rdcPot
index
/home/schwitrs/bzr-repo/xplor-python3/bin.Linux_x86_64/rdcPot.py

residual dipolar coupling potential
 
 One normally creates RDCPot objects using the create_RDCPot function within 
the rdcPotTools module.
 
constructor:   
        RDCPot1(instanceName,
                oTensor
                restraints,
                simulation)
  
  instanceName is a user-specified identifier. oTensor specifies an 
  orientational varTensor.VarTensor object. restraints is an optional 
  XPLOR-style sani or dipo restraint table. simulation is an optional 
  simulation.Simulation specification. 
 
  This potential term is described in G.M. Clore and C.D. Schwieters,
  J. Am. Chem. Soc. 126, 2923-2938 (2004). 
 
members:
  oTensor - the VarTensor orientational tensor object.
 
methods:
  addRestraints(restraintList,,
                warnOnEmpty=False,
                selectionFilter="") -add the specified XPLOR sani- or
                                     dipo-style restraints. Note that
                                     this is a string, and not a
                                     filename. If the optional warnOnEmpty
                                     argument is True, the warning given
                                     for an empty restraintList will
                                     be suppressed. selectionFilter is
                                     an optional additional selection
                                     string which can be used to specify
                                     that restraints apply to only a 
                                     subset of the atoms matched by the        
                                     strings in the ASSIgnment statements
                                     in the restraintList.
 
  removeRestraint(num)         - remove the specified restraint. Restraints
                                 are numbered from zero. Note that
                                 after a restraint is removed, all
                                 restraints with larger indices will be
                                 renumbered.
 
  calcEnergy()                 - calc energy, returns the energy value.
  calcEnergyAndDerivs(derivs)  - calc energy, derivs, returns the energy value.
 
 
 
  rms()           - return the rms of the restriants' diff() values.
  deviation()     - return average of deviation of ensemble members
  numRestraints() - return the number of restraints defined for this term.
  violations()    - return number of violations
  
  info()                    - current info about the state of this instance
  showViolations()          - return a string listing violated restraints.
  showRestraints(violated)  - return info on restraints. Argument violated is
                              boolean specifying whether to return only 
                              violated restraints.
 
 
  restraints() - return the list of restraints. See the description of the
                 Restraint class below. Restraint properties can thus be
                 modified.
  rawRestraints() - return a list of restraints, without calling calcEnergy
                 to update calculated values. See the description of the
                 Restraint class below.
  simulation() - return the associated simulation.Simulation.
 
  setLocalTensors(list) - Specify atoms to use to define a local reference
                          frame used to specify the alignment tensor. The
                          list is a sequence of tuples containing three atoms, 
                          the first of which must appear in the first selection
                          of one or more restraints' selPairs. If one is 
                          specified, then all atoms in all first selections of
                          all restraints must be present in list. If the
                          specified atoms of a tuple are A,B,C, which
                          positions qA,qB,qC, then the local frame for the 
                          alignment tensor of all interactions involving
                          atom A is given by the rotation matrix RA
 
                                 /              \
                           RA =  | c1 , c2 , c3  |
                                 \              /
 
                          where c1, c2, c3 are the column vectors:
 
                            c1 = unitVec(qBA X (qBA X qCA))
                            c2 = unitVec(qBA)
                            c3 = unitVec(qBA X qCA)
 
                          with qBA=qB-qA and X denoting cross product.
                          The principal components of the alignment tensor
                          associated with center A become
 
                                  ux -> RA ux
                                  uy -> RA uy
                                  uz -> RA uz
 
                          This local tensor representation is appropriate for
                          pseudo-contact shifts caused by one or more 
                          paramagnetic tags attached to a molecule of interest. 
 
  getLocalTensors() - return a dictionary of LocalTensors indexed by the atom 
                      index of center atoms. See below for a description of
                      the contents of a LocalTensor
 
  ensWeight(index) - return the ensemble weight associated with the
                     specified member.
 
 
 The following parameters can be set [defaults in square brackets]
 
  allowBadRestraints - By default, restraint definitions given to
                       addRestraints which select no atoms cause an
                       exception to be raised. If this flag is set to
                       True, only a warning message will be written. [False]
  deltaDFS  - constant offset in dipolar couplings [0]
  verbose   - if true, sporadically spit out info [False]
  useDistance- if True, include the 1/r^3 dependence in the calcedShift
               calculation. Note that this feature changes the meaning
               and units of Da [False].
  useSign   - default value for useSign of each restraint (see restraint
               description below) [True]. When set with setUseSign(), the
               default value, and values of all restraints are set.
  gyroA     
  gyroB     - linear scaling factors for the calculated dipolar coupling.
  scale            - energy scale factor (force constant) [1]
  threshold - threshold in violation calculation [0]
  potType   - type of potential: "harmonic" or "square" ["harmonic"]
  aveType   - type of averaging to use for indistinguishable atoms:
              "sum" , "average" , or "pairwise". Pairwise is appropriate for
              symmetric multimers for which the segid is not specified in
              the restraint atom selection. ["sum"]
  showAllRestraints - boolean which changes the behavior of showViolations. If 
                      this parameter is set to True, the behavior of
                      showViolations is modified such that all restraints are
                      printed. Violated restraints are indicated by an
                      asterisk in the first column. [0]
  useLocalTensor  - whether or not to use the local tensor interpretation of
                    of the alignment tensor. It is set to True if 
                    setLocalTensors() is called with non-null argument. 
                    Otherwise, it is False.
  useSimEnsWeight - whether to use the ensemble wieghts set with setEnsWeights
                    or to use those of the underlying EnsembleSimulation.
  ensWeights      - a sequence of ensemble weights to use when calculating 
                    the ensemble- averaged value of each dipolar coupling. By 
                    default, the weights of the underlying EnsembleSimulation 
                    are used. If these are overridden by calling the 
                    setEnsWeights method, and useSimEnsWeight is set to False. 
 
use the specified ensemble weights instead of those
                        in the underlying EnsembleSimulation.
  setEnsWeights(vals) - use the specified ensemble weights instead of those
                        in the underlying EnsembleSimulation.
 
 the above quantities may be retrieved using the member function form
 quantity(), while they are set using the form setQuantity(value).
 
assignment table:
  entries in the restraint list have the following form
 
      assign ( sel OO ) ( sel  Z ) ( sel  X ) ( sel  Y )
             ( sel m  ) ( sel n  )  obsShift error1 [error2]
      [or ( sel m1 ) ( sel n1) ...]
 
  where the first four selections are present for compatibility with
  XPLOR assignment tables- they can be any string with properly nested
  parentheses.  The m and n selections specify the atoms involved in
  the interaction. The observed dipolar shift is given by the obsShift
  argument, and the error bounds are given by error1 and error2.  If
  error2 is absent, it defaults to error1. One or more optional OR
  statements can be used to add additional pairs of atom
  selections. For instance, is residue 4 is a phenylalanine, the
  following assign..or statement will correctly allow averaging of the
  CE1-HE1 CE2-HE2 contributions:
 
      assign ( resid 500  and name OO  )
             ( resid 500  and name Z   )
             ( resid 500  and name X   )
             ( resid 500  and name Y   )
             ( resid 4    and name CE1 )
             ( resid 4    and name HE1 )  -4.62 4.62  0.1000
      or     ( resid 4    and name CE2 ) 
             ( resid 4    and name HE2 )
  [ If a single pair of wildcard atom selections is used, four
    contributions are computed. For these cases, the RDCPot assignment
    statement is not compatible with XPLOR DIPO ASSIgnment
    statements. ]
 
 The dipolar shift is given by the equation
 
   calcedShift =  DFS + Da (3 vz^2 -1) + 3/2 Da*R ( vx^2 - vy^2 )
 
 where R is the rhombic tensor component, and vx,vy,vz are the
 projections of the unit vector in the direction mn onto the
 corresponding coordinate axis representing tensor orientation. Da is scaled 
 by gyroA and gyroB. Typically, these are set to one, or are set to scale
 factors such that a single Da value can be used with experiments 
 involving different nuclei. These scale factors are usually set 
 using the helper function rdcPotTools.scale_toNH.
 
 If useDistance is True, the Da is scaled by 1 / |q_m - q_n|^3. Note that
 this changes the units of Da. This feature is frequently used in
 proton-proton experiments. If the Da is fixed, one will need an
 additional experiment to obtain a value for Da, and the value scaled
 appropriately. For example, if Da(NH) is available from a 15N-1H
 experiment in the same medium, the H-H Da would be set as Da(NH) *
 r(NH)^3 * gamma(N) gamma(N) = 10.47*Da(NH), where r(NH) is the NH
 bond distance, and gamma(N) and  gamma(H) are the gyromagnetic ratio
 of 15N and 1H, respectively.  
 
 
 The energy function is defined as
 
        1/2 * scale * (calcedShift - effShift)^2       [for useSign==True]
                      or
        1/2 * scale * (|calcedShift| - |effShift|)^2   [for useSign==False]
 
 where for potType=harmonic, effShift = obsShift. For potType=square,
 
       effShift = calcedShift, if 
                    obsShift-error1 < calcedShift < obsShift+error2
                = calcedShift+error1, if calcedShift < obsShift-error1
                = calcedShift-error2, if calcedShift > obsShift+error2
 
 
  
 
Restraint class
 
methods:
  energy() - energy due to this restraint
    
  calcd()  - calculated value of dipolar coupling (ensemble average).
  obs()    - observed value of dipolar coupling.
  diff()   - difference between calcd and obs, adjusted for the useSign setting.
             For square and linearsquare potential types, the plus/minus
             bounds are subtracted (so that restraints with zero energy have
             zero diff).
 
  plusErr(), minusErr() - bounds for the square well potential
 
  setObs(val) - set the observed value.
  setErr(val) - set both plus and minus errors to the given value.
 
  selPairs() - pairs of atom selections. Each pair is an object with 
               atomSel.AtomSel members named a and b,
               corresponding to the first and second selections in the
               ASSIgn or OR statements
 
  comment()  - return the (optional) comment string supplied in the
               assignment table.
  selectionFilter() - return the (optional) selectrionFilter string
                      specified in addRestraints()
 
  scale(), setScale() - get, set per-restraint energy scale factor
                       (force constant) [1]
 
  aSelection() - deprecated - synonym for selPairs()[0].a
  bSelection() - deprecated - synonym for selPairs()[0].b
 
  calced_contrib() - list of contributions due to each ensemble member.
 
  deviation() - measure of spread between different ensemble members
 
  useSign()   - if false, ignore the sign of the calculated and observed
                dipolar coupling; this if the sign of the shift is
                unknown [True]. Set this using the setUseSign accessor.
 
  aveSize(mem=-1) - return the number of atom pairs averaged over in
                    ambiguous assignments. The optional mem argument
                    specifies which ensemble member to report on.
 
LocalTensor class
 
  atom1, atom2, atom3 - atoms A, B and C as speicified above in the 
                        documentation of setLocalTensors.
 
  uMat                - the current definition of the rotation matrix RA.
 
  U                   - a sequence of the local values of the alignment tensor
                        principal components: ux, uy, uz.
 
 
 
# 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_RDCPot1_Restraint
CDSList_RDCSelPair
EnsemblePot
RDCPot1_LetterClass
LocalTensor
Modified
ModifiedBase
RDCPot1
RDCSelPair
Restraint_RDCPot1
RDCPot1_Restraint
VarEnsWeights
rc_EnsemblePot
rc_ptr_RDCPot1_Restraint

 
class CDSList_RDCPot1_Restraint(builtins.object)
    CDSList_RDCPot1_Restraint(*args)
 

 
  Methods defined here:
__delitem__(self, *args, **kwargs) -> 'void'
__getitem__(self, *args) -> 'CDSList< CDS::rc_ptr< RDCPot1_Restraint > >'
__getslice__(self, *args, **kwargs) -> 'CDSList< CDS::rc_ptr< RDCPot1_Restraint > >'
__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_RDCPot1_Restraint(...)

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_RDCSelPair(builtins.object)
    CDSList_RDCSelPair(*args)
 

 
  Methods defined here:
__delitem__(self, *args, **kwargs) -> 'void'
__getitem__(self, *args) -> 'CDSList< Pair< AtomSel,AtomSel > >'
__getslice__(self, *args, **kwargs) -> 'CDSList< Pair< AtomSel,AtomSel > >'
__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_RDCSelPair(...)

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 EnsemblePot(builtins.object)
    EnsemblePot(*args, **kwargs)
 

 
  Methods defined here:
__init__(self, *args, **kwargs)
Initialize self.  See help(type(self)) for accurate signature.
__repr__ = _swig_repr(self)
addEnsWeights(self, *args, **kwargs) -> 'void'
calcEnergy(self, *args, **kwargs) -> 'float_type'
calcEnergyAndDerivs(self, *args, **kwargs) -> 'float_type'
calcWDerivs(self, *args, **kwargs) -> 'bool const'
clearEnsWeights(self, *args, **kwargs) -> 'void'
energyMaybeDerivs0(self, *args, **kwargs) -> 'float_type'
energyMaybeDerivs1(self, *args, **kwargs) -> 'float_type'
energyMaybeDerivs2(self, *args, **kwargs) -> 'float_type'
energyMaybeDerivs3(self, *args, **kwargs) -> 'float_type'
energyMaybeDerivs4(self, *args, **kwargs) -> 'float_type'
energyMaybeDerivsPost(self, *args, **kwargs) -> 'float_type'
energyMaybeDerivsPre(self, *args, **kwargs) -> 'float_type'
ensWeight(self, *args, **kwargs) -> 'float_type'
ensWeights(self, *args, **kwargs) -> 'CDSList< float_type >'
ensWeightsInfo(self, *args, **kwargs) -> 'String'
getEnsWeights(self, *args, **kwargs) -> 'CDSList< VarEnsWeights > &'
setCalcWDerivs(self, *args, **kwargs) -> 'void'
setEnsWeights(self, *args, **kwargs) -> 'void'
setUseSimEnsWeights(self, *args, **kwargs) -> 'void'
simulation(self, *args) -> 'EnsembleSimulation const *'
updateEnsWeights(self, *args, **kwargs) -> 'void'
useSimEnsWeights(self, *args, **kwargs) -> 'bool const'

Static methods defined here:
__swig_destroy__ = delete_EnsemblePot(...)

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 LocalTensor(builtins.object)
    LocalTensor(*args)
 

 
  Methods defined here:
__init__(self, *args)
Initialize self.  See help(type(self)) for accurate signature.
__repr__ = _swig_repr(self)
update(self, *args, **kwargs) -> 'void'
updateGradients(self, *args, **kwargs) -> 'void'

Static methods defined here:
__swig_destroy__ = delete_LocalTensor(...)

Data descriptors defined here:
U

 
__dict__

 
dictionary for instance variables (if defined)
__weakref__

 
list of weak references to the object (if defined)
atom1

 
atom2

 
atom3

 
dUp_dq2

 
dUp_dq3

 
thisown

 
The membership flag
uMat

 

 
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)
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 RDCPot1_LetterClass(EnsemblePot)
    RDCPot1_LetterClass(*args, **kwargs)
 

 
 
Method resolution order:
RDCPot1_LetterClass
EnsemblePot
builtins.object

Methods defined here:
__init__(self, *args, **kwargs)
Initialize self.  See help(type(self)) for accurate signature.
__repr__ = _swig_repr(self)
addRestraint(self, *args, **kwargs) -> 'void'
addRestraints(self, *args, **kwargs) -> 'void'
allowBadRestraints(self, *args, **kwargs) -> 'bool const'
aveType(self, *args, **kwargs) -> 'RDCPot1::RDCAveType'
bondLength(self, *args, **kwargs) -> 'float_type const'
deltaDFS(self, *args, **kwargs) -> 'float_type const'
deviation(self, *args, **kwargs) -> 'double'
energyMaybeDerivs0(self, *args, **kwargs) -> 'float_type'
energyMaybeDerivs1(self, *args, **kwargs) -> 'float_type'
energyMaybeDerivs2(self, *args, **kwargs) -> 'float_type'
energyMaybeDerivsPost(self, *args, **kwargs) -> 'float_type'
getLocalTensors(self, *args, **kwargs) -> 'CDSMap< int,LocalTensor >'
gyroA(self, *args, **kwargs) -> 'float_type const'
gyroB(self, *args, **kwargs) -> 'float_type const'
info(self, *args, **kwargs) -> 'String'
numRestraints(self, *args, **kwargs) -> 'int'
potType(self, *args, **kwargs) -> 'RDCPot1::RDCPotType'
pyXplorHelp(self, *args, **kwargs) -> 'String'
rawRestraints(self, *args, **kwargs) -> 'CDSList< CDS::rc_ptr< RDCPot1_Restraint > > &'
removeRestraint(self, *args, **kwargs) -> 'void'
restraints(self, *args, **kwargs) -> 'CDSList< CDS::rc_ptr< RDCPot1_Restraint > > &'
rms(self, *args, **kwargs) -> 'double'
setAllowBadRestraints(self, *args, **kwargs) -> 'void'
setAveType(self, *args, **kwargs) -> 'void'
setBondLength(self, *args, **kwargs) -> 'void'
setDeltaDFS(self, *args, **kwargs) -> 'void'
setGyroA(self, *args, **kwargs) -> 'void'
setGyroB(self, *args, **kwargs) -> 'void'
setLocalTensors(self, *args, **kwargs) -> 'void'
setPotType(self, *args, **kwargs) -> 'void'
setShowAllRestraints(self, *args, **kwargs) -> 'void'
setUseDistance(self, *args, **kwargs) -> 'void'
setUseLocalTensor(self, *args, **kwargs) -> 'void'
setUseSign(self, *args, **kwargs) -> 'void'
setVerbose(self, *args, **kwargs) -> 'void'
showAllRestraints(self, *args, **kwargs) -> 'bool const'
showRestraints(self, *args, **kwargs) -> 'String'
showViolations(self, *args, **kwargs) -> 'String'
simulation(self, *args, **kwargs) -> 'EnsembleSimulation const *'
useDistance(self, *args, **kwargs) -> 'bool const'
useLocalTensor(self, *args, **kwargs) -> 'bool const'
useSign(self, *args, **kwargs) -> 'bool'
verbose(self, *args, **kwargs) -> 'bool const'
violations(self, *args, **kwargs) -> 'float_type'

Static methods defined here:
__swig_destroy__ = delete_RDCPot1_LetterClass(...)

Data descriptors defined here:
localTensors

 
oTensor

 
thisown

 
The membership flag

Data and other attributes defined here:
AVE = 0
HARMONIC = 0
LINEAR = 2
LINEARSQUARE = 3
PAIRWISE = 2
SQUARE = 1
SUM = 1

Methods inherited from EnsemblePot:
addEnsWeights(self, *args, **kwargs) -> 'void'
calcEnergy(self, *args, **kwargs) -> 'float_type'
calcEnergyAndDerivs(self, *args, **kwargs) -> 'float_type'
calcWDerivs(self, *args, **kwargs) -> 'bool const'
clearEnsWeights(self, *args, **kwargs) -> 'void'
energyMaybeDerivs3(self, *args, **kwargs) -> 'float_type'
energyMaybeDerivs4(self, *args, **kwargs) -> 'float_type'
energyMaybeDerivsPre(self, *args, **kwargs) -> 'float_type'
ensWeight(self, *args, **kwargs) -> 'float_type'
ensWeights(self, *args, **kwargs) -> 'CDSList< float_type >'
ensWeightsInfo(self, *args, **kwargs) -> 'String'
getEnsWeights(self, *args, **kwargs) -> 'CDSList< VarEnsWeights > &'
setCalcWDerivs(self, *args, **kwargs) -> 'void'
setEnsWeights(self, *args, **kwargs) -> 'void'
setUseSimEnsWeights(self, *args, **kwargs) -> 'void'
updateEnsWeights(self, *args, **kwargs) -> 'void'
useSimEnsWeights(self, *args, **kwargs) -> 'bool const'

Data descriptors inherited from EnsemblePot:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

 
list of weak references to the object (if defined)

 
class RDCPot1_Restraint(Restraint_RDCPot1)
    RDCPot1_Restraint(*args, **kwargs)
 

 
 
Method resolution order:
RDCPot1_Restraint
Restraint_RDCPot1
builtins.object

Methods defined here:
__init__(self, *args, **kwargs)
Initialize self.  See help(type(self)) for accurate signature.
__repr__ = _swig_repr(self)
aSelection = rdcrestraint_aSel(self)
aveSize(self, *args, **kwargs) -> 'int'
bSelection = rdcrestraint_bSel(self)
calcd(self, *args, **kwargs) -> 'double'
calcd_contrib(self, *args, **kwargs) -> 'CDSList< double >'
comment(self, *args, **kwargs) -> 'String const &'
deriv(self, *args, **kwargs) -> 'void'
deviation(self, *args, **kwargs) -> 'double'
energy(self, *args, **kwargs) -> 'float_type'
minusErr(self, *args, **kwargs) -> 'double'
name(self, *args, **kwargs) -> 'String'
obs(self, *args, **kwargs) -> 'double'
ok(self, *args, **kwargs) -> 'int'
plusErr(self, *args, **kwargs) -> 'double'
scale(self, *args, **kwargs) -> 'float_type const'
selPairs(self, *args, **kwargs) -> 'CDSList< RDCSelPair > const &'
selectionFilter(self, *args, **kwargs) -> 'String const &'
setErr(self, *args, **kwargs) -> 'void'
setObs(self, *args, **kwargs) -> 'void'
setScale(self, *args, **kwargs) -> 'void'
setUseSign(self, *args, **kwargs) -> 'void'
singleDerivContrib(self, *args, **kwargs) -> 'void'
updateAveSize(self, *args, **kwargs) -> 'void'
useSign(self, *args, **kwargs) -> 'bool const'

Static methods defined here:
__swig_destroy__ = delete_RDCPot1_Restraint(...)

Data descriptors defined here:
thisown

 
The membership flag
verbose

 

Methods inherited from Restraint_RDCPot1:
diff(self, *args, **kwargs) -> 'float_type'
setName(self, *args, **kwargs) -> 'void'
violated(self, *args, **kwargs) -> 'bool'

Data descriptors inherited from Restraint_RDCPot1:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

 
list of weak references to the object (if defined)

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

 
  Methods defined here:
__eq__(self, *args, **kwargs) -> 'bool'
Return self==value.
__init__(self, *args)
Initialize self.  See help(type(self)) for accurate signature.
__repr__ = _swig_repr(self)

Static methods defined here:
__swig_destroy__ = delete_RDCSelPair(...)

Data descriptors defined here:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

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

 
b

 
thisown

 
The membership flag

Data and other attributes defined here:
__hash__ = None

 
class Restraint_RDCPot1(builtins.object)
    Restraint_RDCPot1(*args, **kwargs)
 

 
  Methods defined here:
__init__(self, *args, **kwargs)
Initialize self.  See help(type(self)) for accurate signature.
__repr__ = _swig_repr(self)
diff(self, *args, **kwargs) -> 'float_type'
name(self, *args, **kwargs) -> 'String const'
setName(self, *args, **kwargs) -> 'void'
violated(self, *args, **kwargs) -> 'bool'

Static methods defined here:
__swig_destroy__ = delete_Restraint_RDCPot1(...)

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 VarEnsWeights(builtins.object)
    VarEnsWeights(*args, **kwargs)
 

 
  Methods defined here:
__init__(self, *args, **kwargs)
Initialize self.  See help(type(self)) for accurate signature.
__repr__ = _swig_repr(self)

Static methods defined here:
__swig_destroy__ = delete_VarEnsWeights(...)

Data descriptors defined here:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

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

 
mult

 
thisown

 
The membership flag

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

 
  Methods defined here:
__init__(self, *args, **kwargs)
Initialize self.  See help(type(self)) for accurate signature.
__repr__ = _swig_repr(self)

Static methods defined here:
__swig_destroy__ = delete_rc_EnsemblePot(...)

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 rc_ptr_RDCPot1_Restraint(builtins.object)
    rc_ptr_RDCPot1_Restraint(*args)
 

 
  Methods defined here:
__deref__(self, *args, **kwargs) -> 'RDCPot1_Restraint *'
__init__(self, *args)
Initialize self.  See help(type(self)) for accurate signature.
__ref__(self, *args, **kwargs) -> 'RDCPot1_Restraint &'
__repr__ = _swig_repr(self)
aSelection = rdcrestraint_aSel(self)
aveSize(self, *args, **kwargs) -> 'int'
bSelection = rdcrestraint_bSel(self)
calcd(self, *args, **kwargs) -> 'double'
calcd_contrib(self, *args, **kwargs) -> 'CDSList< double >'
comment(self, *args, **kwargs) -> 'String const &'
count(self, *args, **kwargs) -> 'int'
decr(self, *args, **kwargs) -> 'void'
deriv(self, *args, **kwargs) -> 'void'
deviation(self, *args, **kwargs) -> 'double'
diff(self, *args, **kwargs) -> 'float_type'
energy(self, *args, **kwargs) -> 'float_type'
forceDelete(self, *args, **kwargs) -> 'void'
incr(self, *args, **kwargs) -> 'void'
minusErr(self, *args, **kwargs) -> 'double'
name(self, *args, **kwargs) -> 'String'
obs(self, *args, **kwargs) -> 'double'
ok(self, *args, **kwargs) -> 'int'
plusErr(self, *args, **kwargs) -> 'double'
ptr(self, *args, **kwargs) -> 'RDCPot1_Restraint *'
release(self, *args, **kwargs) -> 'RDCPot1_Restraint *'
reset(self, *args, **kwargs) -> 'void'
scale(self, *args, **kwargs) -> 'float_type const'
selPairs(self, *args, **kwargs) -> 'CDSList< RDCSelPair > const &'
selectionFilter(self, *args, **kwargs) -> 'String const &'
setErr(self, *args, **kwargs) -> 'void'
setName(self, *args, **kwargs) -> 'void'
setObs(self, *args, **kwargs) -> 'void'
setScale(self, *args, **kwargs) -> 'void'
setUseSign(self, *args, **kwargs) -> 'void'
singleDerivContrib(self, *args, **kwargs) -> 'void'
updateAveSize(self, *args, **kwargs) -> 'void'
useSign(self, *args, **kwargs) -> 'bool const'
violated(self, *args, **kwargs) -> 'bool'

Static methods defined here:
__swig_destroy__ = delete_rc_ptr_RDCPot1_Restraint(...)

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
verbose

 

 
realRDCPot1 = class RDCPot1(builtins.object)
    realRDCPot1(*args)
 

 
  Methods defined here:
__deref__(self, *args, **kwargs) -> 'RDCPot1 *'
__init__(self, *args)
__oldinit__ = __init__(self, *args, **kwargs)
__ref__(self, *args, **kwargs) -> 'RDCPot1 &'
__repr__ = _swig_repr(self)
addEnsWeights(self, *args, **kwargs) -> 'void'
addRestraint(self, *args, **kwargs) -> 'void'
addRestraints(self, *args, **kwargs) -> 'void'
allowBadRestraints(self, *args, **kwargs) -> 'bool const'
aveType(self, *args, **kwargs) -> 'RDCPot1::RDCAveType'
bondLength(self, *args, **kwargs) -> 'float_type const'
calcEnergy(self, *args, **kwargs) -> 'float_type'
calcEnergyAndDerivs(self, *args, **kwargs) -> 'float_type'
calcWDerivs(self, *args, **kwargs) -> 'bool const'
clearEnsWeights(self, *args, **kwargs) -> 'void'
decrRefCnt(self, *args, **kwargs) -> 'void'
deltaDFS(self, *args, **kwargs) -> 'float_type const'
deviation(self, *args, **kwargs) -> 'double'
energyMaybeDerivs0(self, *args, **kwargs) -> 'float_type'
energyMaybeDerivs1(self, *args, **kwargs) -> 'float_type'
energyMaybeDerivs2(self, *args, **kwargs) -> 'float_type'
energyMaybeDerivs3(self, *args, **kwargs) -> 'float_type'
energyMaybeDerivs4(self, *args, **kwargs) -> 'float_type'
energyMaybeDerivsPost(self, *args, **kwargs) -> 'float_type'
energyMaybeDerivsPre(self, *args, **kwargs) -> 'float_type'
ensWeight(self, *args, **kwargs) -> 'float_type'
ensWeights(self, *args, **kwargs) -> 'CDSList< float_type >'
ensWeightsInfo(self, *args, **kwargs) -> 'String'
getEnsWeights(self, *args, **kwargs) -> 'CDSList< VarEnsWeights > &'
getLocalTensors(self, *args, **kwargs) -> 'CDSMap< int,LocalTensor >'
gyroA(self, *args, **kwargs) -> 'float_type const'
gyroB(self, *args, **kwargs) -> 'float_type const'
incrRefCnt(self, *args, **kwargs) -> 'void'
info(self, *args, **kwargs) -> 'String'
instanceData(self, *args, **kwargs) -> 'PyObject *'
instanceName(self, *args, **kwargs) -> 'char const *'
numRestraints(self, *args, **kwargs) -> 'int'
potName(self, *args, **kwargs) -> 'char const *'
potType(self, *args, **kwargs) -> 'RDCPot1::RDCPotType'
pyXplorHelp(self, *args, **kwargs) -> 'String'
rawRestraints(self, *args, **kwargs) -> 'CDSList< CDS::rc_ptr< RDCPot1_Restraint > > &'
refCnt(self, *args, **kwargs) -> 'int'
registerInstanceData(self, *args, **kwargs) -> 'void'
registerTo(self, *args, **kwargs) -> 'void'
removeRestraint(self, *args, **kwargs) -> 'void'
resetInstanceName(self, *args, **kwargs) -> 'void'
resetPotName(self, *args, **kwargs) -> 'void'
restraints(self, *args, **kwargs) -> 'CDSList< CDS::rc_ptr< RDCPot1_Restraint > > &'
rms(self, *args, **kwargs) -> 'double'
scale(self, *args, **kwargs) -> 'float_type const'
setAllowBadRestraints(self, *args, **kwargs) -> 'void'
setAveType(self, *args, **kwargs) -> 'void'
setBondLength(self, *args, **kwargs) -> 'void'
setCalcWDerivs(self, *args, **kwargs) -> 'void'
setDeltaDFS(self, *args, **kwargs) -> 'void'
setEnsWeights(self, *args, **kwargs) -> 'void'
setGyroA(self, *args, **kwargs) -> 'void'
setGyroB(self, *args, **kwargs) -> 'void'
setLocalTensors(self, *args, **kwargs) -> 'void'
setPotType(self, *args, **kwargs) -> 'void'
setScale(self, *args, **kwargs) -> 'void'
setShowAllRestraints(self, *args, **kwargs) -> 'void'
setThreshold(self, *args, **kwargs) -> 'void'
setUseDistance(self, *args, **kwargs) -> 'void'
setUseLocalTensor(self, *args, **kwargs) -> 'void'
setUseSign(self, *args, **kwargs) -> 'void'
setUseSimEnsWeights(self, *args, **kwargs) -> 'void'
setVerbose(self, *args, **kwargs) -> 'void'
showAllRestraints(self, *args, **kwargs) -> 'bool const'
showRestraints(self, *args, **kwargs) -> 'String'
showViolations(self, *args, **kwargs) -> 'String'
simulation(self, *args, **kwargs) -> 'EnsembleSimulation const *'
threshold(self, *args, **kwargs) -> 'float_type const'
unRegister(self, *args, **kwargs) -> 'void'
updateDelta(self, *args, **kwargs) -> 'void'
updateEnsWeights(self, *args, **kwargs) -> 'void'
updateValues(self, *args, **kwargs) -> 'void'
useDistance(self, *args, **kwargs) -> 'bool const'
useLocalTensor(self, *args, **kwargs) -> 'bool const'
useSign(self, *args, **kwargs) -> 'bool'
useSimEnsWeights(self, *args, **kwargs) -> 'bool const'
verbose(self, *args, **kwargs) -> 'bool const'
violations(self, *args, **kwargs) -> 'float_type'

Static methods defined here:
__swig_destroy__ = delete_RDCPot1(...)

Data descriptors defined here:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

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

 
instanceDataCreate

 
instanceData_

 
localTensors

 
modified

 
oTensor

 
registeredSimulations

 
thisown

 
The membership flag

 
Functions
       
RDCPot1(*args)
pyXplorHelp(*args) -> 'String'
rdcrestraint_aSel(self)
rdcrestraint_bSel(self)