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protocols::noesy_assign::CrossPeak3D Class Reference

#include <CrossPeak.hh>

Inheritance diagram for protocols::noesy_assign::CrossPeak3D:
Inheritance graph
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Public Member Functions

 CrossPeak3D (Spin const &sp1, Spin const &sp2, Spin const &label1, core::Real strength)
 
 CrossPeak3D ()
 
 ~CrossPeak3D () override
 
CrossPeakOP empty_clone () override
 
void assign_spin (core::Size spin_id) override
 assign protons based on chemical shifts and tolerances More...
 
core::Size assign_spin (core::Size spin_id, core::Size res_ids[]) override
 assign protons ass pre-determined More...
 
virtual void assign_labelled_spin (core::Size proton)
 
bool has_label (core::Size i) const override
 
Spinlabel (core::Size) override
 
Spin const & label (core::Size) const override
 
- Public Member Functions inherited from protocols::noesy_assign::CrossPeak
 CrossPeak (Spin const &, Spin const &, core::Real strength)
 
 CrossPeak ()
 
 ~CrossPeak () override
 
Spin const & proton (core::Size i) const
 
Spinproton (core::Size i)
 
bool has_proton (core::Size) const
 
Spin const & spin (core::Size i) const
 flat access to spins in [ a, b, h(a), h(b) ] order More...
 
Spinspin (core::Size i)
 
core::Size dimension () const
 
virtual void add_full_assignment (core::Size res_ids[])
 expect res_ids in order: spin1, spin2, label1, label2 More...
 
FoldResonance const & folder (core::Size i)
 
core::Real fold_resonance (core::Real freq, core::Size i)
 
virtual void find_assignments ()
 find all possible assignments based on chemical shifts and tolerances More...
 
core::Real volume () const
 the measured integral of the peak More...
 
void set_volume (core::Real val)
 
void set_resonances (ResonanceListOP res_in)
 
ResonanceList const & resonances () const
 
core::Real cumulative_peak_volume () const
 the cumulative cyana-type weights for all assignments Vk More...
 
void set_cumulative_peak_volume (core::Real setting)
 
core::Real max_volume_contribution () const
 the largest volume contribution (normalized) any of the assignments has More...
 
core::Real probability () const
 
void set_eliminated_due_to_dist_violations (bool setting)
 
void set_elimination_candidate (bool setting=true)
 
void set_elimination_comment (std::string const &str)
 
bool is_elimination_candidate ()
 
bool eliminated (bool recompute=false, bool do_not_compute=false) const
 returns true if this peak is to be ignored due to points (i)-(iv) on p215 of JMB 2002, 319,209-227 do_not_compute ... for outputter that does not want to change state... More...
 
std::string elimination_reason () const
 
core::Size min_seq_separation_residue_assignment (core::Real volume_threshold) const
 do we have a inter residue assignment with at least volume_threshold contribution ? More...
 
void create_fa_and_cen_constraint (core::scoring::constraints::ConstraintOP &fa_cst, core::scoring::constraints::ConstraintOP &cen_cst, core::pose::Pose const &pose, core::pose::Pose const &centroid_pose, core::Size normalization, core::Real padding=0.0, bool fa_only=false) const
 
bool assigned () const
 
bool ambiguous () const
 
core::Size n_assigned () const
 
core::Size n_Vmin_assignments ()
 number of assignments with peak volume higher than params.min_volume_ More...
 
PeakAssignments const & assignments () const
 
const_iterator begin () const
 
const_iterator end () const
 
iterator begin ()
 
iterator end ()
 
core::Real distance_bound () const
 
void nudge_distance_bound (core::Real offset)
 
core::Size peak_id () const
 
std::string const & filename () const
 
std::size_t exp_hash () const
 
bool same_peak (CrossPeak const &other) const
 
void set_peak_id (core::Size val)
 
CrossPeakInfo const & info (core::Size i) const
 
void set_info (core::Size i, CrossPeakInfoCOP info)
 
void calibrate (PeakCalibrator const &, CalibrationTypeCumulator &calibration_types)
 
core::Real tolerance (core::Size d)
 
bool is4D () const
 
void print_peak_info (std::ostream &) const
 
QualityClass quality_class () const
 
std::string quality_class_str () const
 
core::Real smallest_native_violation () const
 

Private Attributes

Spin label1_
 

Additional Inherited Members

- Public Types inherited from protocols::noesy_assign::CrossPeak
enum  EliminationReason {
  NOT_ELIMINATED = 0, EL_DISTVIOL, EL_NETWORK, EL_MINPEAKVOL,
  EL_MAXASSIGN
}
 
enum  QualityClass {
  HI_UNAMBIG = 0, HI_NEAR_UNAMBIG, HI_AMBIG, MED_AMBIG,
  UNAMBIG_MED_PROB, BAD_LOW_PROB, MAX_CLASS
}
 
typedef utility::vector1
< PeakAssignmentOP
PeakAssignments
 
typedef
PeakAssignments::const_iterator 
const_iterator
 
typedef PeakAssignments::iterator iterator
 

Constructor & Destructor Documentation

protocols::noesy_assign::CrossPeak3D::CrossPeak3D ( Spin const &  sp1,
Spin const &  sp2,
Spin const &  label1,
core::Real  strength 
)
protocols::noesy_assign::CrossPeak3D::CrossPeak3D ( )
default
protocols::noesy_assign::CrossPeak3D::~CrossPeak3D ( )
overridedefault

Member Function Documentation

void protocols::noesy_assign::CrossPeak3D::assign_labelled_spin ( core::Size  proton)
virtual
void protocols::noesy_assign::CrossPeak3D::assign_spin ( core::Size  spin_id)
overridevirtual
Size protocols::noesy_assign::CrossPeak3D::assign_spin ( core::Size  spin_id,
core::Size  res_ids[] 
)
overridevirtual
CrossPeakOP protocols::noesy_assign::CrossPeak3D::empty_clone ( )
inlineoverridevirtual
bool protocols::noesy_assign::CrossPeak3D::has_label ( core::Size  i) const
inlineoverridevirtual
Spin& protocols::noesy_assign::CrossPeak3D::label ( core::Size  )
inlineoverridevirtual
Spin const& protocols::noesy_assign::CrossPeak3D::label ( core::Size  ) const
inlineoverridevirtual

Reimplemented from protocols::noesy_assign::CrossPeak.

Reimplemented in protocols::noesy_assign::CrossPeak4D.

References label1_.

Member Data Documentation

Spin protocols::noesy_assign::CrossPeak3D::label1_
private

Referenced by label().


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