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protocols::noesy_assign::CrossPeakList Class Reference

#include <CrossPeakList.hh>

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

typedef std::list< CrossPeakOP > CrossPeaks
 
typedef CrossPeaks::const_iterator const_iterator
 
typedef CrossPeaks::iterator iterator
 

Public Member Functions

 CrossPeakList ()
 
virtual ~CrossPeakList ()
 
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
 
PeakAssignmentResidueMap & assignments ()
 
core::Size count_assignments () const
 
void delete_diagonal_peaks ()
 
void update_peak_volumina ()
 
void network_analysis (ResonanceList const &)
 
void set_trivial_decoy_compatibility_score ()
 
CrossPeaks const & peaks () const
 
const_iterator begin () const
 
const_iterator end () const
 
iterator begin ()
 
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_
 

Detailed Description

Definition at line 58 of file CrossPeakList.hh.

Member Typedef Documentation

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

Definition at line 61 of file CrossPeakList.hh.

typedef std::list< CrossPeakOP > protocols::noesy_assign::CrossPeakList::CrossPeaks

Definition at line 60 of file CrossPeakList.hh.

typedef CrossPeaks::iterator protocols::noesy_assign::CrossPeakList::iterator

Definition at line 62 of file CrossPeakList.hh.

Constructor & Destructor Documentation

protocols::noesy_assign::CrossPeakList::CrossPeakList ( )

Definition at line 75 of file CrossPeakList.cc.

protocols::noesy_assign::CrossPeakList::~CrossPeakList ( )
virtual

Definition at line 79 of file CrossPeakList.cc.

Member Function Documentation

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

Definition at line 100 of file CrossPeakList.hh.

References assignments_.

Referenced by update_symmetry_score().

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

Definition at line 104 of file CrossPeakList.hh.

References assignments_.

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

Definition at line 118 of file CrossPeakList.hh.

References peaks_.

Referenced by protocols::noesy_assign::DistanceScoreMover::apply(), calibrate(), count_assignments(), delete_diagonal_peaks(), protocols::noesy_assign::DistanceScoreMover::DistanceScoreMover(), eliminate_spurious_peaks(), protocols::noesy_assign::DistanceScoreMover::finalize_scoring(), generate_fa_and_cen_constraints(), protocols::noesy_assign::PeakCalibratorMap::PeakCalibratorMap(), protocols::noesy_assign::DistanceScoreMover::prepare_scoring(), set_trivial_decoy_compatibility_score(), update_assignment_list(), update_chemshiftscore(), update_peak_volumina(), and update_upperdistance_score().

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

Definition at line 120 of file CrossPeakList.hh.

References peaks_.

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

Definition at line 102 of file CrossPeakList.impl.hh.

References protocols::noesy_assign::PeakAssignmentParameters::calibration_cycles_, protocols::noesy_assign::PeakAssignmentParameters::calibration_eliminate_, protocols::noesy_assign::PeakAssignmentParameters::calibration_target_, protocols::noesy_assign::PeakAssignmentParameters::dcalibrate_, protocols::noesy_assign::PeakCalibratorMap::do_calibration(), protocols::noesy_assign::PeakCalibratorMap::eliminate_violated_constraints(), end(), protocols::noesy_assign::PeakAssignmentParameters::get_instance(), protocols::jumping::JumpSample::remove_chainbreaks(), protocols::noesy_assign::PeakCalibratorMap::set_target_and_tolerance(), and core::chemical::tr().

Real protocols::noesy_assign::CrossPeakList::calibrate ( PeakCalibrator const &  calibrator)
private

return average upper distance bound

Definition at line 279 of file CrossPeakList.cc.

References begin(), and end().

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

Definition at line 81 of file CrossPeakList.cc.

References begin(), and end().

Referenced by network_analysis().

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

Definition at line 89 of file CrossPeakList.cc.

References assignments_, begin(), end(), peaks_, and tr().

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

Definition at line 273 of file CrossPeakList.cc.

References begin(), and end().

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

Definition at line 119 of file CrossPeakList.hh.

References peaks_.

Referenced by protocols::noesy_assign::DistanceScoreMover::apply(), calibrate(), count_assignments(), delete_diagonal_peaks(), protocols::noesy_assign::DistanceScoreMover::DistanceScoreMover(), eliminate_spurious_peaks(), protocols::noesy_assign::DistanceScoreMover::finalize_scoring(), generate_fa_and_cen_constraints(), protocols::noesy_assign::PeakCalibratorMap::PeakCalibratorMap(), protocols::noesy_assign::DistanceScoreMover::prepare_scoring(), set_trivial_decoy_compatibility_score(), update_assignment_list(), update_chemshiftscore(), update_peak_volumina(), and update_upperdistance_score().

void protocols::noesy_assign::CrossPeakList::find_assignments ( )

Definition at line 184 of file CrossPeakList.cc.

References assignments_, peaks_, and tr().

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

Definition at line 292 of file CrossPeakList.cc.

References core::id::EXCN_AtomNotFound::atom(), begin(), end(), protocols::noesy_assign::CrossPeak::MAX_CLASS, core::pose::Pose::residue_type(), core::id::NamedAtomID::rsd(), and tr().

void protocols::noesy_assign::CrossPeakList::network_analysis ( ResonanceList const &  resonances)

Definition at line 258 of file CrossPeakList.cc.

References assignments_, count_assignments(), protocols::noesy_assign::PeakAssignmentParameters::get_instance(), protocols::noesy_assign::PeakAssignmentParameters::network_mode_, tr(), and update_assignment_list().

CrossPeaks const& protocols::noesy_assign::CrossPeakList::peaks ( ) const
inline

Definition at line 117 of file CrossPeakList.hh.

References peaks_.

Referenced by protocols::noesy_assign::PeakAssignmentResidueMap::add(), protocols::noesy_assign::PeakAssignmentResidueMap::check_for_symmetric_peaks(), and update_assignment_list().

void protocols::noesy_assign::CrossPeakList::read_from_stream ( std::istream &  is,
PeakFileFormat &  input_adaptor,
ResonanceListOP  resonances 
)

Definition at line 110 of file CrossPeakList.cc.

References protocols::noesy_assign::PeakFileFormat_Base::ignore_negative_intensity(), protocols::noesy_assign::PeakFileFormat::output_diagnosis(), peaks_, protocols::noesy_assign::PeakFileFormat::read_header(), protocols::noesy_assign::PeakFileFormat::read_peak(), tr(), and protocols::noesy_assign::PeakFileFormat::write_peak().

void protocols::noesy_assign::CrossPeakList::set_trivial_decoy_compatibility_score ( )

Definition at line 238 of file CrossPeakList.cc.

References begin(), end(), and tr().

core::Size protocols::noesy_assign::CrossPeakList::size ( ) const
inline

Definition at line 121 of file CrossPeakList.hh.

References peaks_.

void protocols::noesy_assign::CrossPeakList::update_assignment_list ( )
private

Definition at line 193 of file CrossPeakList.cc.

References assignments_, begin(), end(), protocols::noesy_assign::PeakAssignmentParameters::get_instance(), protocols::noesy_assign::PeakAssignmentParameters::network_use_all_covalent_atoms_, and peaks().

Referenced by network_analysis(), and update_symmetry_score().

void protocols::noesy_assign::CrossPeakList::update_chemshiftscore ( )

Definition at line 218 of file CrossPeakList.cc.

References begin(), end(), and tr().

template<class DecoyIterator >
void protocols::noesy_assign::CrossPeakList::update_decoy_compatibility_score ( DecoyIterator const &  begin,
DecoyIterator const &  end 
)

Definition at line 62 of file CrossPeakList.impl.hh.

References protocols::noesy_assign::PeakAssignmentParameters::dcut_, core::pose::Pose::fold_tree(), protocols::noesy_assign::PeakAssignmentParameters::get_instance(), protocols::jumping::JumpSample::remove_chainbreaks(), and core::chemical::tr().

void protocols::noesy_assign::CrossPeakList::update_peak_volumina ( )

Definition at line 205 of file CrossPeakList.cc.

References begin(), end(), and tr().

void protocols::noesy_assign::CrossPeakList::update_symmetry_score ( )

Definition at line 249 of file CrossPeakList.cc.

References assignments(), assignments_, protocols::noesy_assign::PeakAssignmentResidueMap::check_for_symmetric_peaks(), protocols::noesy_assign::PeakAssignmentParameters::get_instance(), protocols::noesy_assign::PeakAssignmentParameters::min_contribution_symmetric_peaks_, tr(), and update_assignment_list().

void protocols::noesy_assign::CrossPeakList::update_upperdistance_score ( )

Definition at line 227 of file CrossPeakList.cc.

References begin(), end(), and tr().

void protocols::noesy_assign::CrossPeakList::write_peak_files ( std::string const &  prefix,
PeakFileFormat &  output_adaptor 
) const

Definition at line 161 of file CrossPeakList.cc.

References protocols::abinitio::filename(), protocols::noesy_assign::open_stream(), peaks_, protocols::noesy_assign::PeakFileFormat::set_format_from_peak(), protocols::noesy_assign::PeakFileFormat::write_header(), and protocols::noesy_assign::PeakFileFormat::write_peak().

void protocols::noesy_assign::CrossPeakList::write_to_stream ( std::ostream &  os,
PeakFileFormat &  output_adaptor 
) const

Definition at line 140 of file CrossPeakList.cc.

References peaks_, protocols::noesy_assign::PeakFileFormat::set_format_from_peak(), protocols::noesy_assign::PeakFileFormat::write_header(), and protocols::noesy_assign::PeakFileFormat::write_peak().

Member Data Documentation

PeakAssignmentResidueMapOP protocols::noesy_assign::CrossPeakList::assignments_
private

Definition at line 130 of file CrossPeakList.hh.

Referenced by assignments(), delete_diagonal_peaks(), find_assignments(), network_analysis(), update_assignment_list(), and update_symmetry_score().

CrossPeaks protocols::noesy_assign::CrossPeakList::peaks_
private

Definition at line 127 of file CrossPeakList.hh.

Referenced by begin(), delete_diagonal_peaks(), end(), find_assignments(), peaks(), read_from_stream(), size(), write_peak_files(), and write_to_stream().

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