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protocols::noesy_assign::CrossPeak Class Reference

#include <CrossPeak.hh>

Inheritance diagram for protocols::noesy_assign::CrossPeak:
Inheritance graph
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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 ()
 
 ~CrossPeak () override
 
virtual CrossPeakOP empty_clone ()
 
virtual bool has_label (core::Size) const
 
virtual Spinlabel (core::Size)
 
virtual Spin const & label (core::Size) const
 
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...
 
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
 
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

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_
 

Member Typedef Documentation

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

Member Enumeration Documentation

Enumerator
NOT_ELIMINATED 
EL_DISTVIOL 
EL_NETWORK 
EL_MINPEAKVOL 
EL_MAXASSIGN 
Enumerator
HI_UNAMBIG 
HI_NEAR_UNAMBIG 
HI_AMBIG 
MED_AMBIG 
UNAMBIG_MED_PROB 
BAD_LOW_PROB 
MAX_CLASS 

Constructor & Destructor Documentation

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

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)

References assign_spin(), and assignments_.

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

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

References assignments_.

void protocols::noesy_assign::CrossPeak::assign_spin ( core::Size  spin_id)
virtual
core::Size protocols::noesy_assign::CrossPeak::assign_spin ( core::Size  spin_id,
core::Size  res_ids[] 
)
virtual
bool protocols::noesy_assign::CrossPeak::assigned ( ) const
inline

References assignments_.

PeakAssignments const& protocols::noesy_assign::CrossPeak::assignments ( ) const
inline
const_iterator protocols::noesy_assign::CrossPeak::begin ( ) const
inline
iterator protocols::noesy_assign::CrossPeak::begin ( )
inline

References assignments_.

void protocols::noesy_assign::CrossPeak::calibrate ( PeakCalibrator const &  calibrator,
CalibrationTypeCumulator calibration_types 
)
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
core::Real protocols::noesy_assign::CrossPeak::cumulative_peak_volume ( ) const
inline
core::Size protocols::noesy_assign::CrossPeak::dimension ( ) const
inline
core::Real protocols::noesy_assign::CrossPeak::distance_bound ( ) const
inline
bool protocols::noesy_assign::CrossPeak::eliminated ( bool  recompute = false,
bool  do_not_compute = false 
) const
std::string protocols::noesy_assign::CrossPeak::elimination_reason ( ) const
virtual CrossPeakOP protocols::noesy_assign::CrossPeak::empty_clone ( )
inlinevirtual
const_iterator protocols::noesy_assign::CrossPeak::end ( ) const
inline
iterator protocols::noesy_assign::CrossPeak::end ( )
inline

References assignments_.

std::size_t protocols::noesy_assign::CrossPeak::exp_hash ( ) const
inline
std::string const& protocols::noesy_assign::CrossPeak::filename ( ) const
inline

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

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

References info1_, info2_, and core::id::to_string().

FoldResonance const& protocols::noesy_assign::CrossPeak::folder ( core::Size  i)
inline
virtual bool protocols::noesy_assign::CrossPeak::has_label ( core::Size  ) const
inlinevirtual
bool protocols::noesy_assign::CrossPeak::has_proton ( core::Size  select) const
CrossPeakInfo const& protocols::noesy_assign::CrossPeak::info ( core::Size  i) const
inline
bool protocols::noesy_assign::CrossPeak::is4D ( ) const
inline

References has_label(), info1_, and info2_.

bool protocols::noesy_assign::CrossPeak::is_elimination_candidate ( )
inline
virtual Spin& protocols::noesy_assign::CrossPeak::label ( core::Size  )
inlinevirtual
virtual Spin const& protocols::noesy_assign::CrossPeak::label ( core::Size  ) const
inlinevirtual
core::Real protocols::noesy_assign::CrossPeak::max_volume_contribution ( ) const

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

References protocols::mean_field::max().

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 ?

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

number of assignments with peak volume higher than params.min_volume_

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)

References distance_bound_.

core::Size protocols::noesy_assign::CrossPeak::peak_id ( ) const
inline
void protocols::noesy_assign::CrossPeak::print_peak_info ( std::ostream &  os) const
core::Real protocols::noesy_assign::CrossPeak::probability ( ) const
Spin const& protocols::noesy_assign::CrossPeak::proton ( core::Size  i) const
inline
Spin& protocols::noesy_assign::CrossPeak::proton ( core::Size  i)
inline

References proton1_, and proton2_.

CrossPeak::QualityClass protocols::noesy_assign::CrossPeak::quality_class ( ) const
std::string protocols::noesy_assign::CrossPeak::quality_class_str ( ) const
ResonanceList const& protocols::noesy_assign::CrossPeak::resonances ( ) const
inline
bool protocols::noesy_assign::CrossPeak::same_peak ( CrossPeak const &  other) const
inline
void protocols::noesy_assign::CrossPeak::set_cumulative_peak_volume ( core::Real  setting)
inline
void protocols::noesy_assign::CrossPeak::set_eliminated_due_to_dist_violations ( bool  setting)
inline
void protocols::noesy_assign::CrossPeak::set_elimination_candidate ( bool  setting = true)
inline
void protocols::noesy_assign::CrossPeak::set_elimination_comment ( std::string const &  str)
inline
void protocols::noesy_assign::CrossPeak::set_info ( core::Size  i,
CrossPeakInfoCOP  info 
)
inline

References info(), info1_, and info2_.

void protocols::noesy_assign::CrossPeak::set_peak_id ( core::Size  val)
inline
void protocols::noesy_assign::CrossPeak::set_resonances ( ResonanceListOP  res_in)
inline

References resonances_.

void protocols::noesy_assign::CrossPeak::set_volume ( core::Real  val)
inline
Real protocols::noesy_assign::CrossPeak::smallest_native_violation ( ) const
Spin const& protocols::noesy_assign::CrossPeak::spin ( core::Size  i) const
inline

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

References label(), and proton().

Referenced by protocols::noesy_assign::PeakAssignment::update_chemshiftscore_from_peak().

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

References label(), and proton().

core::Real protocols::noesy_assign::CrossPeak::tolerance ( core::Size  d)
inline
core::Real protocols::noesy_assign::CrossPeak::volume ( ) const
inline

the measured integral of the peak

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
core::Real protocols::noesy_assign::CrossPeak::cumulative_peak_volume_
private
core::Real protocols::noesy_assign::CrossPeak::distance_bound_
private
EliminationReason protocols::noesy_assign::CrossPeak::eliminated_
mutableprivate
bool protocols::noesy_assign::CrossPeak::eliminated_due_to_dist_violations_
private
bool protocols::noesy_assign::CrossPeak::elimination_candidate_
private
std::string protocols::noesy_assign::CrossPeak::elimination_comment_
private
CrossPeakInfoCOP protocols::noesy_assign::CrossPeak::info1_
private
CrossPeakInfoCOP protocols::noesy_assign::CrossPeak::info2_
private
core::Size protocols::noesy_assign::CrossPeak::peak_id_
private

Referenced by peak_id(), and set_peak_id().

Spin protocols::noesy_assign::CrossPeak::proton1_
private

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

Spin protocols::noesy_assign::CrossPeak::proton2_
private

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

ResonanceListOP protocols::noesy_assign::CrossPeak::resonances_
private

Referenced by resonances(), and set_resonances().

FoldResonance protocols::noesy_assign::CrossPeak::UNFOLDED_
private

Referenced by folder().

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

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


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