters::FilterScanFilter::unbind ( core::pose::Pose pose) const
private
bool protocols::protein_interface_design::filters::FilterScanFilter::unbound ( ) const

References unbound_.

Referenced by parse_my_tag(), and unbind().

void protocols::protein_interface_design::filters::FilterScanFilter::unbound ( bool const  u)

Member Data Documentation

bool protocols::protein_interface_design::filters::FilterScanFilter::delta_
private

Referenced by delta().

utility::vector1< core::Real > protocols::protein_interface_design::filters::FilterScanFilter::delta_filter_thresholds_
private
utility::vector1< protocols::simple_filters::DeltaFilterOP > protocols::protein_interface_design::filters::FilterScanFilter::delta_filters_
private
bool protocols::protein_interface_design::filters::FilterScanFilter::dump_pdb_
private

Referenced by dump_pdb().

std::string protocols::protein_interface_design::filters::FilterScanFilter::dump_pdb_name_
private

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

protocols::filters::FilterOP protocols::protein_interface_design::filters::FilterScanFilter::filter_
private

Referenced by filter().

core::Size protocols::protein_interface_design::filters::FilterScanFilter::jump_
private

Referenced by jump().

bool protocols::protein_interface_design::filters::FilterScanFilter::keep_native_
private

Referenced by keep_native().

protocols::moves::MoverOP protocols::protein_interface_design::filters::FilterScanFilter::relax_mover_
private

Referenced by relax_mover().

bool protocols::protein_interface_design::filters::FilterScanFilter::report_all_
private

Referenced by apply(), and report_all().

std::string protocols::protein_interface_design::filters::FilterScanFilter::resfile_general_property_
private
std::string protocols::protein_interface_design::filters::FilterScanFilter::resfile_name_
private

Referenced by resfile_name().

bool protocols::protein_interface_design::filters::FilterScanFilter::rtmin_
private

Referenced by rtmin().

std::string protocols::protein_interface_design::filters::FilterScanFilter::score_log_file_
private

Referenced by score_log_file().

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

Referenced by scorefxn().

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

Referenced by task_factory().

protocols::filters::FilterOP protocols::protein_interface_design::filters::FilterScanFilter::triage_filter_
private

Referenced by triage_filter().

bool protocols::protein_interface_design::filters::FilterScanFilter::unbound_
private

Referenced by unbound().


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