Rosetta Protocols  2014.35
Public Member Functions | Private Attributes | List of all members
protocols::noesy_assign::CrossPeak4D Class Reference

#include <CrossPeak.hh>

Public Member Functions

 CrossPeak4D (Spin const &sp1, Spin const &sp2, Spin const &label1, Spin const &label2, core::Real strength)
 CrossPeak4D ()
 ~CrossPeak4D ()
virtual CrossPeakOP empty_clone ()
virtual void assign_spin (Size proton)
 assign protons based on chemical shifts and tolerances More...
virtual core::Size assign_spin (core::Size spin_id, core::Size res_ids[])
 assign protons ass pre-determined More...
virtual bool has_label (core::Size) const
Spinlabel (core::Size i)
Spin const & label (core::Size i) const
- Public Member Functions inherited from protocols::noesy_assign::CrossPeak3D
 CrossPeak3D (Spin const &sp1, Spin const &sp2, Spin const &label1, core::Real strength)
 CrossPeak3D ()
 ~CrossPeak3D ()
virtual void assign_labelled_spin (Size proton)
- Public Member Functions inherited from protocols::noesy_assign::CrossPeak
 CrossPeak (Spin const &, Spin const &, core::Real strength)
 CrossPeak ()
virtual ~CrossPeak ()
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
iterator begin ()
const_iterator end () const
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 label2_

Additional Inherited Members

- Public Types inherited from protocols::noesy_assign::CrossPeak
enum  EliminationReason {
enum  QualityClass {
typedef utility::vector1
< PeakAssignmentOP
typedef PeakAssignments::iterator iterator

Constructor & Destructor Documentation

protocols::noesy_assign::CrossPeak4D::CrossPeak4D ( Spin const &  sp1,
Spin const &  sp2,
Spin const &  label1,
Spin const &  label2,
core::Real  strength 
protocols::noesy_assign::CrossPeak4D::CrossPeak4D ( )

Referenced by empty_clone().

protocols::noesy_assign::CrossPeak4D::~CrossPeak4D ( )

Member Function Documentation

void protocols::noesy_assign::CrossPeak4D::assign_spin ( Size  spin_id)

assign protons based on chemical shifts and tolerances

Reimplemented from protocols::noesy_assign::CrossPeak3D.

References protocols::noesy_assign::CrossPeak3D::assign_labelled_spin().

Size protocols::noesy_assign::CrossPeak4D::assign_spin ( core::Size  spin_id,
core::Size  res_ids[] 
virtual CrossPeakOP protocols::noesy_assign::CrossPeak4D::empty_clone ( )

Reimplemented from protocols::noesy_assign::CrossPeak3D.

References CrossPeak4D().

virtual bool protocols::noesy_assign::CrossPeak4D::has_label ( core::Size  ) const
Spin& protocols::noesy_assign::CrossPeak4D::label ( core::Size  i)
Spin const& protocols::noesy_assign::CrossPeak4D::label ( core::Size  i) const

Member Data Documentation

Spin protocols::noesy_assign::CrossPeak4D::label2_

Referenced by label().

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