#include <CrossPeak.hh>

Inheritance diagram for protocols::noesy_assign::CrossPeak:

Collaboration diagram for protocols::noesy_assign::CrossPeak:

Classes
class	Spin
	a single dimension of a multidimensional peak, stores putative assignments as indices into Resonance table More...

Public Types
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

Public Member Functions
	CrossPeak (Spin const &, Spin const &, core::Real strength)

	CrossPeak ()

virtual	~CrossPeak ()

virtual CrossPeakOP	empty_clone ()

virtual bool	has_label (core::Size) const

virtual Spin &	label (core::Size)

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

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...

virtual void	assign_spin (core::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...

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

Static Protected Attributes
static std::set < core::id::NamedAtomID >	unknown_resonances_

Detailed Description

Definition at line 52 of file CrossPeak.hh.

Member Typedef Documentation

typedef PeakAssignments::const_iterator protocols::noesy_assign::CrossPeak::const_iterator

Definition at line 89 of file CrossPeak.hh.

typedef PeakAssignments::iterator protocols::noesy_assign::CrossPeak::iterator

Definition at line 90 of file CrossPeak.hh.

typedef utility::vector1< PeakAssignmentOP > protocols::noesy_assign::CrossPeak::PeakAssignments

Definition at line 88 of file CrossPeak.hh.

Member Enumeration Documentation

enum protocols::noesy_assign::CrossPeak::EliminationReason

Enumerator
NOT_ELIMINATED
EL_DISTVIOL
EL_NETWORK
EL_MINPEAKVOL
EL_MAXASSIGN

Definition at line 91 of file CrossPeak.hh.

enum protocols::noesy_assign::CrossPeak::QualityClass

Enumerator
HI_UNAMBIG
HI_NEAR_UNAMBIG
HI_AMBIG
MED_AMBIG
UNAMBIG_MED_PROB
BAD_LOW_PROB
MAX_CLASS

Definition at line 99 of file CrossPeak.hh.

Constructor & Destructor Documentation

protocols::noesy_assign::CrossPeak::CrossPeak	(	Spin const &	sp1,
		Spin const &	sp2,
		core::Real	strength
	)

Definition at line 84 of file CrossPeak.cc.

protocols::noesy_assign::CrossPeak::CrossPeak ( )

Definition at line 95 of file CrossPeak.cc.

Referenced by empty_clone().

protocols::noesy_assign::CrossPeak::~CrossPeak ( )

virtual

Definition at line 103 of file CrossPeak.cc.

Member Function Documentation

void protocols::noesy_assign::CrossPeak::add_full_assignment ( core::Size res_ids[])

virtual

expect res_ids in order: spin1, spin2, label1, label2

use for reading of assignments from file pass as spin1, spin2, label1, label2 (indices 1..4)

Definition at line 107 of file CrossPeak.cc.

References assign_spin(), and assignments_.

Referenced by protocols::noesy_assign::PeakFileFormat::read_assignments().

bool protocols::noesy_assign::CrossPeak::ambiguous ( ) const

inline

Definition at line 259 of file CrossPeak.hh.

References assignments_.

void protocols::noesy_assign::CrossPeak::assign_spin ( core::Size spin_id)

virtual

assign protons based on chemical shifts and tolerances

Reimplemented in protocols::noesy_assign::CrossPeak4D, and protocols::noesy_assign::CrossPeak3D.

Definition at line 156 of file CrossPeak.cc.

References protocols::noesy_assign::CrossPeak::Spin::add_assignment(), begin(), protocols::noesy_assign::ResonanceList::end(), folder(), info(), proton(), and resonances().

Referenced by add_full_assignment(), protocols::noesy_assign::CrossPeak3D::assign_spin(), protocols::noesy_assign::CrossPeak4D::assign_spin(), and find_assignments().

core::Size protocols::noesy_assign::CrossPeak::assign_spin	(	core::Size	spin_id,
		core::Size	res_ids[]
	)

virtual

assign protons ass pre-determined

Reimplemented in protocols::noesy_assign::CrossPeak4D, and protocols::noesy_assign::CrossPeak3D.

Definition at line 169 of file CrossPeak.cc.

References protocols::noesy_assign::CrossPeak::Spin::add_assignment(), protocols::noesy_assign::CrossPeak::Spin::assignment_index(), protocols::noesy_assign::CrossPeak::Spin::n_assigned(), and proton().

bool protocols::noesy_assign::CrossPeak::assigned ( ) const

inline

Definition at line 258 of file CrossPeak.hh.

References assignments_.

PeakAssignments const& protocols::noesy_assign::CrossPeak::assignments ( ) const

inline

Definition at line 267 of file CrossPeak.hh.

References assignments_.

Referenced by eliminated(), and protocols::noesy_assign::PeakFileFormat::write_assignments().

const_iterator protocols::noesy_assign::CrossPeak::begin ( ) const

inline

Definition at line 268 of file CrossPeak.hh.

References assignments_.

Referenced by protocols::noesy_assign::CrossPeak3D::assign_labelled_spin(), assign_spin(), calibrate(), create_fa_and_cen_constraint(), eliminated(), max_volume_contribution(), min_seq_separation_residue_assignment(), n_Vmin_assignments(), probability(), quality_class(), and smallest_native_violation().

iterator protocols::noesy_assign::CrossPeak::begin ( )

inline

Definition at line 269 of file CrossPeak.hh.

References assignments_.

void protocols::noesy_assign::CrossPeak::calibrate	(	PeakCalibrator const &	calibrator,
		CalibrationTypeCumulator &	calibration_types
	)

Definition at line 561 of file CrossPeak.cc.

References begin(), distance_bound_, end(), protocols::noesy_assign::PeakAssignmentParameters::get_instance(), info(), protocols::noesy_assign::PeakAssignmentParameters::min_volume_, peak_id_, resonances(), and volume_.

void protocols::noesy_assign::CrossPeak::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

Definition at line 188 of file CrossPeak.cc.

References begin(), protocols::noesy_assign::PeakAssignmentParameters::centroid_mapping_distance_padding_, protocols::noesy_assign::PeakAssignmentParameters::cst_strength_, distance_bound(), end(), filename(), protocols::noesy_assign::PeakAssignmentParameters::get_instance(), HI_NEAR_UNAMBIG, HI_UNAMBIG, protocols::noesy_assign::PeakAssignmentParameters::map_to_cen_atom_, protocols::noesy_assign::PeakAssignmentParameters::min_volume_, n_assigned(), peak_id(), quality_class(), protocols::noesy_assign::round(), and volume().

core::Real protocols::noesy_assign::CrossPeak::cumulative_peak_volume ( ) const

inline

the cumulative cyana-type weights for all assignments Vk

Definition at line 184 of file CrossPeak.hh.

References cumulative_peak_volume_.

Referenced by probability(), and protocols::noesy_assign::PeakFileFormat::write_peak().

core::Size protocols::noesy_assign::CrossPeak::dimension ( ) const

inline

Definition at line 128 of file CrossPeak.hh.

References has_label().

core::Real protocols::noesy_assign::CrossPeak::distance_bound ( ) const

inline

Definition at line 272 of file CrossPeak.hh.

References distance_bound_.

Referenced by create_fa_and_cen_constraint(), protocols::noesy_assign::PeakFileFormat_xpk::write_peak(), protocols::noesy_assign::PeakFileFormat_Sparky::write_peak(), and protocols::noesy_assign::PeakFileFormat::write_peak().

bool protocols::noesy_assign::CrossPeak::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...

Definition at line 506 of file CrossPeak.cc.

References assignments(), begin(), EL_DISTVIOL, EL_MAXASSIGN, EL_MINPEAKVOL, EL_NETWORK, eliminated_, eliminated_due_to_dist_violations_, end(), protocols::noesy_assign::PeakAssignmentParameters::get_instance(), protocols::noesy_assign::PeakAssignmentParameters::min_volume_, protocols::noesy_assign::PeakAssignmentParameters::network_atom_min_, protocols::noesy_assign::PeakAssignmentParameters::network_reswise_high_, protocols::noesy_assign::PeakAssignmentParameters::network_reswise_min_, protocols::noesy_assign::PeakAssignmentParameters::nmax_, NOT_ELIMINATED, and core::io::serialization::size().

Referenced by protocols::noesy_assign::PeakFileFormat_Sparky::write_peak(), protocols::noesy_assign::PeakFileFormat_xpk::write_peak(), and protocols::noesy_assign::PeakFileFormat::write_peak().

std::string protocols::noesy_assign::CrossPeak::elimination_reason ( ) const

Definition at line 493 of file CrossPeak.cc.

References EL_DISTVIOL, EL_MAXASSIGN, EL_MINPEAKVOL, EL_NETWORK, eliminated_, and elimination_comment_.

Referenced by protocols::noesy_assign::PeakFileFormat_Sparky::write_peak(), protocols::noesy_assign::PeakFileFormat_xpk::write_peak(), and protocols::noesy_assign::PeakFileFormat::write_peak().

virtual CrossPeakOP protocols::noesy_assign::CrossPeak::empty_clone ( )

inlinevirtual

Reimplemented in protocols::noesy_assign::CrossPeak4D, and protocols::noesy_assign::CrossPeak3D.

Definition at line 112 of file CrossPeak.hh.

References CrossPeak().

const_iterator protocols::noesy_assign::CrossPeak::end ( ) const

inline

Definition at line 270 of file CrossPeak.hh.

References assignments_.

Referenced by calibrate(), create_fa_and_cen_constraint(), eliminated(), max_volume_contribution(), min_seq_separation_residue_assignment(), n_Vmin_assignments(), probability(), quality_class(), and smallest_native_violation().

size_t protocols::noesy_assign::CrossPeak::exp_hash ( ) const

inline

Definition at line 277 of file CrossPeak.hh.

References info1_.

Referenced by protocols::noesy_assign::PeakAssignment::is_symmetric_partner_of(), and same_peak().

std::string const& protocols::noesy_assign::CrossPeak::filename ( ) const

inline

Definition at line 276 of file CrossPeak.hh.

References info1_.

Referenced by create_fa_and_cen_constraint().

void protocols::noesy_assign::CrossPeak::find_assignments ( )

virtual

find all possible assignments based on chemical shifts and tolerances

Definition at line 126 of file CrossPeak.cc.

References assign_spin(), assignments_, protocols::noesy_assign::CrossPeak::Spin::n_assigned(), n_assigned(), proton(), proton1_, and proton2_.

core::Real protocols::noesy_assign::CrossPeak::fold_resonance	(	core::Real	freq,
		core::Size	i
	)

inline

Definition at line 146 of file CrossPeak.hh.

References info1_, and info2_.

FoldResonance const& protocols::noesy_assign::CrossPeak::folder ( core::Size i)

inline

Definition at line 132 of file CrossPeak.hh.

References info1_, info2_, and UNFOLDED_.

Referenced by protocols::noesy_assign::CrossPeak3D::assign_labelled_spin(), and assign_spin().

virtual bool protocols::noesy_assign::CrossPeak::has_label ( core::Size ) const

inlinevirtual

Reimplemented in protocols::noesy_assign::CrossPeak4D, and protocols::noesy_assign::CrossPeak3D.

Definition at line 116 of file CrossPeak.hh.

Referenced by protocols::noesy_assign::CrossPeak3D::assign_labelled_spin(), dimension(), is4D(), print_peak_info(), protocols::noesy_assign::PeakFileFormat::read_assignments(), protocols::noesy_assign::PeakFileFormat::read_resonances(), protocols::noesy_assign::PeakFileFormat::write_assignment_indent(), and protocols::noesy_assign::PeakFileFormat::write_resonances().

bool protocols::noesy_assign::CrossPeak::has_proton ( core::Size select) const

Definition at line 121 of file CrossPeak.cc.

References info(), and protocols::noesy_assign::CrossPeakInfo::proton_tolerance().

CrossPeakInfo const& protocols::noesy_assign::CrossPeak::info ( core::Size i) const

inline

Definition at line 288 of file CrossPeak.hh.

References info1_, and info2_.

Referenced by protocols::noesy_assign::CrossPeak3D::assign_labelled_spin(), assign_spin(), calibrate(), protocols::noesy_assign::PeakFileFormat::compatible_with_current_format(), has_proton(), print_peak_info(), protocols::noesy_assign::PeakFileFormat_xpk::set_format_from_peak(), protocols::noesy_assign::PeakFileFormat_Sparky::set_format_from_peak(), protocols::noesy_assign::PeakFileFormat::set_format_from_peak(), and set_info().

bool protocols::noesy_assign::CrossPeak::is4D ( ) const

inline

Definition at line 309 of file CrossPeak.hh.

References has_label(), info1_, and info2_.

bool protocols::noesy_assign::CrossPeak::is_elimination_candidate ( )

inline

Definition at line 211 of file CrossPeak.hh.

References elimination_candidate_.

virtual Spin& protocols::noesy_assign::CrossPeak::label ( core::Size )

inlinevirtual

Reimplemented in protocols::noesy_assign::CrossPeak4D, and protocols::noesy_assign::CrossPeak3D.

Definition at line 117 of file CrossPeak.hh.

References proton1_.

Referenced by protocols::noesy_assign::CrossPeak3D::assign_labelled_spin(), protocols::noesy_assign::CrossPeak3D::assign_spin(), protocols::noesy_assign::PeakFileFormat::read_resonances(), spin(), and protocols::noesy_assign::PeakFileFormat::write_resonances().

virtual Spin const& protocols::noesy_assign::CrossPeak::label ( core::Size ) const

inlinevirtual

Reimplemented in protocols::noesy_assign::CrossPeak4D, and protocols::noesy_assign::CrossPeak3D.

Definition at line 118 of file CrossPeak.hh.

References proton2_.

core::Real protocols::noesy_assign::CrossPeak::max_volume_contribution ( ) const

the largest volume contribution (normalized) any of the assignments has

Definition at line 401 of file CrossPeak.cc.

References begin(), and end().

Size protocols::noesy_assign::CrossPeak::min_seq_separation_residue_assignment ( core::Real volume_threshold) const

do we have a inter residue assignment with at least volume_threshold contribution ?

Definition at line 481 of file CrossPeak.cc.

References begin(), and end().

core::Size protocols::noesy_assign::CrossPeak::n_assigned ( ) const

inline

Definition at line 260 of file CrossPeak.hh.

References assignments_.

Referenced by protocols::noesy_assign::CrossPeak3D::assign_spin(), protocols::noesy_assign::CrossPeak4D::assign_spin(), create_fa_and_cen_constraint(), and find_assignments().

core::Size protocols::noesy_assign::CrossPeak::n_Vmin_assignments ( )

number of assignments with peak volume higher than params.min_volume_

Definition at line 547 of file CrossPeak.cc.

References begin(), end(), protocols::noesy_assign::PeakAssignmentParameters::get_instance(), and protocols::noesy_assign::PeakAssignmentParameters::min_volume_.

void protocols::noesy_assign::CrossPeak::nudge_distance_bound ( core::Real offset)

Definition at line 557 of file CrossPeak.cc.

References distance_bound_.

core::Size protocols::noesy_assign::CrossPeak::peak_id ( ) const

inline

Definition at line 274 of file CrossPeak.hh.

References peak_id_.

Referenced by create_fa_and_cen_constraint(), print_peak_info(), and same_peak().

void protocols::noesy_assign::CrossPeak::print_peak_info ( std::ostream & os) const

Definition at line 146 of file CrossPeak.cc.

References has_label(), info(), protocols::noesy_assign::CrossPeakInfo::label_atom_type(), protocols::noesy_assign::CrossPeakInfo::main_atom(), and peak_id().

Referenced by protocols::noesy_assign::operator<<().

core::Real protocols::noesy_assign::CrossPeak::probability ( ) const

Definition at line 315 of file CrossPeak.cc.

References begin(), cumulative_peak_volume(), end(), protocols::noesy_assign::PeakAssignmentParameters::get_instance(), protocols::noesy_assign::PeakAssignmentParameters::prob_sigmoid_m_, protocols::noesy_assign::PeakAssignmentParameters::prob_sigmoid_tau_, protocols::noesy_assign::PeakAssignmentParameters::prob_sigmoid_w_, and protocols::noesy_assign::sigmoid().

Referenced by quality_class(), and protocols::noesy_assign::PeakFileFormat::write_peak().

Spin const& protocols::noesy_assign::CrossPeak::proton ( core::Size i) const

inline

Definition at line 120 of file CrossPeak.hh.

References proton1_, and proton2_.

Referenced by protocols::noesy_assign::CrossPeak3D::assign_labelled_spin(), assign_spin(), find_assignments(), protocols::noesy_assign::PeakFileFormat::read_resonances(), spin(), and protocols::noesy_assign::PeakFileFormat::write_resonances().

Spin& protocols::noesy_assign::CrossPeak::proton ( core::Size i)

inline

Definition at line 121 of file CrossPeak.hh.

References proton1_, and proton2_.

CrossPeak::QualityClass protocols::noesy_assign::CrossPeak::quality_class ( ) const

Definition at line 357 of file CrossPeak.cc.

References BAD_LOW_PROB, begin(), end(), protocols::noesy_assign::PeakAssignmentParameters::get_instance(), HI_AMBIG, HI_NEAR_UNAMBIG, HI_UNAMBIG, MED_AMBIG, protocols::noesy_assign::PeakAssignmentParameters::prob_level_, probability(), and UNAMBIG_MED_PROB.

Referenced by create_fa_and_cen_constraint(), quality_class_str(), smallest_native_violation(), and protocols::noesy_assign::PeakFileFormat::write_peak().

std::string protocols::noesy_assign::CrossPeak::quality_class_str ( ) const

Definition at line 352 of file CrossPeak.cc.

References quality_class().

Referenced by protocols::noesy_assign::PeakFileFormat::write_peak().

ResonanceList const& protocols::noesy_assign::CrossPeak::resonances ( ) const

inline

Definition at line 181 of file CrossPeak.hh.

References resonances_.

Referenced by protocols::noesy_assign::CrossPeak3D::assign_labelled_spin(), assign_spin(), and calibrate().

bool protocols::noesy_assign::CrossPeak::same_peak ( CrossPeak const & other) const

inline

Definition at line 279 of file CrossPeak.hh.

References exp_hash(), and peak_id().

void protocols::noesy_assign::CrossPeak::set_cumulative_peak_volume ( core::Real setting)

inline

Definition at line 188 of file CrossPeak.hh.

References cumulative_peak_volume_.

void protocols::noesy_assign::CrossPeak::set_eliminated_due_to_dist_violations ( bool setting)

inline

Definition at line 197 of file CrossPeak.hh.

References EL_DISTVIOL, eliminated_, eliminated_due_to_dist_violations_, and NOT_ELIMINATED.

void protocols::noesy_assign::CrossPeak::set_elimination_candidate ( bool setting = true)

inline

Definition at line 203 of file CrossPeak.hh.

References elimination_candidate_.

void protocols::noesy_assign::CrossPeak::set_elimination_comment ( std::string const & str)

inline

Definition at line 207 of file CrossPeak.hh.

References elimination_comment_, and protocols::kinmatch::str().

void protocols::noesy_assign::CrossPeak::set_info	(	core::Size	i,
		CrossPeakInfoCOP	info
	)

inline

Definition at line 290 of file CrossPeak.hh.

References info(), info1_, and info2_.

void protocols::noesy_assign::CrossPeak::set_peak_id ( core::Size val)

inline

Definition at line 283 of file CrossPeak.hh.

References peak_id_.

void protocols::noesy_assign::CrossPeak::set_resonances ( ResonanceListOP res_in)

inline

Definition at line 177 of file CrossPeak.hh.

References resonances_.

void protocols::noesy_assign::CrossPeak::set_volume ( core::Real val)

inline

Definition at line 175 of file CrossPeak.hh.

References volume_.

Referenced by protocols::noesy_assign::PeakFileFormat::read_strength().

Real protocols::noesy_assign::CrossPeak::smallest_native_violation ( ) const

Definition at line 340 of file CrossPeak.cc.

References begin(), end(), HI_UNAMBIG, MED_AMBIG, and quality_class().

Referenced by protocols::noesy_assign::PeakFileFormat::write_peak().

Spin const& protocols::noesy_assign::CrossPeak::spin ( core::Size i) const

inline

flat access to spins in [ a, b, h(a), h(b) ] order

Definition at line 125 of file CrossPeak.hh.

References label(), and proton().

Spin& protocols::noesy_assign::CrossPeak::spin ( core::Size i)

inline

Definition at line 126 of file CrossPeak.hh.

References label(), and proton().

core::Real protocols::noesy_assign::CrossPeak::tolerance ( core::Size d)

inline

Definition at line 294 of file CrossPeak.hh.

References info1_, and info2_.

core::Real protocols::noesy_assign::CrossPeak::volume ( ) const

inline

the measured integral of the peak

Definition at line 174 of file CrossPeak.hh.

References volume_.

Referenced by create_fa_and_cen_constraint(), and protocols::noesy_assign::PeakFileFormat::write_strength().

Member Data Documentation

PeakAssignments protocols::noesy_assign::CrossPeak::assignments_

private

Definition at line 322 of file CrossPeak.hh.

Referenced by add_full_assignment(), ambiguous(), assigned(), protocols::noesy_assign::CrossPeak::Spin::assignment_index(), assignments(), begin(), end(), find_assignments(), and n_assigned().

core::Real protocols::noesy_assign::CrossPeak::cumulative_peak_volume_

private

Definition at line 329 of file CrossPeak.hh.

Referenced by cumulative_peak_volume(), and set_cumulative_peak_volume().

core::Real protocols::noesy_assign::CrossPeak::distance_bound_

private

Definition at line 330 of file CrossPeak.hh.

Referenced by calibrate(), distance_bound(), and nudge_distance_bound().

EliminationReason protocols::noesy_assign::CrossPeak::eliminated_

mutableprivate

Definition at line 331 of file CrossPeak.hh.

Referenced by eliminated(), elimination_reason(), and set_eliminated_due_to_dist_violations().

bool protocols::noesy_assign::CrossPeak::eliminated_due_to_dist_violations_

private

Definition at line 332 of file CrossPeak.hh.

Referenced by eliminated(), and set_eliminated_due_to_dist_violations().

bool protocols::noesy_assign::CrossPeak::elimination_candidate_

private

Definition at line 333 of file CrossPeak.hh.

Referenced by is_elimination_candidate(), and set_elimination_candidate().

std::string protocols::noesy_assign::CrossPeak::elimination_comment_

private

Definition at line 334 of file CrossPeak.hh.

Referenced by elimination_reason(), and set_elimination_comment().

CrossPeakInfoCOP protocols::noesy_assign::CrossPeak::info1_

private

Definition at line 324 of file CrossPeak.hh.

Referenced by exp_hash(), filename(), fold_resonance(), folder(), info(), is4D(), set_info(), and tolerance().

CrossPeakInfoCOP protocols::noesy_assign::CrossPeak::info2_

private

Definition at line 324 of file CrossPeak.hh.

Referenced by fold_resonance(), folder(), info(), is4D(), set_info(), and tolerance().

core::Size protocols::noesy_assign::CrossPeak::peak_id_

private

Definition at line 328 of file CrossPeak.hh.

Referenced by calibrate(), peak_id(), and set_peak_id().

Spin protocols::noesy_assign::CrossPeak::proton1_

private

Definition at line 325 of file CrossPeak.hh.

Referenced by find_assignments(), label(), and proton().

Spin protocols::noesy_assign::CrossPeak::proton2_

private

Definition at line 326 of file CrossPeak.hh.

Referenced by find_assignments(), label(), and proton().

ResonanceListOP protocols::noesy_assign::CrossPeak::resonances_

private

Definition at line 323 of file CrossPeak.hh.

Referenced by resonances(), and set_resonances().

FoldResonance protocols::noesy_assign::CrossPeak::UNFOLDED_

private

Definition at line 321 of file CrossPeak.hh.

Referenced by folder().

std::set< core::id::NamedAtomID > protocols::noesy_assign::CrossPeak::unknown_resonances_

staticprotected

Definition at line 337 of file CrossPeak.hh.

Referenced by protocols::noesy_assign::CrossPeak3D::assign_labelled_spin().

core::Real protocols::noesy_assign::CrossPeak::volume_

private

Definition at line 327 of file CrossPeak.hh.

Referenced by calibrate(), set_volume(), and volume().

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

src/protocols/noesy_assign/CrossPeak.hh
src/protocols/noesy_assign/CrossPeak.cc

Private Attributes
FoldResonance	UNFOLDED_

PeakAssignments	assignments_

ResonanceListOP	resonances_

CrossPeakInfoCOP	info1_

CrossPeakInfoCOP	info2_

Spin	proton1_

Spin	proton2_

core::Real	volume_

core::Size	peak_id_

core::Real	cumulative_peak_volume_

core::Real	distance_bound_

EliminationReason	eliminated_

bool	eliminated_due_to_dist_violations_

bool	elimination_candidate_

std::string	elimination_comment_

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