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protocols::evolution::AlignmentAAFinder Class Reference

test whether a pose contains a comment that evaluates to a predefined value. This is useful in controlling execution flow in RosettaScripts. More...

#include <AlignmentAAFinderFilter.hh>

Inheritance diagram for protocols::evolution::AlignmentAAFinder:
Inheritance graph
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Public Member Functions

 AlignmentAAFinder ()
 
 ~AlignmentAAFinder () override
 
filters::FilterOP clone () const override
 
filters::FilterOP fresh_instance () const override
 
bool apply (core::pose::Pose const &p) const override
 Returns true if the given pose passes the filter, false otherwise. 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...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
 Called by FilterFactory when constructing new Filter. Takes care of the specific mover's parsing. More...
 
core::Real exclude_AA_threshold () const
 
void exclude_AA_threshold (core::Real const &t)
 
std::string alignment_file () const
 
void alignment_file (std::string const &a)
 
std::string available_AAs_file () const
 
void available_AAs_file (std::string const &a)
 
core::Size indel_motif_radius () const
 
void indel_motif_radius (core::Size const &r)
 
core::Real loop_seqid_threshold () const
 
void loop_seqid_threshold (core::Real const &t)
 
core::scoring::ScoreFunctionOP scorefxn () const
 
void scorefxn (core::scoring::ScoreFunctionOP scorefxn)
 
protocols::moves::MoverOP relax_mover () const
 
void relax_mover (protocols::moves::MoverOP mover)
 
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::Real exclude_AA_threshold_
 
std::string alignment_file_
 
std::string available_AAs_file_
 
core::Size indel_motif_radius_
 
core::Real loop_seqid_threshold_
 
core::scoring::ScoreFunctionOP scorefxn_
 
protocols::moves::MoverOP relax_mover_
 

Additional Inherited Members

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

Detailed Description

test whether a pose contains a comment that evaluates to a predefined value. This is useful in controlling execution flow in RosettaScripts.

Constructor & Destructor Documentation

protocols::evolution::AlignmentAAFinder::AlignmentAAFinder ( )
protocols::evolution::AlignmentAAFinder::~AlignmentAAFinder ( )
overridedefault

Member Function Documentation

std::string protocols::evolution::AlignmentAAFinder::alignment_file ( ) const
inline

References alignment_file_.

Referenced by apply(), and parse_my_tag().

void protocols::evolution::AlignmentAAFinder::alignment_file ( std::string const &  a)
inline
bool protocols::evolution::AlignmentAAFinder::apply ( core::pose::Pose const &  pose) const
overridevirtual
std::string protocols::evolution::AlignmentAAFinder::available_AAs_file ( ) const
inline

References available_AAs_file_.

Referenced by apply(), and parse_my_tag().

void protocols::evolution::AlignmentAAFinder::available_AAs_file ( std::string const &  a)
inline
std::string protocols::evolution::AlignmentAAFinder::class_name ( )
static
filters::FilterOP protocols::evolution::AlignmentAAFinder::clone ( ) const
inlineoverridevirtual
core::Real protocols::evolution::AlignmentAAFinder::exclude_AA_threshold ( ) const
inline

References exclude_AA_threshold_.

Referenced by apply(), and parse_my_tag().

void protocols::evolution::AlignmentAAFinder::exclude_AA_threshold ( core::Real const &  t)
inline
filters::FilterOP protocols::evolution::AlignmentAAFinder::fresh_instance ( ) const
inlineoverridevirtual
core::Size protocols::evolution::AlignmentAAFinder::indel_motif_radius ( ) const
inline

References indel_motif_radius_.

Referenced by apply(), and parse_my_tag().

void protocols::evolution::AlignmentAAFinder::indel_motif_radius ( core::Size const &  r)
inline

References indel_motif_radius_.

core::Real protocols::evolution::AlignmentAAFinder::loop_seqid_threshold ( ) const
inline

References loop_seqid_threshold_.

Referenced by apply(), and parse_my_tag().

void protocols::evolution::AlignmentAAFinder::loop_seqid_threshold ( core::Real const &  t)
inline
std::string protocols::evolution::AlignmentAAFinder::name ( ) const
overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

void protocols::evolution::AlignmentAAFinder::parse_my_tag ( utility::tag::TagCOP  ,
basic::datacache::DataMap &   
)
overridevirtual

Called by FilterFactory when constructing new Filter. Takes care of the specific mover's parsing.

Reimplemented from protocols::filters::Filter.

References alignment_file(), available_AAs_file(), exclude_AA_threshold(), indel_motif_radius(), loop_seqid_threshold(), protocols::rosetta_scripts::parse_mover(), core::scoring::parse_score_function(), relax_mover(), and scorefxn().

void protocols::evolution::AlignmentAAFinder::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
protocols::moves::MoverOP protocols::evolution::AlignmentAAFinder::relax_mover ( ) const
inline

References relax_mover_.

Referenced by parse_my_tag().

void protocols::evolution::AlignmentAAFinder::relax_mover ( protocols::moves::MoverOP  mover)
inline

References relax_mover_.

void protocols::evolution::AlignmentAAFinder::report ( std::ostream &  out,
core::pose::Pose const &  pose 
) const
overridevirtual

Reimplemented from protocols::filters::Filter.

core::Real protocols::evolution::AlignmentAAFinder::report_sm ( core::pose::Pose const &  ) const
overridevirtual

used to report filter internals through a score or silent file

Reimplemented from protocols::filters::Filter.

core::scoring::ScoreFunctionOP protocols::evolution::AlignmentAAFinder::scorefxn ( ) const
inline

References scorefxn_.

Referenced by apply(), and parse_my_tag().

void protocols::evolution::AlignmentAAFinder::scorefxn ( core::scoring::ScoreFunctionOP  scorefxn)
inline

References scorefxn(), and scorefxn_.

Referenced by scorefxn().

Member Data Documentation

std::string protocols::evolution::AlignmentAAFinder::alignment_file_
private

Referenced by alignment_file().

std::string protocols::evolution::AlignmentAAFinder::available_AAs_file_
private

Referenced by available_AAs_file().

core::Real protocols::evolution::AlignmentAAFinder::exclude_AA_threshold_
private

Referenced by exclude_AA_threshold().

core::Size protocols::evolution::AlignmentAAFinder::indel_motif_radius_
private

Referenced by indel_motif_radius().

core::Real protocols::evolution::AlignmentAAFinder::loop_seqid_threshold_
private

Referenced by loop_seqid_threshold().

protocols::moves::MoverOP protocols::evolution::AlignmentAAFinder::relax_mover_
private

Referenced by relax_mover().

core::scoring::ScoreFunctionOP protocols::evolution::AlignmentAAFinder::scorefxn_
private

Referenced by scorefxn().


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