#include <CrossPeak.hh>

Inheritance diagram for protocols::noesy_assign::CrossPeak3D:

Collaboration diagram for protocols::noesy_assign::CrossPeak3D:

Public Member Functions
	CrossPeak3D (Spin const &sp1, Spin const &sp2, Spin const &label1, core::Real strength)

	CrossPeak3D ()

	~CrossPeak3D ()

virtual CrossPeakOP	empty_clone ()

virtual void	assign_spin (Size spin_id)
	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 void	assign_labelled_spin (Size proton)

virtual bool	has_label (core::Size i) const

virtual Spin &	label (core::Size)

virtual Spin const &	label (core::Size) const

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

Spin &	proton (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...

Spin &	spin (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

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

Static Protected Attributes inherited from protocols::noesy_assign::CrossPeak
static std::set < core::id::NamedAtomID >	unknown_resonances_