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protocols::simple_filters::SSMotifFinder Class Reference

#include <SSMotifFinderFilter.hh>

Inheritance diagram for protocols::simple_filters::SSMotifFinder:
Inheritance graph
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Public Member Functions

 SSMotifFinder ()
 
 ~SSMotifFinder () override
 
filters::FilterOP clone () const override
 
filters::FilterOP fresh_instance () const override
 
bool apply (core::pose::Pose const &pose) 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 &) override
 Called by FilterFactory when constructing new Filter. Takes care of the specific mover's parsing. More...
 
core::Size from_res () const
 
void from_res (core::Size const r)
 
core::Size to_res () const
 
void to_res (core::Size const r)
 
core::Size template_stem1 () const
 
void template_stem1 (core::Size const r)
 
core::Size template_stem2 () const
 
void template_stem2 (core::Size const r)
 
core::Real rmsd () const
 
void rmsd (core::Real const c)
 
core::kinematics::Jump jump () const
 
core::kinematics::Jump compute_jump (core::pose::Pose const &pose, core::Size const start, core::Size const end) const
 
std::string filename () const
 
void filename (std::string const s)
 
std::string pdbname () const
 
void pdbname (std::string const s)
 
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 Member Functions

void superimpose_pose_on_template (core::pose::Pose const &, core::pose::Pose &, core::Size const, core::Size const ) const
 

Private Attributes

core::Size from_res_
 
core::Size to_res_
 
core::pose::PoseOP template_pose_
 
core::Size template_stem1_
 
core::Size template_stem2_
 
core::kinematics::Jump jump_
 
core::Real rmsd_
 
std::string filename_
 
std::string pdbname_
 

Additional Inherited Members

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

Constructor & Destructor Documentation

protocols::simple_filters::SSMotifFinder::SSMotifFinder ( )
protocols::simple_filters::SSMotifFinder::~SSMotifFinder ( )
overridedefault

Member Function Documentation

bool protocols::simple_filters::SSMotifFinder::apply ( core::pose::Pose const &  pose) const
overridevirtual
std::string protocols::simple_filters::SSMotifFinder::class_name ( )
static
filters::FilterOP protocols::simple_filters::SSMotifFinder::clone ( ) const
inlineoverridevirtual
core::kinematics::Jump protocols::simple_filters::SSMotifFinder::compute_jump ( core::pose::Pose const &  pose,
core::Size const  start,
core::Size const  end 
) const
std::string protocols::simple_filters::SSMotifFinder::filename ( ) const
inline

References filename_.

Referenced by parse_my_tag().

void protocols::simple_filters::SSMotifFinder::filename ( std::string const  s)
inline

References filename_.

filters::FilterOP protocols::simple_filters::SSMotifFinder::fresh_instance ( ) const
inlineoverridevirtual
core::Size protocols::simple_filters::SSMotifFinder::from_res ( ) const
inline

References from_res_.

Referenced by apply(), and parse_my_tag().

void protocols::simple_filters::SSMotifFinder::from_res ( core::Size const  r)
inline

References from_res_.

core::kinematics::Jump protocols::simple_filters::SSMotifFinder::jump ( ) const

References jump_.

std::string protocols::simple_filters::SSMotifFinder::name ( ) const
overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

void protocols::simple_filters::SSMotifFinder::parse_my_tag ( utility::tag::TagCOP  ,
basic::datacache::DataMap &   
)
overridevirtual
std::string protocols::simple_filters::SSMotifFinder::pdbname ( ) const
inline

References pdbname_.

Referenced by parse_my_tag().

void protocols::simple_filters::SSMotifFinder::pdbname ( std::string const  s)
inline

References pdbname_.

void protocols::simple_filters::SSMotifFinder::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::simple_filters::SSMotifFinder::report ( std::ostream &  out,
core::pose::Pose const &  pose 
) const
overridevirtual

Reimplemented from protocols::filters::Filter.

core::Real protocols::simple_filters::SSMotifFinder::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::Real protocols::simple_filters::SSMotifFinder::rmsd ( ) const
inline

References rmsd_.

Referenced by apply(), and parse_my_tag().

void protocols::simple_filters::SSMotifFinder::rmsd ( core::Real const  c)
inline

References core::pack::dunbrack::c, and rmsd_.

void protocols::simple_filters::SSMotifFinder::superimpose_pose_on_template ( core::pose::Pose const &  template_pose,
core::pose::Pose copy_pose,
core::Size const  pose_stem1,
core::Size const  pose_stem2 
) const
private
core::Size protocols::simple_filters::SSMotifFinder::template_stem1 ( ) const
inline
void protocols::simple_filters::SSMotifFinder::template_stem1 ( core::Size const  r)
inline

References template_stem1_.

core::Size protocols::simple_filters::SSMotifFinder::template_stem2 ( ) const
inline
void protocols::simple_filters::SSMotifFinder::template_stem2 ( core::Size const  r)
inline

References template_stem2_.

core::Size protocols::simple_filters::SSMotifFinder::to_res ( ) const
inline

References to_res_.

Referenced by apply(), and parse_my_tag().

void protocols::simple_filters::SSMotifFinder::to_res ( core::Size const  r)
inline

References to_res_.

Member Data Documentation

std::string protocols::simple_filters::SSMotifFinder::filename_
private

Referenced by apply(), and filename().

core::Size protocols::simple_filters::SSMotifFinder::from_res_
private

Referenced by from_res().

core::kinematics::Jump protocols::simple_filters::SSMotifFinder::jump_
private

Referenced by jump(), and parse_my_tag().

std::string protocols::simple_filters::SSMotifFinder::pdbname_
private

Referenced by apply(), and pdbname().

core::Real protocols::simple_filters::SSMotifFinder::rmsd_
private

Referenced by rmsd().

core::pose::PoseOP protocols::simple_filters::SSMotifFinder::template_pose_
private

Referenced by apply(), and parse_my_tag().

core::Size protocols::simple_filters::SSMotifFinder::template_stem1_
private

Referenced by template_stem1().

core::Size protocols::simple_filters::SSMotifFinder::template_stem2_
private

Referenced by template_stem2().

core::Size protocols::simple_filters::SSMotifFinder::to_res_
private

Referenced by to_res().


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