Objects associated with pasdPot.PASDPot energy terms: Peak,
PeakAssignment and ShiftAssignment
 
class Peak
 
  A Peak is associated with each peak in an NOE spectrum.
 
 It can have several possible assignments. It has an upper and lower
 distance bound, which each assignment can correct (for things like
 methyl groups).
 
Constructor: 
 
  Peak(name="")
 
Read-only accessor:
 
  name() - return name given during construction
 
Read/Write accessors:
 
  upBound            - upper distance bound
  lowBound           - lower distance bound
  fromProtonShift    - chemical shift value for from proton
  toProtonShift      - chemical shift value for to proton
  fromHeavyatomShift - chemical shift value for from heavy atom
  toHeavyatomShift   - chemical shift value for to heavy atom
  intensity          - peak intensity
 
Functions to manipulate notations in the note member:
 
  note()            - return the notation string.
  setNote(val)      - set note to string val
  appendToNote(val) - append string val to existing note
 
  
These accessors are used to set the corresponding quantity
to invalid values.
 
   resetFromProtonShift()
   resetToProtonShift()
   resetFromHeavyatomShift()
   resetToHeavyatomShift()
   resetIntensity()
 
These accessors return boolean indicating whether the corresponding
value has been set to a valid value:
 
   hasFromProtonShift()
   hasToProtonShift()
   hasFromHeavyatomShift()
   hasToHeavyatomShift()
   hasIntensity()
 
 
  peakAssignments()               - return the list of PeakAssignment objects 
  addPeakAssignment()             - add a PeakAssignment.
  removePeakAssignmentNamed(name) - remove the PeakAssignment with the
                                    specified name (a string). If no
                                    PeakAssigment is found, an exception
                                    is raised.
  removeAllPeakAssignments()      - remove all PeakAssignments.
  hasPeakAssignmentNamed(name)    - return boolean value indicating whether
                                    a PeakAssignment exists with the
                                    specified name.
  peakAssignmentNamed(name)       - return the PeakAssignment with the
                                    specified name. If no PeakAssigment is 
                                    found, an exception is raised.
  numPeakAssignments()            - return len(peakAssignments)
  isAssigned()                    - return True if len(peakAssignments)>0,
                                    otherwise False.
 
  fromShiftAssignments()     - return a list of from ShiftAssignments
  toShiftAssignments()       - return a list of to ShiftAssignments
  numFromShiftAssignments()  - return len(fromShiftAssignments)
  numToShiftAssignments()    - return len(toShiftAssignments)
  addShiftAssignment(val)    - add val, a ShiftAssignment
  removeShiftAssignmentNamed(name) - remove the ShiftAssignment with the
                                     specified name (a string). If no
                                     ShiftAssigment is found, an exception
                                     is raised.
  removeAllShiftAssignments()      - remove all ShiftAssignments
  hasShiftAssignmentNamed(name)    - return boolean value indicating whether
                                     a ShiftAssignment exists with the
                                     specified name.
  shiftAssignmentNamed(name)       - return the ShiftAssignment with the
                                     specified name. If no ShiftAssigment is 
                                     found, an exception is raised.
 
 
  peakAssignmentsWithShiftAssignmentNamed(name) -
      Return a list of PeakAssignments with the specified
      ShiftAssignment name.
      
 
Accessors querying difference in primary sequence of the
PeakAssignment with the smallest such distance.
 
  updatePrimarySeqDist() - call each PeakAssignment's updatePrimarySeqDist()
  primarySeqDist()       - return the smallest sequence difference. If the
                           PeakAssignment is intermolecular, a value
                           of 99999 is returned.
 
  Convenience sequence distance query accessors:
  
    isIntraresidue()       
    isSequential()
    isShortRange(cutoff)  - True if sequence differs by more than one residue,
                            and and less than cutoff.
    isLongRange(cutoff)   - True if sequence differs by more than cutoff,
                            or it is intermolecular.
    isIntermolecular()    - True if the PeakAssignment is intermolecular.
 
  
  lowestViolation()  - return the lowest distance violation of all
                       constituent PeakAssignments.
  prevLikelihood()   - likelihood of this PeakAssignment with the
                       largest such value.
                       
  lowestViolationsPrimarySeqDist() - return the primary sequence distance 
                                     of the PeakAssignment with the smallest
                                     distance violation.
  isGood()                         - return True if any PeakAssignment
                                     has been marked as good.
                                     
 
                                     
 Methods for activating PeakAssignments:
 
  activateAllPeakAssigns()   - make all PeakAssignments active
  inactivateAllPeakAssigns() - make no PeakAssignment active
 
  updateActivation(useSingleAssignment,
                   characteristicDist, 
                   violationWeight,
                   previousLikelihoodWeight) -
 
     This method updates PeakAssignment activation.
       PeakAssignments are activated by a Monte Carlo procedure
       based on a weighted sum of previousLikelihoods and likelihoods
       generated from distance violations in the current coordinates,
       weighted by previousLikelihoodWeight and violationWeight,
       respectively. The value characteristicDist is used to 
       scale distance violations in this calculation. 
 
     For useSingleAssignment=True, a single PeakAssignment is activated,
     whie for useSingleAssignment=False, zero or more PeakAssignments
     are activated using an analogous procedure.
 
  Results are queried with these accessor methods:
 
   numActivePeakAssigns() - self-explanatory
   isActive()             - True if at least one PeakAssignment is active
   isInactive()           - True if no PeakAssignment is active
   chosenPeakAssignment() - return PeakAssignment chosen by updateActivation(),
                            only if useSingleAssignment=True.
 
  updateInWrongNeighborhood(cutoff) - support for marking PeakAssignments as 
                                      in wrong neighborhood, based on their
                                      distance and their shiftAssignments'
                                      neighborhood flags
 
  updateShiftAssignmentActivePeakPositions() - support for shiftAssignment's 
                                               likelihood calculation
 
  State-saving:
    resetSavedState()
    saveCurrentState()
    revertToSavedState()
 
 Peak-wise energy:
  EnergyReport calcEnergy(useQuadraticPotential, 
                          forceConst, 
                          switchViol) 
 
  Currently, the crowded concept is not implemented, and the following
  methods are not used:
  
   isCrowded()
   setIsCrowded()
   setNotCrowded()
 
class PeakAssignment;:
 
 A PeakAssignment is a type that correlates a pair of ShiftAssignments
 with a Peak.
 
 PeakAssignments can specfify multiple "to" and "from" atoms, with R-6 sum
 averaging of their distances.  They can be given corrections to apply
 to the upper and lower distance bounds used in their violation
 calculation (eg., if this PeakAssignment involves a methyl, one might
 like to add  half an Angstrom to the distance estimated from the 
 NOE's intensity). PeakAssignments can also be assigned an estimate of
 their likelihood, based on the previous pass's results. PeakAssignments do
 not calculate that likelihood themselves.
 
  Constructor:
 
    PeakAssignment(name) - name is a string argument
 
  Methods:
 
  name() - return name given during construction
 
Functions to manipulate notations in the note member:
 
  note()            - return the notation string.
  setNote(val)      - set note to string val
  appendToNote(val) - append string val to existing note
 
Read/Write Accessors (read using value(), set using setValue(newVal)):
 
  toAssignment       - the to ShiftAssignment
  fromAssignment     - the from ShiftAssignment
  upBoundCorrection  - distance correction to apply to this PeakAssignment's
                       upper bound
  lowBoundCorrection - distance correction to apply to this PeakAssignment's
                       lower bound
  nMono              - value used in distance calculation for
                       ambiguous ShiftAssignments in symmetric multimers - 
                       should be set to the number of subunits. See
                       documentation for noePot.NOEPot. [Default: 1]
  aveExp             - exponent to use in computation of distance for
                       ambiguous ShiftAssignments. See documentation for
                       noePot.NOEPot. [Default: 6]
 
Read-only Accessors (read using value()):
 
  toAssignmentName   - return toAssignment.name()
  fromAssignmentName - return fromAssignment.name()
 
  toProtonSelection   - toAssignment.protonSelection
  fromProtonSelection - an atomSel.AtomSel
 
  distance() - distance computed between atoms in the to and from
               ShiftAssignment proton selections.
 
  violation(upBound,lowBound) - violation given the upper and lower
                                distance bounds, the current
                                distance() value, and the upper and
                                lower bounds corrections.
 
    Accessors for the shift table entries that matched this peakAssignment to
    its peak
 
  hasFromProtonShift()    - whether the specified shift is present
  hasToProtonShift()
  hasFromHeavyatomShift()
  hasToHeavyatomShift()
  fromProtonShift()    - the value of the specified chemical shift
  toProtonShift()
  fromHeavyatomShift()
  toHeavyatomShift()
 
 
    Accessors for the unfolded position of this PeakAssignment's NOE peak 
    position
 
  resetUnfoldedFromProtonPeakPosition()   - set specified value to invalid
  resetUnfoldedFromHeavyatomPeakPosition()  value
  resetUnfoldedToProtonPeakPosition()
  resetUnfoldedToHeavyatomPeakPosition()
 
  hasUnfoldedFromProtonPeakPosition()   - return boolean indicating presence
  hasUnfoldedFromHeavyatomPeakPosition()  of specified shift value
  hasUnfoldedToProtonPeakPosition() 
  hasUnfoldedToHeavyatomPeakPosition() 
 
  unfoldedFromProtonPeakPosition()    - chemical shift value of specified
  unfoldedFromHeavyatomPeakPosition()   peak dimension. These are settable
  unfoldedToProtonPeakPosition()
  unfoldedToHeavyatomPeakPosition()
 
    Accessors for the good/bad flag which indicates whether this PeakAssignment
    is violated in some reference structure.
 
  setGood()
  setBad()
  isGood()
 
   Manipulate the previousLikelihood member:
 
  resetPreviousLikelihood()  - set to invalid value
  hasPreviousLikelihood()    - has a valid value
  previousLikelihood()       - the value
  setPreviousLikelihood(val) - set the value
  
    Set/query the activation state
 
  isActive()  - query
  activate()  - setters
  inactivate()
 
      Manipulate inWrongNeighborhood state
 
  updateInWrongNeighborhood(cutoff) - marks this PeakAssignment as being in
                                      the right or wrong neighborhood,
                                      based on its distance violation
                                      (relative to cutoff) and its 
                                      ShiftAssignments' neighborhood flags
  inWrongNeighborhood()        - getter
  setInWrongNeighborhood(bool) - setter
 
 
    Saving activation state
 
  resetSavedState()
  saveCurrentState()
  revertToSavedState()
 
    PeakAssignments whose activation is linked to this one -
    manipulated by name or value
 
  addLinkedPeakAssignmentName(peakName, assName)
  resetLinkedPeakAssignmentNames();
  linkedPeakAssignmentNames()
  removeLinkedPeakAssignmentName(peakName, assName)
  resetLinkedPeakAssignments();
  addLinkedPeakAssignment(peakAssignment)
  linkedPeakAssignments()
 
    Primary sequence distance - see description above for the Peak class
 
  updatePrimarySeqDist() - compute
  primarySeqDist()       - read-only accessors
  isIntraresidue()
  isBackboneSequential()
  isSequential()         - return True if any of the from- and to-
                           shiftAssigments are between adjacent
                           residues, else False. 
  isShortRange(deltaRes) - return True if none of the from- and to-
                           shiftAssigments are between adjacent
                           residues, and the smallest primary sequence
                           distance is less than deltaRes, else False.
  isLongRange(deltaRes)  - return True if the smallest primary sequence
                           distance is greater than or equal to deltaRes,
                           else False.
  isIntermolecular()     - return True if the assignments are intermolecular,
                           and none is intramolecular, else False
 
    isBackbone flag - the selection is hard-wired, and this flag is
    not currently used in PASD functionality. If it were to be used,
    the selection should be made settable. It is currently hard-wired
    to the selection string "name HA HA* HB HB* HN HT* H"
 
  isBackbone() - boolean: whether or not this PeakAssignment's
                 proton selections only involve protein backbone atoms.
  updateIsBackbone() - recompute this value.
 
 
    Intersecting selections flag: True if the atom selections of the
    ShiftAssignments for the from and to protons overlap.
 
  selectionsIntersect()       - query value - returns a bool
  updateSelectionsIntersect() - recompute value
 
    Number of peakAssign filters that this PeakAssignment failed -
    this value is manipulated and used by the network filter.
 
  numFiltersFailed()          - query accessor
  resetNumFiltersFailed()     - reset to zero
  incrementNumFiltersFailed() - increment the value
 
     Not Documented:
 
  calcEnergy(useQuadraticPotential,
             forceConst,
             switchViol,
             upBound,
             lowBound)
 
  updateActivation(upBound, 
                   lowBound,
                   characteristicDist, 
                   violationWeight,
                   previousLikelihoodWeight)
 
 
class ShiftAssignment:
 
 This object contains an atomSel for the proton, an optional atomSel for its 
 connected heavy atom, the raw shift values for both (in ppm), and indication
 as to whether it represents an assignment along the "from" or "to" axis/axes.
 It is intended for use with both normal NOE assignments and inverse 
 (repulsive) NOEs.
 
// It also has flags for whether it's a methyl group, 
// whether , whether it's currently in the correct neighborhood, and 
// whether it's compatible with a reference structure.
 
  Constructor:
  
    ShiftAssignment(name) - name is a string argument
 
Functions to manipulate notations in the note member:
 
  note()            - return the notation string.
  setNote(val)      - set note to string val
  appendToNote(val) - append string val to existing note
 
   These read/write accessors correspond to the primary quantities of
   the ShiftAssignment: the specified selection or its string, the
   associated chemical shift(s) and the axis identity.
 
  protonSelection
  protonSelectionString
  heavyatomSelection
  heavyatomSelectionString
  protonShift
  heavyatomShift
  isFrom
  isTo
  foldedSign       - the value +/-1
  foldedProtonShift
  foldedHeavyatomShift
  protonTolerance
  heavyatomTolerance
  previousLikelihood
  noeCompleteness
 
    Associated are these query accessors and resetters:
 
  hasProtonSelection()     - return bool value
  hasHeavyatomSelection()
  hasProtonShift()
  hasHeavyatomShift()
  hasFoldedProtonShift()
  hasFoldedHeavyatomShift()
  hasProtonTolerance()
  hasHeavyatomTolerance()
  hasPreviousLikelihood()
  hasNoeCompleteness()
 
  resetProtonShift()
  resetHeavyatomShift()
  resetFoldedProtonShift()
  resetFoldedHeavyatomShift()
  resetProtonTolerance()
  resetHeavyatomTolerance()
  resetPreviousLikelihood()
  resetNoeCompleteness()
 
    The toFromPartner ShiftAssignment for protons which appear in both
    from and to axes.
 
    Read/write accessors
    
      toFromPartner     - ShiftAssignment of partner
      toFromPartnerName - name of partner ShiftAssignment
 
    Query accessors - returns a bool
 
       hasToFromPartner()
       hasToFromPartnerName()
 
    Resetters - to a blank state
 
      resetToFromPartner()
      resetToFromPartnerName()
  
    The stereoPartner ShiftAssignment (e.g. for methylene protons)
 
    Read/write accessors
 
      stereoPartner     - by ShiftAssignment value
      stereoPartnerName - by name
 
    Query accessors - returns a bool
 
      hasStereoPartner() 
      hasStereoPartnerName()
 
    Resetters - to a blank state
 
      resetStereoPartnerName()
      resetStereoPartner()
 
    Linked ShiftAssignment manipulation
 
      addLinkedShiftAssignment(val)
      addLinkedShiftAssignmentName(name)
      linkedShiftAssignments()           - returns a list of ShiftAssignments
      linkedShiftAssignmentNames()
      numLinkedShiftAssignments()
      removeAllLinkedShiftAssignments()
      removeLinkedShiftAssignmentName(name)
 
 
 
  void resetProtonPeakPositions();
  void recordProtonPeakPosition(const String& newName,
                                      float_type newVal,
                                      int bothInRightNeighborhood);
  float_type protonPeakPositionScatter();
  CDSList<float_type> scatterValues(int rightNeighborhoodsOnly);
 
  updateInWrongNeighborhood(charNoeCompleteness,
                            charScatter,
                            prevLikeliWeight,
                            completenessWeight,
                            scatterWeight)
 
   Probabilistic updating of inWrongNeighborhood flags of all
   linkedShiftAssignments (including this ShiftAssignment, and any
   possible to/FromPartner), based on an overall likelihood computed as the
   scaled sum of weighted completeness, scatter and previous likelihoods.
  
      Access with:
      inWrongNeighborhood()          - getter
      setInWrongNeighborhood( bool ) - setter
 
 
 
  float_type distanceToShiftAssignment(const ShiftAssignment *otherShiftAssignment) const;
 
  int shiftAssignWithinDist(const ShiftAssignment* otherShiftAssignment, 
                            const float_type&      cutoff) const;
 
  int primarySeqDistToSA(const ShiftAssignment *otherShiftAssignment) const;
 
  int isMonomericallyEqualTo(const ShiftAssignment* otherShiftAssignment) const;
 
 
    Methods to manipulate various boolean flags:
 
      isMethyl()    - isMethyl
      setIsMethyl()
      setNotMethyl()
  
      isGood()   - isGood
      setGood()
      setBad()
 
    State-saving:
 
      resetSavedState()
      saveCurrentState()
      revertToSavedState()
 
    Undocumented:
    
      cachedIndex()
      resetCachedIndex()
      hasCachedIndex()
      setCachedIndex(val)
 
      numAccountedNeighbors()
      resetNumAccountedNeighbors()
      incrementNumAccountedNeighbors()
      
      numUnaccountedNeighbors()
      resetNumUnaccountedNeighbors()
      incrementNumUnaccountedNeighbors()
 
 
 
# This file was automatically generated by SWIG (http://www.swig.org).
# Version 4.0.2
#
# Do not make changes to this file unless you know what you are doing--modify
# the SWIG interface file instead.

Classes
		builtins.object CDSlist_PeakAssignmentPtr CDSlist_ShiftAssignmentPtr Peak PeakAssignment ShiftAssignment   class CDSlist_PeakAssignmentPtr(builtins.object)     CDSlist_PeakAssignmentPtr(*args)       Methods defined here: __delitem__(self, *args, **kwargs) -> 'void' __getitem__(self, *args) -> 'CDSList< PeakAssignment * >' __getslice__(self, *args, **kwargs) -> 'CDSList< PeakAssignment * >' __init__(self, *args) Initialize self.  See help(type(self)) for accurate signature. __len__(self, *args, **kwargs) -> 'int' __repr__ = _swig_repr(self) __setitem__(self, *args, **kwargs) -> 'void' append(self, *args, **kwargs) -> 'void' help(self, *args, **kwargs) -> 'String' remove(self, *args, **kwargs) -> 'void' removeAll(self, *args, **kwargs) -> 'void' Static methods defined here: __swig_destroy__ = delete_CDSlist_PeakAssignmentPtr(...) Data descriptors defined here: __dict__   dictionary for instance variables (if defined) __weakref__   list of weak references to the object (if defined) thisown   The membership flag   class CDSlist_ShiftAssignmentPtr(builtins.object)     CDSlist_ShiftAssignmentPtr(*args)       Methods defined here: __delitem__(self, *args, **kwargs) -> 'void' __getitem__(self, *args) -> 'CDSList< ShiftAssignment * >' __getslice__(self, *args, **kwargs) -> 'CDSList< ShiftAssignment * >' __init__(self, *args) Initialize self.  See help(type(self)) for accurate signature. __len__(self, *args, **kwargs) -> 'int' __repr__ = _swig_repr(self) __setitem__(self, *args, **kwargs) -> 'void' append(self, *args, **kwargs) -> 'void' help(self, *args, **kwargs) -> 'String' remove(self, *args, **kwargs) -> 'void' removeAll(self, *args, **kwargs) -> 'void' Static methods defined here: __swig_destroy__ = delete_CDSlist_ShiftAssignmentPtr(...) Data descriptors defined here: __dict__   dictionary for instance variables (if defined) __weakref__   list of weak references to the object (if defined) thisown   The membership flag   class Peak(builtins.object)     Peak(*args, **kwargs)       Methods defined here: __init__(self, *args, **kwargs) Initialize self.  See help(type(self)) for accurate signature. __repr__ = _swig_repr(self) activateAllPeakAssigns(self, *args, **kwargs) -> 'void' addPeakAssignment(self, *args, **kwargs) -> 'void' addShiftAssignment(self, *args, **kwargs) -> 'void' appendToNote(self, *args, **kwargs) -> 'void' calcEnergy(self, *args, **kwargs) -> 'EnergyReport' calcEnergyAndDerivs(self, *args, **kwargs) -> 'EnergyReport' chosenPeakAssignment(self, *args, **kwargs) -> 'PeakAssignment *' fromHeavyatomShift(self, *args, **kwargs) -> 'float_type' fromProtonShift(self, *args, **kwargs) -> 'float_type' fromShiftAssignments(self, *args, **kwargs) -> 'CDSList< ShiftAssignment const * >' hasFromHeavyatomShift(self, *args, **kwargs) -> 'int' hasFromProtonShift(self, *args, **kwargs) -> 'int' hasIntensity(self, *args, **kwargs) -> 'int' hasPeakAssignmentNamed(self, *args, **kwargs) -> 'int' hasShiftAssignmentNamed(self, *args, **kwargs) -> 'bool' hasToHeavyatomShift(self, *args, **kwargs) -> 'int' hasToProtonShift(self, *args, **kwargs) -> 'int' inactivateAllPeakAssigns(self, *args, **kwargs) -> 'void' intensity(self, *args, **kwargs) -> 'float_type' isActive(self, *args, **kwargs) -> 'int' isAssigned(self, *args, **kwargs) -> 'int' isCrowded(self, *args, **kwargs) -> 'int' isGood(self, *args, **kwargs) -> 'int' isInactive(self, *args, **kwargs) -> 'int' isIntermolecular(self, *args, **kwargs) -> 'int' isIntraresidue(self, *args, **kwargs) -> 'int' isLongRange(self, *args, **kwargs) -> 'int' isSequential(self, *args, **kwargs) -> 'int' isShortRange(self, *args, **kwargs) -> 'int' lowBound(self, *args, **kwargs) -> 'float_type' lowestViolation(self, *args, **kwargs) -> 'float_type' lowestViolationsPrimarySeqDist(self, *args, **kwargs) -> 'int' name(self, *args, **kwargs) -> 'String const &' note(self, *args, **kwargs) -> 'String const &' numActivePeakAssigns(self, *args, **kwargs) -> 'int' numFromShiftAssignments(self, *args, **kwargs) -> 'int' numPeakAssignments(self, *args, **kwargs) -> 'int' numToShiftAssignments(self, *args, **kwargs) -> 'int' peakAssignmentNamed(self, *args, **kwargs) -> 'PeakAssignment *' peakAssignments(self, *args, **kwargs) -> 'CDSList< PeakAssignmentPtr >' peakAssignmentsWithShiftAssignmentNamed(self, *args, **kwargs) -> 'CDSList< PeakAssignmentPtr >' peakAssignments_sorted(self, *args, **kwargs) -> 'CDSList< PeakAssignmentPtr >' prevLikelihood(self, *args, **kwargs) -> 'float_type' primarySeqDist(self, *args, **kwargs) -> 'int' pyXplorHelp(self, *args, **kwargs) -> 'String' removeAllPeakAssignments(self, *args, **kwargs) -> 'void' removeAllShiftAssignments(self, *args, **kwargs) -> 'void' removePeakAssignmentNamed(self, *args, **kwargs) -> 'void' removeShiftAssignmentNamed(self, *args, **kwargs) -> 'void' resetFromHeavyatomShift(self, *args, **kwargs) -> 'void' resetFromProtonShift(self, *args, **kwargs) -> 'void' resetIntensity(self, *args, **kwargs) -> 'void' resetSavedState(self, *args, **kwargs) -> 'void' resetToHeavyatomShift(self, *args, **kwargs) -> 'void' resetToProtonShift(self, *args, **kwargs) -> 'void' revertToSavedState(self, *args, **kwargs) -> 'void' saveCurrentState(self, *args, **kwargs) -> 'void' setFromHeavyatomShift(self, *args, **kwargs) -> 'void' setFromProtonShift(self, *args, **kwargs) -> 'void' setIntensity(self, *args, **kwargs) -> 'void' setIsCrowded(self, *args, **kwargs) -> 'void' setLowBound(self, *args, **kwargs) -> 'void' setNotCrowded(self, *args, **kwargs) -> 'void' setNote(self, *args, **kwargs) -> 'void' setToHeavyatomShift(self, *args, **kwargs) -> 'void' setToProtonShift(self, *args, **kwargs) -> 'void' setUpBound(self, *args, **kwargs) -> 'void' shiftAssignmentNamed(self, *args, **kwargs) -> 'ShiftAssignment const *' toHeavyatomShift(self, *args, **kwargs) -> 'float_type' toProtonShift(self, *args, **kwargs) -> 'float_type' toShiftAssignments(self, *args, **kwargs) -> 'CDSList< ShiftAssignment const * >' upBound(self, *args, **kwargs) -> 'float_type' updateActivation(self, *args, **kwargs) -> 'void' updateInWrongNeighborhood(self, *args, **kwargs) -> 'void' updatePrimarySeqDist(self, *args, **kwargs) -> 'void' updateShiftAssignmentActivePeakPositions(self, *args, **kwargs) -> 'void' Static methods defined here: __swig_destroy__ = delete_Peak(...) match4d(*args, **kwargs) -> 'void' Data descriptors defined here: __dict__   dictionary for instance variables (if defined) __weakref__   list of weak references to the object (if defined) thisown   The membership flag   class PeakAssignment(builtins.object)     PeakAssignment(*args, **kwargs)       Methods defined here: __init__(self, *args, **kwargs) Initialize self.  See help(type(self)) for accurate signature. __repr__ = _swig_repr(self) active(self, *args, **kwargs) -> 'bool const' addLinkedPeakAssignment(self, *args, **kwargs) -> 'void' addLinkedPeakAssignmentName(self, *args, **kwargs) -> 'void' appendToNote(self, *args, **kwargs) -> 'void' aveExp(self, *args, **kwargs) -> 'float_type const' calcEnergy(self, *args, **kwargs) -> 'EnergyReport' calcEnergyAndDerivs(self, *args, **kwargs) -> 'EnergyReport' distance(self, *args, **kwargs) -> 'float_type' fromAssignment(self, *args, **kwargs) -> 'ShiftAssignment *' fromAssignmentName(self, *args, **kwargs) -> 'String' fromHeavyatomShift(self, *args, **kwargs) -> 'float_type' fromProtonSelection(self, *args, **kwargs) -> 'AtomSel *' fromProtonShift(self, *args, **kwargs) -> 'float_type' hasFromHeavyatomShift(self, *args, **kwargs) -> 'int' hasFromProtonShift(self, *args, **kwargs) -> 'int' hasPreviousLikelihood(self, *args, **kwargs) -> 'int' hasToHeavyatomShift(self, *args, **kwargs) -> 'int' hasToProtonShift(self, *args, **kwargs) -> 'int' hasUnfoldedFromHeavyatomPeakPosition(self, *args, **kwargs) -> 'int' hasUnfoldedFromProtonPeakPosition(self, *args, **kwargs) -> 'int' hasUnfoldedToHeavyatomPeakPosition(self, *args, **kwargs) -> 'int' hasUnfoldedToProtonPeakPosition(self, *args, **kwargs) -> 'int' inWrongNeighborhood(self, *args, **kwargs) -> 'bool const' incrementNumFiltersFailed(self, *args, **kwargs) -> 'void' isBackbone(self, *args, **kwargs) -> 'int' isBackboneSequential(self, *args, **kwargs) -> 'int' isGood(self, *args, **kwargs) -> 'int' isIntermolecular(self, *args, **kwargs) -> 'int' isIntraresidue(self, *args, **kwargs) -> 'int' isLongRange(self, *args, **kwargs) -> 'int' isSequential(self, *args, **kwargs) -> 'int' isShortRange(self, *args, **kwargs) -> 'int' linkedPeakAssignmentNames(self, *args, **kwargs) -> 'CDSList< String >' linkedPeakAssignments(self, *args, **kwargs) -> 'CDSList< PeakAssignment * >' lowBoundCorrection(self, *args, **kwargs) -> 'float_type' nMono(self, *args, **kwargs) -> 'int const' name(self, *args, **kwargs) -> 'String const &' note(self, *args, **kwargs) -> 'String const &' numFiltersFailed(self, *args, **kwargs) -> 'int' previousLikelihood(self, *args, **kwargs) -> 'float_type' primarySeqDist(self, *args, **kwargs) -> 'int' removeLinkedPeakAssignmentName(self, *args, **kwargs) -> 'void' resetLinkedPeakAssignmentNames(self, *args, **kwargs) -> 'void' resetLinkedPeakAssignments(self, *args, **kwargs) -> 'void' resetNumFiltersFailed(self, *args, **kwargs) -> 'void' resetPreviousLikelihood(self, *args, **kwargs) -> 'void' resetSavedState(self, *args, **kwargs) -> 'void' resetUnfoldedFromHeavyatomPeakPosition(self, *args, **kwargs) -> 'void' resetUnfoldedFromProtonPeakPosition(self, *args, **kwargs) -> 'void' resetUnfoldedToHeavyatomPeakPosition(self, *args, **kwargs) -> 'void' resetUnfoldedToProtonPeakPosition(self, *args, **kwargs) -> 'void' revertToSavedState(self, *args, **kwargs) -> 'void' saveCurrentState(self, *args, **kwargs) -> 'void' selectionsIntersect(self, *args, **kwargs) -> 'int' setActive(self, *args, **kwargs) -> 'void' setAveExp(self, *args, **kwargs) -> 'void' setBad(self, *args, **kwargs) -> 'void' setFromAssignment(self, *args, **kwargs) -> 'void' setGood(self, *args, **kwargs) -> 'void' setInWrongNeighborhood(self, *args, **kwargs) -> 'void' setLowBoundCorrection(self, *args, **kwargs) -> 'void' setNMono(self, *args, **kwargs) -> 'void' setNote(self, *args, **kwargs) -> 'void' setPreviousLikelihood(self, *args, **kwargs) -> 'void' setToAssignment(self, *args, **kwargs) -> 'void' setUnfoldedFromHeavyatomPeakPosition(self, *args, **kwargs) -> 'void' setUnfoldedFromProtonPeakPosition(self, *args, **kwargs) -> 'void' setUnfoldedToHeavyatomPeakPosition(self, *args, **kwargs) -> 'void' setUnfoldedToProtonPeakPosition(self, *args, **kwargs) -> 'void' setUpBoundCorrection(self, *args, **kwargs) -> 'void' toAssignment(self, *args, **kwargs) -> 'ShiftAssignment *' toAssignmentName(self, *args, **kwargs) -> 'String' toHeavyatomShift(self, *args, **kwargs) -> 'float_type' toProtonSelection(self, *args, **kwargs) -> 'AtomSel *' toProtonShift(self, *args, **kwargs) -> 'float_type' unfoldedFromHeavyatomPeakPosition(self, *args, **kwargs) -> 'float_type' unfoldedFromProtonPeakPosition(self, *args, **kwargs) -> 'float_type' unfoldedToHeavyatomPeakPosition(self, *args, **kwargs) -> 'float_type' unfoldedToProtonPeakPosition(self, *args, **kwargs) -> 'float_type' upBoundCorrection(self, *args, **kwargs) -> 'float_type' updateActivation(self, *args, **kwargs) -> 'void' updateInWrongNeighborhood(self, *args, **kwargs) -> 'void' updateIsBackbone(self, *args, **kwargs) -> 'void' updatePrimarySeqDist(self, *args, **kwargs) -> 'void' updateSelectionsIntersect(self, *args, **kwargs) -> 'void' violation(self, *args, **kwargs) -> 'float_type' Static methods defined here: __swig_destroy__ = delete_PeakAssignment(...) Data descriptors defined here: __dict__   dictionary for instance variables (if defined) __weakref__   list of weak references to the object (if defined) thisown   The membership flag Data and other attributes defined here: defaultAveExp = 6   class ShiftAssignment(builtins.object)     ShiftAssignment(*args, **kwargs)       Methods defined here: __init__(self, *args, **kwargs) Initialize self.  See help(type(self)) for accurate signature. __repr__ = _swig_repr(self) addLinkedShiftAssignment(self, *args, **kwargs) -> 'void' addLinkedShiftAssignmentName(self, *args, **kwargs) -> 'void' appendToNote(self, *args, **kwargs) -> 'void' cachedIndex(self, *args, **kwargs) -> 'int' distanceToShiftAssignment(self, *args, **kwargs) -> 'float_type' foldedHeavyatomShift(self, *args, **kwargs) -> 'float_type' foldedProtonShift(self, *args, **kwargs) -> 'float_type' foldedSign(self, *args, **kwargs) -> 'int' hasCachedIndex(self, *args, **kwargs) -> 'int' hasFoldedHeavyatomShift(self, *args, **kwargs) -> 'int' hasFoldedProtonShift(self, *args, **kwargs) -> 'int' hasHeavyatomSelection(self, *args, **kwargs) -> 'bool' hasHeavyatomShift(self, *args, **kwargs) -> 'bool' hasHeavyatomTolerance(self, *args, **kwargs) -> 'bool' hasNoeCompleteness(self, *args, **kwargs) -> 'int' hasPreviousLikelihood(self, *args, **kwargs) -> 'int' hasProtonSelection(self, *args, **kwargs) -> 'int' hasProtonShift(self, *args, **kwargs) -> 'int' hasProtonTolerance(self, *args, **kwargs) -> 'int' hasStereoPartner(self, *args, **kwargs) -> 'int' hasStereoPartnerName(self, *args, **kwargs) -> 'int' hasToFromPartner(self, *args, **kwargs) -> 'int' hasToFromPartnerName(self, *args, **kwargs) -> 'int' heavyatomSelection(self, *args, **kwargs) -> 'AtomSel *' heavyatomSelectionString(self, *args, **kwargs) -> 'String' heavyatomShift(self, *args, **kwargs) -> 'float_type' heavyatomTolerance(self, *args, **kwargs) -> 'float_type' inWrongNeighborhood(self, *args, **kwargs) -> 'bool const' incrementNumAccountedNeighbors(self, *args, **kwargs) -> 'void' incrementNumUnaccountedNeighbors(self, *args, **kwargs) -> 'void' isFrom(self, *args, **kwargs) -> 'int' isGood(self, *args, **kwargs) -> 'int' isMethyl(self, *args, **kwargs) -> 'int' isMonomericallyEqualTo(self, *args, **kwargs) -> 'int' isTo(self, *args, **kwargs) -> 'int' linkedShiftAssignmentNames(self, *args, **kwargs) -> 'CDSList< String >' linkedShiftAssignments(self, *args, **kwargs) -> 'CDSList< ShiftAssignment * >' name(self, *args, **kwargs) -> 'String const &' noeCompleteness(self, *args, **kwargs) -> 'float_type' note(self, *args, **kwargs) -> 'String const &' numAccountedNeighbors(self, *args, **kwargs) -> 'int' numLinkedShiftAssignments(self, *args, **kwargs) -> 'int' numUnaccountedNeighbors(self, *args, **kwargs) -> 'int' previousLikelihood(self, *args, **kwargs) -> 'float_type' primarySeqDistToSA(self, *args, **kwargs) -> 'int' protonPeakPositionScatter(self, *args, **kwargs) -> 'float_type' protonSelection(self, *args, **kwargs) -> 'AtomSel *' protonSelectionString(self, *args, **kwargs) -> 'String' protonShift(self, *args, **kwargs) -> 'float_type' protonTolerance(self, *args, **kwargs) -> 'float_type' recordProtonPeakPosition(self, *args, **kwargs) -> 'void' removeAllLinkedShiftAssignments(self, *args, **kwargs) -> 'void' removeLinkedShiftAssignmentName(self, *args, **kwargs) -> 'void' resetCachedIndex(self, *args, **kwargs) -> 'void' resetFoldedHeavyatomShift(self, *args, **kwargs) -> 'void' resetFoldedProtonShift(self, *args, **kwargs) -> 'void' resetHeavyatomShift(self, *args, **kwargs) -> 'void' resetHeavyatomTolerance(self, *args, **kwargs) -> 'void' resetNoeCompleteness(self, *args, **kwargs) -> 'void' resetNumAccountedNeighbors(self, *args, **kwargs) -> 'void' resetNumUnaccountedNeighbors(self, *args, **kwargs) -> 'void' resetPreviousLikelihood(self, *args, **kwargs) -> 'void' resetProtonPeakPositions(self, *args, **kwargs) -> 'void' resetProtonShift(self, *args, **kwargs) -> 'void' resetProtonTolerance(self, *args, **kwargs) -> 'void' resetSavedState(self, *args, **kwargs) -> 'void' resetStereoPartner(self, *args, **kwargs) -> 'void' resetStereoPartnerName(self, *args, **kwargs) -> 'void' resetToFromPartner(self, *args, **kwargs) -> 'void' resetToFromPartnerName(self, *args, **kwargs) -> 'void' revertToSavedState(self, *args, **kwargs) -> 'void' saveCurrentState(self, *args, **kwargs) -> 'void' scatterValues(self, *args, **kwargs) -> 'CDSList< float_type >' setBad(self, *args, **kwargs) -> 'void' setCachedIndex(self, *args, **kwargs) -> 'void' setFoldedHeavyatomShift(self, *args, **kwargs) -> 'void' setFoldedProtonShift(self, *args, **kwargs) -> 'void' setFoldedSign(self, *args, **kwargs) -> 'void' setGood(self, *args, **kwargs) -> 'void' setHeavyatomSelection(self, *args, **kwargs) -> 'void' setHeavyatomSelectionString(self, *args, **kwargs) -> 'void' setHeavyatomShift(self, *args, **kwargs) -> 'void' setHeavyatomTolerance(self, *args, **kwargs) -> 'void' setInWrongNeighborhood(self, *args, **kwargs) -> 'void' setIsFrom(self, *args, **kwargs) -> 'void' setIsMethyl(self, *args, **kwargs) -> 'void' setIsTo(self, *args, **kwargs) -> 'void' setNoeCompleteness(self, *args, **kwargs) -> 'void' setNotMethyl(self, *args, **kwargs) -> 'void' setNote(self, *args, **kwargs) -> 'void' setPreviousLikelihood(self, *args, **kwargs) -> 'void' setProtonSelection(self, *args, **kwargs) -> 'void' setProtonSelectionString(self, *args, **kwargs) -> 'void' setProtonShift(self, *args, **kwargs) -> 'void' setProtonTolerance(self, *args, **kwargs) -> 'void' setStereoPartner(self, *args, **kwargs) -> 'void' setStereoPartnerName(self, *args, **kwargs) -> 'void' setToFromPartner(self, *args, **kwargs) -> 'void' setToFromPartnerName(self, *args, **kwargs) -> 'void' shiftAssignWithinDist(self, *args, **kwargs) -> 'int' stereoPartner(self, *args, **kwargs) -> 'ShiftAssignment *' stereoPartnerName(self, *args, **kwargs) -> 'String' toFromPartner(self, *args, **kwargs) -> 'ShiftAssignment *' toFromPartnerName(self, *args, **kwargs) -> 'String' updateInWrongNeighborhood(self, *args, **kwargs) -> 'void' Static methods defined here: __swig_destroy__ = delete_ShiftAssignment(...) overlappingSAsByIndex(*args, **kwargs) -> 'CDSList< CDSList< int > >' Data descriptors defined here: __dict__   dictionary for instance variables (if defined) __weakref__   list of weak references to the object (if defined) thisown   The membership flag

Functions
		Peak_match4d(*args, **kwargs) -> 'void' ShiftAssignment_overlappingSAsByIndex(*args, **kwargs) -> 'CDSList< CDSList< int > >' overlappingSAs(sas) pyXplorHelp(*args) -> 'String'

Data
		cvar = <Swig global variables>