Rosetta Protocols  2014.35
Public Types | Public Member Functions | Private Attributes | List of all members
protocols::fldsgn::filters::SecondaryStructureFilter Class Reference

#include <SecondaryStructureFilter.hh>

Public Types

typedef protocols::filters::Filter Super
 
typedef protocols::filters::Filter Filter
 
typedef std::string String
 
typedef
protocols::filters::FilterOP 
FilterOP
 
typedef core::pose::Pose Pose
 
typedef utility::tag::TagCOP TagCOP
 
typedef
protocols::filters::Filters_map 
Filters_map
 
typedef basic::datacache::DataMap DataMap
 
typedef
protocols::moves::Movers_map 
Movers_map
 

Public Member Functions

 SecondaryStructureFilter ()
 
 SecondaryStructureFilter (String const &ss)
 
 SecondaryStructureFilter (SecondaryStructureFilter const &rval)
 
virtual ~SecondaryStructureFilter ()
 
virtual FilterOP clone () const
 
virtual FilterOP fresh_instance () const
 
void filtered_ss (String const &s)
 
void filtered_abego (String const &s)
 
virtual std::string name () const
 
void set_blueprint (std::string const blueprint_file)
 sets the blueprint file based on filename. If a strand pairing is impossible (i.e. the structure has two strands, 5 and 6 residues, respectively, it sets the unpaired residues to 'h' so that they still match. More...
 
virtual void parse_my_tag (TagCOP tag, basic::datacache::DataMap &, Filters_map const &, Movers_map const &, Pose const &)
 parse xml More...
 
virtual bool apply (Pose const &pose) const
 Returns true if the given pose passes the filter, false otherwise. More...
 
virtual core::Real report_sm (Pose const &pose) const
 used to report filter internals through a score or silent file More...
 
virtual core::Size compute (Pose const &pose) const
 
- Public Member Functions inherited from protocols::filters::Filter
 Filter ()
 
 Filter (std::string const &)
 
 Filter (Filter const &)
 
virtual ~Filter ()
 
virtual void report (std::ostream &, core::pose::Pose const &) const
 
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 void apply (core::io::serialization::PipeMap &pmap)
 
virtual void score (core::io::serialization::PipeMap &pmap)
 
virtual core::Real score (core::pose::Pose &pose)
 
virtual void parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks)
 

Private Attributes

String filtered_ss_
 
utility::vector1< Stringfiltered_abego_
 
bool use_abego_
 

Additional Inherited Members

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

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::fldsgn::filters::SecondaryStructureFilter::SecondaryStructureFilter ( )

Referenced by clone(), and fresh_instance().

protocols::fldsgn::filters::SecondaryStructureFilter::SecondaryStructureFilter ( String const &  ss)
protocols::fldsgn::filters::SecondaryStructureFilter::SecondaryStructureFilter ( SecondaryStructureFilter const &  rval)
virtual protocols::fldsgn::filters::SecondaryStructureFilter::~SecondaryStructureFilter ( )
inlinevirtual

Member Function Documentation

bool protocols::fldsgn::filters::SecondaryStructureFilter::apply ( Pose const &  pose) const
virtual
virtual FilterOP protocols::fldsgn::filters::SecondaryStructureFilter::clone ( ) const
inlinevirtual
core::Size protocols::fldsgn::filters::SecondaryStructureFilter::compute ( Pose const &  pose) const
virtual

returns the number of residues in the protein that have matching secondary structure WARNING: ignores abegos for now, since abegomanager only returns a bool The filter score will report only secondary structures, but if you specify abego, the 'apply' function will return false if abegos don't match

References abego, core::util::ABEGOManager::check_rama(), filtered_abego_, filtered_ss_, core::util::ABEGOManager::get_abego_string(), core::conformation::Residue::is_protein(), core::pose::Pose::omega(), core::pose::Pose::phi(), core::pose::Pose::psi(), core::pose::Pose::residue(), sec(), core::pose::Pose::secstruct(), core::pose::Pose::total_residue(), tr, and use_abego_.

Referenced by apply(), and report_sm().

void protocols::fldsgn::filters::SecondaryStructureFilter::filtered_abego ( String const &  s)

References filtered_abego_, and use_abego_.

void protocols::fldsgn::filters::SecondaryStructureFilter::filtered_ss ( String const &  s)

References filtered_ss_.

virtual FilterOP protocols::fldsgn::filters::SecondaryStructureFilter::fresh_instance ( ) const
inlinevirtual
virtual std::string protocols::fldsgn::filters::SecondaryStructureFilter::name ( ) const
inlinevirtual

Reimplemented from protocols::filters::Filter.

void protocols::fldsgn::filters::SecondaryStructureFilter::parse_my_tag ( TagCOP  tag,
basic::datacache::DataMap ,
Filters_map const &  ,
Movers_map const &  ,
Pose const &   
)
virtual
core::Real protocols::fldsgn::filters::SecondaryStructureFilter::report_sm ( Pose const &  ) const
virtual

used to report filter internals through a score or silent file

Reimplemented from protocols::filters::Filter.

References compute().

void protocols::fldsgn::filters::SecondaryStructureFilter::set_blueprint ( std::string const  blueprint_file)

sets the blueprint file based on filename. If a strand pairing is impossible (i.e. the structure has two strands, 5 and 6 residues, respectively, it sets the unpaired residues to 'h' so that they still match.

References filtered_abego_, filtered_ss_, runtime_assert, s1, s2, ss, protocols::loops::loop_closure::ccd::strand, and tr.

Referenced by parse_my_tag().

Member Data Documentation

utility::vector1< String > protocols::fldsgn::filters::SecondaryStructureFilter::filtered_abego_
private
String protocols::fldsgn::filters::SecondaryStructureFilter::filtered_ss_
private
bool protocols::fldsgn::filters::SecondaryStructureFilter::use_abego_
private

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