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bit Xplor-NIH VMD-XPLOR
Pydoc: module pasdPot
 
pasdPot		 index

FIX: add contents
 
int
PASDPot::computeRawPAScores(      CDSMap<String,float_type>& paScore,
                                  StringListStringMap&       peakToPAname,
                                  StringIntPairMap&          paToSApairIndex,
                            const String&                    initScoresFrom,
                            const AtomSel&                   bbSel,
                            const CDSList<String>&           fromSAnames,
                            const CDSList<String>&           toSAnames,
                            const CDSMap<String,int>&        nameToSAindex,
                            const CDSList<StringPair>&       knownContacts,
                            const bool                       preferIntra,
                            const float_type&                maxFailed)
 
    initScoresFrom: string with possible values:
       "previous", "degen", "uniform". Value "contacts" needs to be
       re-implemented.
 
 
  //
  // constructor/destructor
  //
 
  PASDPot(const String&     instanceName,
                           Simulation* defaultSimulation)
 
  PASD_DistPot distPot()
  PASD_InvPot  invPot()
  float_type distEnergy;
  float_type invEnergy;
  bool staleGradient;
  //
  // accessors
  //
 
  CDSList<ShiftAssignmentPtr> shiftAssignments();
  CDSList<ShiftAssignmentPtr> fromShiftAssignments();
  CDSList<ShiftAssignmentPtr> toShiftAssignments();
  int numShiftAssignments() const;
  int numFromShiftAssignments() const;
  int numToShiftAssignments() const;
  void addShiftAssignment(ShiftAssignmentPtr newVal);
  void removeShiftAssignmentNamed(const String &targetName);
  ShiftAssignmentPtr shiftAssignmentNamed(const String &targetName) const;
  int hasShiftAssignmentNamed(const String &targetName) const;
 
  Simulation* simulation() { return sim; }
 
  CDSList< PeakPtr > peaks();
  int numPeaks() const;
  void addPeak(Peak* newVal);
  void removePeakNamed(const String& targetName);
  PeakPtr peakNamed(const String& targetName) const;
  int hasPeakNamed(const String& targetName) const;
  void removePeakAssignmentsInvolving(const String& targetName);
 
  void clearMissingLinksToPeakAssignments();
 
  CDSList< PeakPtr > peaksWithShiftAssignmentNamed(const String& targetName);
  CDSList< PeakPtr > peaksWithShiftAssignmentsNamed(const String& targetName1, 
                                                    const String& targetName2);
 
  CDSList< ShiftAssignmentPtr > shiftAssignmentsWithPeakNamed(const String &targetName);
 
  void addException(const String& targetName1,
                    const String& targetName2);
 
  bool hasException(const String& targetName1,
                   const String& targetName2) const;
 
  void removeAllExceptions();
  void removeExceptionsInvolving(const String& targetName);
 
  CDSList< String > exceptions();
 
  void resetLinkedPeakAssignmentNames();
  void resetLinkedPeakAssignments();
  void updateLinkedPeakAssignments();
 
  void updatePrimarySeqDists();
  ACCESSOR(longRangePrimarySeqCutoff,LongRangePrimarySeqCutoff,int);
 
  void allowShiftAssignmentInactivation();
  void disallowShiftAssignmentInactivation();
  int allowsShiftAssignmentInactivation();
 
  void setSwitchViolation(float_type newVal);
  float_type switchViolation() const;
 
  float_type inverseBound() const;
  void setInverseBound(float_type newVal);
 
  float_type inverseMethylCorrection() const;
  void setInverseMethylCorrection(float_type newVal);
 
  ACCESSOR(previousLikelihoodWeight,PreviousLikelihoodWeight,float_type);
  ACCESSOR(distanceViolationWeight,DistanceViolationWeight,float_type );
  ACCESSOR(noeCompletenessWeight,NoeCompletenessWeight,float_type);
  ACCESSOR(scatterWeight,ScatterWeight,float_type);
  ACCESSOR(violationCutoff,ViolationCutoff,float_type);
  ACCESSOR(characteristicDistanceViol,CharacteristicDistanceViol, float_type );
  ACCESSOR(characteristicNoeCompleteness,CharacteristicNoeCompleteness,float_type);
  ACCESSOR(characteristicScatter,CharacteristicScatter, float_type );
 
  void setInverseNoeNeighborhoodSize(float_type newVal);
  float_type inverseNoeNeighborhoodSize() const;
 
  // false: useSingleAssignment
  ACCESSOR(useSingleAssignment,UseSingleAssignment,bool);
  ACCESSOR(maxMonteCarloAttempts,MaxMonteCarloAttempts,int);
  ACCESSOR(characteristicDeltaDV,CharacteristicDeltaDV,float_type);
  ACCESSOR(characteristicDeltaPL,CharacteristicDeltaPL,float_type);
  ACCESSOR(characteristicDeltaNoeCompleteness,
           CharacteristicDeltaNoeCompleteness,float_type);
  ACCESSOR(characteristicDeltaScatter,CharacteristicDeltaScatter,float_type);
  ACCESSOR(useQuadraticPot,UseQuadraticPot,bool);
  ACCESSOR(useOriginalViolationScore,UseOriginalViolationScore,bool);
 
  void saveCurrentState();
  void resetSavedState();
  void revertToSavedState();
 
  CDSList< float_type > updateActivation();
  void activateAllAssigns();
  void inactivateAllAssigns();
  void setAllShiftAssignmentsInRightNeighborhood();
 
 
  int numInactivePeaks() const;
  int numActivePeaks() const;
  int numShiftAssignmentsInWrongNeighborhood() const;
  float_type fracPeakAssignsInactive() const;
 
  float_type previousLikelihoodScore() const;
  float_type noeCompletenessScore() const;
  int numCloseShiftAssignmentPairs() const;
  int numCloseAccountedShiftAssignmentPairs() const;
  int numClosePAAccountedShiftAssignmentPairs() const;
 
  float_type scatterScore() const;
  float_type violationScore();
  float_type peakCoverageScore() const;
 
 
  float_type goodScore1() const;
  float_type goodScore2() const;
 
  //
  // likelihood calculation for shiftAssignments
  //
 
  void recordActivePeakAssignments();
  void updateNoeCompleteness();
  void updatePeakPositionScatter();
 
  //
  // NOE completeness-related reporting
  //
 
  CDSList< ShiftAssignmentPtr >expectedNeighbors(ShiftAssignmentPtr target);
  CDSList< ShiftAssignmentPtr >accountedNeighbors(ShiftAssignmentPtr target);
  CDSList< ShiftAssignmentPtr >unaccountedNeighbors(ShiftAssignmentPtr target);
 
  //
  // calculate energy without calculating derivs
  //
 
  float_type calcEnergy();
 
  EnergyReport calcNormalEnergy()  { return calcNormalEnergyAndDerivs(0); }
  EnergyReport calcInverseEnergy() { return calcInverseEnergyAndDerivs(0); }
 
  //
  // calculate energy & derivatives w/respect to atom positions. 
  // Records these derivs in the passed-in DerivList.
  //
 
  float_type calcEnergyAndDerivs(DerivList* aDerivList);
  
  // 
  // These are pure virtual functions defined by Pot.
  // They don't return anything useful yet
  //
  
  float_type rms()           { return deviation; }
  float_type violations()    { return -1; }
  int        numRestraints() const { return -1; }
 
  //
  // neighbor list support for inverse energy calc
  //
 
  void cacheNeighbors();
  int neighborsNeedUpdate();
 
calcNormalEnergyAndDerivs(DerivList* derivsp) - OpenMP parallelized
calcInverseEnergyAndDerivs(DerivList* derivs) - OpenMP parallelized
 
 
 
# 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_PeakPtr
Modified
ModifiedBase
PASDPot
PASDPot_LetterClass
PASD_DistPot
PASD_DistPot_LetterClass
PASD_InvPot
PASD_InvPot_LetterClass

 
class CDSList_PeakPtr(builtins.object)
    CDSList_PeakPtr(*args)
 

 
  Methods defined here:
__delitem__(self, *args, **kwargs) -> 'void'
__getitem__(self, *args) -> 'CDSList< Peak * >'
__getslice__(self, *args, **kwargs) -> 'CDSList< Peak * >'
__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_PeakPtr(...)
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 Modified(builtins.object)
    Modified(*args, **kwargs)
 

 
  Methods defined here:
__call__(self, *args, **kwargs) -> 'int'
Call self as a function.
__init__(self, *args, **kwargs)
Initialize self.  See help(type(self)) for accurate signature.
__repr__ = _swig_repr(self)
asString(self, *args, **kwargs) -> 'String'
assertClear(self, *args, **kwargs) -> 'void'
clear(self, *args, **kwargs) -> 'void'
set(self, *args, **kwargs) -> 'void'
update(self, *args, **kwargs) -> 'void'
value(self, *args, **kwargs) -> 'int'
Static methods defined here:
__swig_destroy__ = delete_Modified(...)
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:
MOD_SELF = 1
MOD_SIMULATION = 2

 
class ModifiedBase(builtins.object)
    ModifiedBase(*args, **kwargs)
 

 
  Methods defined here:
__init__(self, *args, **kwargs)
Initialize self.  See help(type(self)) for accurate signature.
__repr__ = _swig_repr(self)
registerTo(self, *args, **kwargs) -> 'void'
unRegister(self, *args, **kwargs) -> 'void'
updateValues(self, *args, **kwargs) -> 'void'
Static methods defined here:
__swig_destroy__ = delete_ModifiedBase(...)
Data descriptors defined here:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

 
list of weak references to the object (if defined)
modified

 
registeredSimulations

 
thisown

 
The membership flag

 
class PASDPot_LetterClass(builtins.object)
    PASDPot_LetterClass(*args, **kwargs)
 

 
  Methods defined here:
__init__(self, *args, **kwargs)
Initialize self.  See help(type(self)) for accurate signature.
__repr__ = _swig_repr(self)
accountedNeighbors(self, *args, **kwargs) -> 'CDSList< ShiftAssignmentPtr >'
activateAllAssigns(self, *args, **kwargs) -> 'void'
addException(self, *args, **kwargs) -> 'void'
addPeak(self, *args, **kwargs) -> 'void'
addShiftAssignment(self, *args, **kwargs) -> 'void'
allowShiftAssignmentInactivation(self, *args, **kwargs) -> 'void'
allowsShiftAssignmentInactivation(self, *args, **kwargs) -> 'int'
cacheNeighbors(self, *args, **kwargs) -> 'void'
calcEnergy(self, *args, **kwargs) -> 'float_type'
calcEnergyAndDerivs(self, *args, **kwargs) -> 'float_type'
calcInverseEnergy(self, *args, **kwargs) -> 'EnergyReport'
calcNormalEnergy(self, *args, **kwargs) -> 'EnergyReport'
characteristicDeltaDV(self, *args, **kwargs) -> 'float_type const'
characteristicDeltaNoeCompleteness(self, *args, **kwargs) -> 'float_type const'
characteristicDeltaPL(self, *args, **kwargs) -> 'float_type const'
characteristicDeltaScatter(self, *args, **kwargs) -> 'float_type const'
characteristicDistanceViol(self, *args, **kwargs) -> 'float_type const'
characteristicNoeCompleteness(self, *args, **kwargs) -> 'float_type const'
characteristicScatter(self, *args, **kwargs) -> 'float_type const'
clearMissingLinksToPeakAssignments(self, *args, **kwargs) -> 'void'
computeRawPAScores(self, *args, **kwargs) -> 'int'
disallowShiftAssignmentInactivation(self, *args, **kwargs) -> 'void'
distPot_cxx(self, *args, **kwargs) -> 'rc_DerivedPot< PASD_DistPot >'
distanceViolationWeight(self, *args, **kwargs) -> 'float_type const'
exceptions(self, *args, **kwargs) -> 'CDSList< String >'
expectedNeighbors(self, *args, **kwargs) -> 'CDSList< ShiftAssignmentPtr >'
fracPeakAssignsInactive(self, *args, **kwargs) -> 'float_type'
fromShiftAssignments(self, *args, **kwargs) -> 'CDSList< ShiftAssignmentPtr >'
goodScore1(self, *args, **kwargs) -> 'float_type'
goodScore2(self, *args, **kwargs) -> 'float_type'
hasException(self, *args, **kwargs) -> 'bool'
hasPeakNamed(self, *args, **kwargs) -> 'int'
hasShiftAssignmentNamed(self, *args, **kwargs) -> 'int'
inactivateAllAssigns(self, *args, **kwargs) -> 'void'
invPot_cxx(self, *args, **kwargs) -> 'rc_DerivedPot< PASD_InvPot >'
inverseBound(self, *args, **kwargs) -> 'float_type'
inverseMethylCorrection(self, *args, **kwargs) -> 'float_type'
inverseNoeNeighborhoodSize(self, *args, **kwargs) -> 'float_type'
longRangePrimarySeqCutoff(self, *args, **kwargs) -> 'int const'
maxMonteCarloAttempts(self, *args, **kwargs) -> 'int const'
neighborsNeedUpdate(self, *args, **kwargs) -> 'int'
noeCompletenessScore(self, *args, **kwargs) -> 'float_type'
noeCompletenessWeight(self, *args, **kwargs) -> 'float_type const'
numActivePeaks(self, *args, **kwargs) -> 'int'
numCloseAccountedShiftAssignmentPairs(self, *args, **kwargs) -> 'int'
numClosePAAccountedShiftAssignmentPairs(self, *args, **kwargs) -> 'int'
numCloseShiftAssignmentPairs(self, *args, **kwargs) -> 'int'
numFromShiftAssignments(self, *args, **kwargs) -> 'int'
numInactivePeaks(self, *args, **kwargs) -> 'int'
numPeaks(self, *args, **kwargs) -> 'int'
numRestraints(self, *args, **kwargs) -> 'int'
numShiftAssignments(self, *args, **kwargs) -> 'int'
numShiftAssignmentsInWrongNeighborhood(self, *args, **kwargs) -> 'int'
numToShiftAssignments(self, *args, **kwargs) -> 'int'
peakCoverageScore(self, *args, **kwargs) -> 'float_type'
peakNamed(self, *args, **kwargs) -> 'PeakPtr'
peaks(self, *args, **kwargs) -> 'CDSList< PeakPtr >'
peaksWithShiftAssignmentNamed(self, *args, **kwargs) -> 'CDSList< PeakPtr >'
peaksWithShiftAssignmentsNamed(self, *args, **kwargs) -> 'CDSList< PeakPtr >'
previousLikelihoodScore(self, *args, **kwargs) -> 'float_type'
previousLikelihoodWeight(self, *args, **kwargs) -> 'float_type const'
pyXplorHelp(self, *args, **kwargs) -> 'String'
recordActivePeakAssignments(self, *args, **kwargs) -> 'void'
removeAllExceptions(self, *args, **kwargs) -> 'void'
removeExceptionsInvolving(self, *args, **kwargs) -> 'void'
removePeakAssignmentsInvolving(self, *args, **kwargs) -> 'void'
removePeakNamed(self, *args, **kwargs) -> 'void'
removeShiftAssignmentNamed(self, *args, **kwargs) -> 'void'
resetLinkedPeakAssignmentNames(self, *args, **kwargs) -> 'void'
resetLinkedPeakAssignments(self, *args, **kwargs) -> 'void'
resetSavedState(self, *args, **kwargs) -> 'void'
revertToSavedState(self, *args, **kwargs) -> 'void'
rms(self, *args, **kwargs) -> 'float_type'
saveCurrentState(self, *args, **kwargs) -> 'void'
scatterScore(self, *args, **kwargs) -> 'float_type'
scatterWeight(self, *args, **kwargs) -> 'float_type const'
setAllShiftAssignmentsInRightNeighborhood(self, *args, **kwargs) -> 'void'
setCharacteristicDeltaDV(self, *args, **kwargs) -> 'void'
setCharacteristicDeltaNoeCompleteness(self, *args, **kwargs) -> 'void'
setCharacteristicDeltaPL(self, *args, **kwargs) -> 'void'
setCharacteristicDeltaScatter(self, *args, **kwargs) -> 'void'
setCharacteristicDistanceViol(self, *args, **kwargs) -> 'void'
setCharacteristicNoeCompleteness(self, *args, **kwargs) -> 'void'
setCharacteristicScatter(self, *args, **kwargs) -> 'void'
setDistanceViolationWeight(self, *args, **kwargs) -> 'void'
setInverseBound(self, *args, **kwargs) -> 'void'
setInverseMethylCorrection(self, *args, **kwargs) -> 'void'
setInverseNoeNeighborhoodSize(self, *args, **kwargs) -> 'void'
setLongRangePrimarySeqCutoff(self, *args, **kwargs) -> 'void'
setMaxMonteCarloAttempts(self, *args, **kwargs) -> 'void'
setNoeCompletenessWeight(self, *args, **kwargs) -> 'void'
setPreviousLikelihoodWeight(self, *args, **kwargs) -> 'void'
setScatterWeight(self, *args, **kwargs) -> 'void'
setSwitchViolation(self, *args, **kwargs) -> 'void'
setUseOriginalViolationScore(self, *args, **kwargs) -> 'void'
setUseQuadraticPot(self, *args, **kwargs) -> 'void'
setUseSingleAssignment(self, *args, **kwargs) -> 'void'
setViolationCutoff(self, *args, **kwargs) -> 'void'
shiftAssignmentNamed(self, *args, **kwargs) -> 'ShiftAssignmentPtr'
shiftAssignments(self, *args, **kwargs) -> 'CDSList< ShiftAssignmentPtr >'
shiftAssignmentsWithPeakNamed(self, *args, **kwargs) -> 'CDSList< ShiftAssignmentPtr >'
simulation(self, *args, **kwargs) -> 'Simulation *'
switchViolation(self, *args, **kwargs) -> 'float_type'
toShiftAssignments(self, *args, **kwargs) -> 'CDSList< ShiftAssignmentPtr >'
unaccountedNeighbors(self, *args, **kwargs) -> 'CDSList< ShiftAssignmentPtr >'
updateActivation(self, *args, **kwargs) -> 'CDSList< float_type >'
updateLinkedPeakAssignments(self, *args, **kwargs) -> 'void'
updateNoeCompleteness(self, *args, **kwargs) -> 'void'
updatePeakPositionScatter(self, *args, **kwargs) -> 'void'
updatePrimarySeqDists(self, *args, **kwargs) -> 'void'
useOriginalViolationScore(self, *args, **kwargs) -> 'bool const'
useQuadraticPot(self, *args, **kwargs) -> 'bool const'
useSingleAssignment(self, *args, **kwargs) -> 'bool const'
violationCutoff(self, *args, **kwargs) -> 'float_type const'
violationScore(self, *args, **kwargs) -> 'float_type'
violations(self, *args, **kwargs) -> 'float_type'
Static methods defined here:
__swig_destroy__ = delete_PASDPot_LetterClass(...)
Readonly properties defined here:
distPot_member

 
invPot_member

 
Data descriptors defined here:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

 
list of weak references to the object (if defined)
distEnergy

 
invEnergy

 
staleGradient

 
thisown

 
The membership flag

 
class PASD_DistPot_LetterClass(builtins.object)
    PASD_DistPot_LetterClass(*args, **kwargs)
 

 
  Methods defined here:
__init__(self, *args, **kwargs)
Initialize self.  See help(type(self)) for accurate signature.
__repr__ = _swig_repr(self)
calcEnergy(self, *args, **kwargs) -> 'float_type'
calcEnergyAndDerivs(self, *args, **kwargs) -> 'float_type'
numRestraints(self, *args, **kwargs) -> 'int'
pyXplorHelp(self, *args, **kwargs) -> 'String'
rms(self, *args, **kwargs) -> 'float_type'
violations(self, *args, **kwargs) -> 'float_type'
Static methods defined here:
__swig_destroy__ = delete_PASD_DistPot_LetterClass(...)
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 PASD_InvPot_LetterClass(builtins.object)
    PASD_InvPot_LetterClass(*args, **kwargs)
 

 
  Methods defined here:
__init__(self, *args, **kwargs)
Initialize self.  See help(type(self)) for accurate signature.
__repr__ = _swig_repr(self)
calcEnergy(self, *args, **kwargs) -> 'float_type'
calcEnergyAndDerivs(self, *args, **kwargs) -> 'float_type'
numRestraints(self, *args, **kwargs) -> 'int'
pyXplorHelp(self, *args, **kwargs) -> 'String'
rms(self, *args, **kwargs) -> 'float_type'
violations(self, *args, **kwargs) -> 'float_type'
Static methods defined here:
__swig_destroy__ = delete_PASD_InvPot_LetterClass(...)
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

 
realPASDPot = class PASDPot(builtins.object)
    realPASDPot(*args, **kwargs)
 

 
  Methods defined here:
__deref__(self, *args, **kwargs) -> 'PASDPot *'
__init__(self, *args, **kwargs)
__oldinit__ = __init__(self, *args, **kwargs)
__ref__(self, *args, **kwargs) -> 'PASDPot &'
__repr__ = _swig_repr(self)
accountedNeighbors(self, *args, **kwargs) -> 'CDSList< ShiftAssignmentPtr >'
activateAllAssigns(self, *args, **kwargs) -> 'void'
addException(self, *args, **kwargs) -> 'void'
addPeak(self, *args, **kwargs) -> 'void'
addShiftAssignment(self, *args, **kwargs) -> 'void'
allowShiftAssignmentInactivation(self, *args, **kwargs) -> 'void'
allowsShiftAssignmentInactivation(self, *args, **kwargs) -> 'int'
cacheNeighbors(self, *args, **kwargs) -> 'void'
calcEnergy(self, *args, **kwargs) -> 'float_type'
calcEnergyAndDerivs(self, *args, **kwargs) -> 'float_type'
calcInverseEnergy(self, *args, **kwargs) -> 'EnergyReport'
calcNormalEnergy(self, *args, **kwargs) -> 'EnergyReport'
characteristicDeltaDV(self, *args, **kwargs) -> 'float_type const'
characteristicDeltaNoeCompleteness(self, *args, **kwargs) -> 'float_type const'
characteristicDeltaPL(self, *args, **kwargs) -> 'float_type const'
characteristicDeltaScatter(self, *args, **kwargs) -> 'float_type const'
characteristicDistanceViol(self, *args, **kwargs) -> 'float_type const'
characteristicNoeCompleteness(self, *args, **kwargs) -> 'float_type const'
characteristicScatter(self, *args, **kwargs) -> 'float_type const'
clearMissingLinksToPeakAssignments(self, *args, **kwargs) -> 'void'
computeRawPAScores(self, *args, **kwargs) -> 'int'
decrRefCnt(self, *args, **kwargs) -> 'void'
disallowShiftAssignmentInactivation(self, *args, **kwargs) -> 'void'
distPot(self)
distPot_cxx(self, *args, **kwargs) -> 'rc_DerivedPot< PASD_DistPot >'
distanceViolationWeight(self, *args, **kwargs) -> 'float_type const'
exceptions(self, *args, **kwargs) -> 'CDSList< String >'
expectedNeighbors(self, *args, **kwargs) -> 'CDSList< ShiftAssignmentPtr >'
fracPeakAssignsInactive(self, *args, **kwargs) -> 'float_type'
fromShiftAssignments(self, *args, **kwargs) -> 'CDSList< ShiftAssignmentPtr >'
goodScore1(self, *args, **kwargs) -> 'float_type'
goodScore2(self, *args, **kwargs) -> 'float_type'
hasException(self, *args, **kwargs) -> 'bool'
hasPeakNamed(self, *args, **kwargs) -> 'int'
hasShiftAssignmentNamed(self, *args, **kwargs) -> 'int'
inactivateAllAssigns(self, *args, **kwargs) -> 'void'
incrRefCnt(self, *args, **kwargs) -> 'void'
instanceData(self, *args, **kwargs) -> 'PyObject *'
instanceName(self, *args, **kwargs) -> 'char const *'
invPot(self)
invPot_cxx(self, *args, **kwargs) -> 'rc_DerivedPot< PASD_InvPot >'
inverseBound(self, *args, **kwargs) -> 'float_type'
inverseMethylCorrection(self, *args, **kwargs) -> 'float_type'
inverseNoeNeighborhoodSize(self, *args, **kwargs) -> 'float_type'
longRangePrimarySeqCutoff(self, *args, **kwargs) -> 'int const'
maxMonteCarloAttempts(self, *args, **kwargs) -> 'int const'
neighborsNeedUpdate(self, *args, **kwargs) -> 'int'
noeCompletenessScore(self, *args, **kwargs) -> 'float_type'
noeCompletenessWeight(self, *args, **kwargs) -> 'float_type const'
numActivePeaks(self, *args, **kwargs) -> 'int'
numCloseAccountedShiftAssignmentPairs(self, *args, **kwargs) -> 'int'
numClosePAAccountedShiftAssignmentPairs(self, *args, **kwargs) -> 'int'
numCloseShiftAssignmentPairs(self, *args, **kwargs) -> 'int'
numFromShiftAssignments(self, *args, **kwargs) -> 'int'
numInactivePeaks(self, *args, **kwargs) -> 'int'
numPeaks(self, *args, **kwargs) -> 'int'
numRestraints(self, *args, **kwargs) -> 'int'
numShiftAssignments(self, *args, **kwargs) -> 'int'
numShiftAssignmentsInWrongNeighborhood(self, *args, **kwargs) -> 'int'
numToShiftAssignments(self, *args, **kwargs) -> 'int'
peakCoverageScore(self, *args, **kwargs) -> 'float_type'
peakNamed(self, *args, **kwargs) -> 'PeakPtr'
peaks(self, *args, **kwargs) -> 'CDSList< PeakPtr >'
peaksWithShiftAssignmentNamed(self, *args, **kwargs) -> 'CDSList< PeakPtr >'
peaksWithShiftAssignmentsNamed(self, *args, **kwargs) -> 'CDSList< PeakPtr >'
potName(self, *args, **kwargs) -> 'char const *'
previousLikelihoodScore(self, *args, **kwargs) -> 'float_type'
previousLikelihoodWeight(self, *args, **kwargs) -> 'float_type const'
pyXplorHelp(self, *args, **kwargs) -> 'String'
recordActivePeakAssignments(self, *args, **kwargs) -> 'void'
refCnt(self, *args, **kwargs) -> 'int'
registerInstanceData(self, *args, **kwargs) -> 'void'
registerTo(self, *args, **kwargs) -> 'void'
removeAllExceptions(self, *args, **kwargs) -> 'void'
removeExceptionsInvolving(self, *args, **kwargs) -> 'void'
removePeakAssignmentsInvolving(self, *args, **kwargs) -> 'void'
removePeakNamed(self, *args, **kwargs) -> 'void'
removeShiftAssignmentNamed(self, *args, **kwargs) -> 'void'
resetInstanceName(self, *args, **kwargs) -> 'void'
resetLinkedPeakAssignmentNames(self, *args, **kwargs) -> 'void'
resetLinkedPeakAssignments(self, *args, **kwargs) -> 'void'
resetPotName(self, *args, **kwargs) -> 'void'
resetSavedState(self, *args, **kwargs) -> 'void'
revertToSavedState(self, *args, **kwargs) -> 'void'
rms(self, *args, **kwargs) -> 'float_type'
saveCurrentState(self, *args, **kwargs) -> 'void'
scale(self, *args, **kwargs) -> 'float_type const'
scatterScore(self, *args, **kwargs) -> 'float_type'
scatterWeight(self, *args, **kwargs) -> 'float_type const'
setAllShiftAssignmentsInRightNeighborhood(self, *args, **kwargs) -> 'void'
setCharacteristicDeltaDV(self, *args, **kwargs) -> 'void'
setCharacteristicDeltaNoeCompleteness(self, *args, **kwargs) -> 'void'
setCharacteristicDeltaPL(self, *args, **kwargs) -> 'void'
setCharacteristicDeltaScatter(self, *args, **kwargs) -> 'void'
setCharacteristicDistanceViol(self, *args, **kwargs) -> 'void'
setCharacteristicNoeCompleteness(self, *args, **kwargs) -> 'void'
setCharacteristicScatter(self, *args, **kwargs) -> 'void'
setDistanceViolationWeight(self, *args, **kwargs) -> 'void'
setInverseBound(self, *args, **kwargs) -> 'void'
setInverseMethylCorrection(self, *args, **kwargs) -> 'void'
setInverseNoeNeighborhoodSize(self, *args, **kwargs) -> 'void'
setLongRangePrimarySeqCutoff(self, *args, **kwargs) -> 'void'
setMaxMonteCarloAttempts(self, *args, **kwargs) -> 'void'
setNoeCompletenessWeight(self, *args, **kwargs) -> 'void'
setPreviousLikelihoodWeight(self, *args, **kwargs) -> 'void'
setScale(self, *args, **kwargs) -> 'void'
setScatterWeight(self, *args, **kwargs) -> 'void'
setSwitchViolation(self, *args, **kwargs) -> 'void'
setThreshold(self, *args, **kwargs) -> 'void'
setUseOriginalViolationScore(self, *args, **kwargs) -> 'void'
setUseQuadraticPot(self, *args, **kwargs) -> 'void'
setUseSingleAssignment(self, *args, **kwargs) -> 'void'
setViolationCutoff(self, *args, **kwargs) -> 'void'
shiftAssignmentNamed(self, *args, **kwargs) -> 'ShiftAssignmentPtr'
shiftAssignments(self, *args, **kwargs) -> 'CDSList< ShiftAssignmentPtr >'
shiftAssignmentsWithPeakNamed(self, *args, **kwargs) -> 'CDSList< ShiftAssignmentPtr >'
simulation(self, *args, **kwargs) -> 'Simulation *'
switchViolation(self, *args, **kwargs) -> 'float_type'
threshold(self, *args, **kwargs) -> 'float_type const'
toShiftAssignments(self, *args, **kwargs) -> 'CDSList< ShiftAssignmentPtr >'
unRegister(self, *args, **kwargs) -> 'void'
unaccountedNeighbors(self, *args, **kwargs) -> 'CDSList< ShiftAssignmentPtr >'
updateActivation(self, *args, **kwargs) -> 'CDSList< float_type >'
updateDelta(self, *args, **kwargs) -> 'void'
updateLinkedPeakAssignments(self, *args, **kwargs) -> 'void'
updateNoeCompleteness(self, *args, **kwargs) -> 'void'
updatePeakPositionScatter(self, *args, **kwargs) -> 'void'
updatePrimarySeqDists(self, *args, **kwargs) -> 'void'
updateValues(self, *args, **kwargs) -> 'void'
useOriginalViolationScore(self, *args, **kwargs) -> 'bool const'
useQuadraticPot(self, *args, **kwargs) -> 'bool const'
useSingleAssignment(self, *args, **kwargs) -> 'bool const'
violationCutoff(self, *args, **kwargs) -> 'float_type const'
violationScore(self, *args, **kwargs) -> 'float_type'
violations(self, *args, **kwargs) -> 'float_type'
Static methods defined here:
__swig_destroy__ = delete_PASDPot(...)
Readonly properties defined here:
distPot_member

 
invPot_member

 
Data descriptors defined here:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

 
list of weak references to the object (if defined)
distEnergy

 
instanceDataCleanup

 
instanceDataCreate

 
instanceData_

 
invEnergy

 
modified

 
registeredSimulations

 
staleGradient

 
thisown

 
The membership flag

 
realPASD_DistPot = class PASD_DistPot(builtins.object)
    realPASD_DistPot(*args, **kwargs)
 

 
  Methods defined here:
__deref__(self, *args, **kwargs) -> 'PASD_DistPot *'
__init__(self, *args, **kwargs)
__oldinit__ = __init__(self, *args, **kwargs)
__ref__(self, *args, **kwargs) -> 'PASD_DistPot &'
__repr__ = _swig_repr(self)
calcEnergy(self, *args, **kwargs) -> 'float_type'
calcEnergyAndDerivs(self, *args, **kwargs) -> 'float_type'
decrRefCnt(self, *args, **kwargs) -> 'void'
incrRefCnt(self, *args, **kwargs) -> 'void'
instanceData(self, *args, **kwargs) -> 'PyObject *'
instanceName(self, *args, **kwargs) -> 'char const *'
numRestraints(self, *args, **kwargs) -> 'int'
potName(self, *args, **kwargs) -> 'char const *'
pyXplorHelp(self, *args, **kwargs) -> 'String'
refCnt(self, *args, **kwargs) -> 'int'
registerInstanceData(self, *args, **kwargs) -> 'void'
registerTo(self, *args, **kwargs) -> 'void'
resetInstanceName(self, *args, **kwargs) -> 'void'
resetPotName(self, *args, **kwargs) -> 'void'
rms(self, *args, **kwargs) -> 'float_type'
scale(self, *args, **kwargs) -> 'float_type const'
setScale(self, *args, **kwargs) -> 'void'
setThreshold(self, *args, **kwargs) -> 'void'
threshold(self, *args, **kwargs) -> 'float_type const'
unRegister(self, *args, **kwargs) -> 'void'
updateDelta(self, *args, **kwargs) -> 'void'
updateValues(self, *args, **kwargs) -> 'void'
violations(self, *args, **kwargs) -> 'float_type'
Static methods defined here:
__swig_destroy__ = delete_PASD_DistPot(...)
Data descriptors defined here:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

 
list of weak references to the object (if defined)
instanceDataCleanup

 
instanceDataCreate

 
instanceData_

 
modified

 
registeredSimulations

 
thisown

 
The membership flag

 
realPASD_InvPot = class PASD_InvPot(builtins.object)
    realPASD_InvPot(*args, **kwargs)
 

 
  Methods defined here:
__deref__(self, *args, **kwargs) -> 'PASD_InvPot *'
__init__(self, *args, **kwargs)
__oldinit__ = __init__(self, *args, **kwargs)
__ref__(self, *args, **kwargs) -> 'PASD_InvPot &'
__repr__ = _swig_repr(self)
calcEnergy(self, *args, **kwargs) -> 'float_type'
calcEnergyAndDerivs(self, *args, **kwargs) -> 'float_type'
decrRefCnt(self, *args, **kwargs) -> 'void'
incrRefCnt(self, *args, **kwargs) -> 'void'
instanceData(self, *args, **kwargs) -> 'PyObject *'
instanceName(self, *args, **kwargs) -> 'char const *'
numRestraints(self, *args, **kwargs) -> 'int'
potName(self, *args, **kwargs) -> 'char const *'
pyXplorHelp(self, *args, **kwargs) -> 'String'
refCnt(self, *args, **kwargs) -> 'int'
registerInstanceData(self, *args, **kwargs) -> 'void'
registerTo(self, *args, **kwargs) -> 'void'
resetInstanceName(self, *args, **kwargs) -> 'void'
resetPotName(self, *args, **kwargs) -> 'void'
rms(self, *args, **kwargs) -> 'float_type'
scale(self, *args, **kwargs) -> 'float_type const'
setScale(self, *args, **kwargs) -> 'void'
setThreshold(self, *args, **kwargs) -> 'void'
threshold(self, *args, **kwargs) -> 'float_type const'
unRegister(self, *args, **kwargs) -> 'void'
updateDelta(self, *args, **kwargs) -> 'void'
updateValues(self, *args, **kwargs) -> 'void'
violations(self, *args, **kwargs) -> 'float_type'
Static methods defined here:
__swig_destroy__ = delete_PASD_InvPot(...)
Data descriptors defined here:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

 
list of weak references to the object (if defined)
instanceDataCleanup

 
instanceDataCreate

 
instanceData_

 
modified

 
registeredSimulations

 
thisown

 
The membership flag

 
Functions
       
NOEPot = PASDPot(*args, **kwargs)
PASDPot(*args, **kwargs)
PASD_DistPot(*args, **kwargs)
PASD_InvPot(*args, **kwargs)
pyXplorHelp(*args) -> 'String'