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protocols::noesy_assign::CrossPeakList Class Reference

#include <CrossPeakList.hh>

Inheritance diagram for protocols::noesy_assign::CrossPeakList:
Inheritance graph
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Public Types

typedef std::list< CrossPeakOPCrossPeaks
 
typedef CrossPeaks::const_iterator const_iterator
 
typedef CrossPeaks::iterator iterator
 

Public Member Functions

 CrossPeakList ()
 
 ~CrossPeakList () override
 
void read_from_stream (std::istream &, PeakFileFormat &input_adaptor, ResonanceListOP resonances)
 
void write_to_stream (std::ostream &, PeakFileFormat &output_adaptor) const
 
void write_peak_files (std::string const &prefix, PeakFileFormat &output_adaptor) const
 
void find_assignments ()
 
void update_chemshiftscore ()
 
void update_symmetry_score ()
 
void update_upperdistance_score ()
 
template<class DecoyIterator >
void update_decoy_compatibility_score (DecoyIterator const &begin, DecoyIterator const &end)
 
void eliminate_spurious_peaks ()
 
template<class DecoyIterator >
void calibrate (DecoyIterator const &begin, DecoyIterator const &end)
 
void generate_fa_and_cen_constraints (core::scoring::constraints::ConstraintSetOP fa_set, core::scoring::constraints::ConstraintSetOP cen_set, core::pose::Pose const &pose, core::pose::Pose const &centroid_pose, core::Size min_seq_separation, core::Size min_quali, core::Size max_quali, core::Real padding=0.0, bool ignore_elimination_candidates=true, bool elimination_candidates=false) const
 
PeakAssignmentResidueMap const & assignments () const
 
PeakAssignmentResidueMapassignments ()
 
core::Size count_assignments () const
 
void delete_diagonal_peaks ()
 
void update_peak_volumina ()
 
void network_analysis ()
 
void set_trivial_decoy_compatibility_score ()
 
CrossPeaks const & peaks () const
 
const_iterator begin () const
 
const_iterator end () const
 
iterator begin ()
 
iterator end ()
 
core::Size size () const
 

Private Member Functions

void update_assignment_list ()
 
core::Real calibrate (PeakCalibrator const &calibrator)
 return average upper distance bound More...
 

Private Attributes

CrossPeaks peaks_
 
PeakAssignmentResidueMapOP assignments_
 

Member Typedef Documentation

typedef CrossPeaks::const_iterator protocols::noesy_assign::CrossPeakList::const_iterator

Constructor & Destructor Documentation

protocols::noesy_assign::CrossPeakList::CrossPeakList ( )
protocols::noesy_assign::CrossPeakList::~CrossPeakList ( )
overridedefault

Member Function Documentation

PeakAssignmentResidueMap const& protocols::noesy_assign::CrossPeakList::assignments ( ) const
inline

References assignments_.

Referenced by update_symmetry_score().

PeakAssignmentResidueMap& protocols::noesy_assign::CrossPeakList::assignments ( )
inline

References assignments_.

const_iterator protocols::noesy_assign::CrossPeakList::begin ( ) const
inline
iterator protocols::noesy_assign::CrossPeakList::begin ( )
inline

References peaks_.

template<class DecoyIterator >
void protocols::noesy_assign::CrossPeakList::calibrate ( DecoyIterator const &  begin,
DecoyIterator const &  end 
)
Real protocols::noesy_assign::CrossPeakList::calibrate ( PeakCalibrator const &  calibrator)
private

return average upper distance bound

References begin(), and end().

Size protocols::noesy_assign::CrossPeakList::count_assignments ( ) const

Referenced by network_analysis().

void protocols::noesy_assign::CrossPeakList::delete_diagonal_peaks ( )
void protocols::noesy_assign::CrossPeakList::eliminate_spurious_peaks ( )

References begin(), and end().

const_iterator protocols::noesy_assign::CrossPeakList::end ( ) const
inline
iterator protocols::noesy_assign::CrossPeakList::end ( )
inline

References peaks_.

void protocols::noesy_assign::CrossPeakList::find_assignments ( )
void protocols::noesy_assign::CrossPeakList::generate_fa_and_cen_constraints ( core::scoring::constraints::ConstraintSetOP  fa_set,
core::scoring::constraints::ConstraintSetOP  cen_set,
core::pose::Pose const &  pose,
core::pose::Pose const &  centroid_pose,
core::Size  min_seq_separation,
core::Size  min_quali,
core::Size  max_quali,
core::Real  padding = 0.0,
bool  ignore_elimination_candidates = true,
bool  elimination_candidates = false 
) const
void protocols::noesy_assign::CrossPeakList::network_analysis ( )
CrossPeaks const& protocols::noesy_assign::CrossPeakList::peaks ( ) const
inline
void protocols::noesy_assign::CrossPeakList::read_from_stream ( std::istream &  is,
PeakFileFormat input_adaptor,
ResonanceListOP  resonances 
)
void protocols::noesy_assign::CrossPeakList::set_trivial_decoy_compatibility_score ( )
core::Size protocols::noesy_assign::CrossPeakList::size ( ) const
inline

References peaks_.

void protocols::noesy_assign::CrossPeakList::update_assignment_list ( )
private
void protocols::noesy_assign::CrossPeakList::update_chemshiftscore ( )
template<class DecoyIterator >
void protocols::noesy_assign::CrossPeakList::update_decoy_compatibility_score ( DecoyIterator const &  begin,
DecoyIterator const &  end 
)
void protocols::noesy_assign::CrossPeakList::update_peak_volumina ( )
void protocols::noesy_assign::CrossPeakList::update_symmetry_score ( )
void protocols::noesy_assign::CrossPeakList::update_upperdistance_score ( )
void protocols::noesy_assign::CrossPeakList::write_peak_files ( std::string const &  prefix,
PeakFileFormat output_adaptor 
) const
void protocols::noesy_assign::CrossPeakList::write_to_stream ( std::ostream &  os,
PeakFileFormat output_adaptor 
) const

Member Data Documentation

PeakAssignmentResidueMapOP protocols::noesy_assign::CrossPeakList::assignments_
private
CrossPeaks protocols::noesy_assign::CrossPeakList::peaks_
private

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