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Python: module varTensor
 
varTensor		 index

variable magnitude orientational tensor object
 
This object is usually constructed using the create_VarTensor() function in 
the varTensorTools module. The VarTensor object is used by 
rdcPot.RDCPot and csaPot.CSAPot potential terms.
 
 The following parameters can be set [defaults in square brackets]
 
  Da        - axial tensor component. Setting this modifies ths position of 
              the p1 atom.
  Rh        - rhombic tensor component. Setting this modifies ths position of 
              the p2 atom.
  DaMax            - maximum possible value of Da [50]
  verbose   - if true, sporadically spit out info [False]
  oAtom            - origin atom
  o2Atom    - origin atom #2 (see below)
  xAtom            - x-axis atom
  yAtom            - y-axis atom
  zAtom            - z-axis atom
  p1Atom    - Da parameter atom
  p2Atom    - rhombicity parameter atom
  potType   - type of potential: "harmonic" or "square" ["harmonic"]
  expts     - the potentials (RDCPots and CSAPots) which depend on this 
              tensor.
  freedom   - string used by varTensorTools.topologySetup to setup IVM
              topology. The freedom language contains the following keywords:
                  fix
                  fixAxis
                  fixDa, varyDa
                  fixRh, varyRh
                  fixAxisTo <name>
                  fixRhTo <name>
                  ignore
              More than one can be specified, using a comma as a seperator.
  useSimEnsWeight - whether to use the ensemble wieghts set with setEnsWeights
                    or to use those of the underlying EnsembleSimulation.
 
 the above quantities may be retrieved using the member function form
 quantity(), while they are set using the form setQuantity(value).
 
  ensWeigth(index) - return the ensemble weight associated with the
                     specified member.
  setEnsWeights(vals) - use the specified ensemble weights instead of those
                        in the underlying EnsembleSimulation.
 
if the associated Simulation object is an EnsembleSimulation, additional
functionality is available:
 
accessors:
 
  ensembleAxis - boolean. If True, there is a separate value for tensor
                 axis orientation for each ensemble member. Default is False.
  ensembleDa - boolean. If true, there is a separate value of Da for 
               each structure. Default is 0(false).
  ensembleRh - boolean. If true, there is a separate value of rhombicity for 
               each structure. Default is 0(false).
  scaleDa    - weight on an energy term which weights spread in
               Da. This is only meaningful if ensembleDa is on. [default: 0]
  scaleRh    - weight on an energy term which weights spread in
               rhombicity. This is only meaningful if ensembleRh is on. 
               [default: 0]
  spreadDa   - Target spread in Da. Deviations in Da of less than
               spreadDa (from the mean) do not count towards the Da
               spread energy term. [default value: 0]
  spreadRh   - Target spread in rhombicity. Deviations in rhombicity
               of less than spreadRh (from the mean) do not count
               towards the rhombicity spread energy term. [default value: 0]
 
In addition the followiong methods are provided:
 
 aveDa()         - return the value of Da averaged over the 
                   ensembleSimulation.EnsembleSimulation
 aveRhombicity() - return the value of Rh averaged over the 
                   ensembleSimulation.EnsembleSimulation
 
The energy term associated with spread in Da and Rh is
     scaleDa * < harmonicSquare( Da - <Da> ) >
and
     scaleRh * < harmonicSquare( Rh - <Rh> ) >,
respectively.
 
 
 Implementation: required topology issues
 
 The VarTensor object is best used with the IVM module for coordinate
 minimization and manipulation. An example of such use is shown in the
 rdcPotTest.py script in the python/tests subdirectory. To exploit the full
 capabilities of the VarTensor object, seven atoms are used to represent
 tensor properties. A second origin atom (named OO2) is placed
 co-incident with atom OO. 
 
  The axial tensor component Da is represented as 
                    Da_max * cos(theta1)
 where theta1 is the angle defined by atomX-atomOO-atomPA1. The
 rhombic tensor component is represented by 
                    2/3 * sin(theta2)
 where theta2 is the angle defined by atomZ-atomOO2-atomPA2.
 
 
 
 
# 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_Pot
EnsemblePot
VarTensor_LetterClass
Modified
ModifiedBase
VarEnsWeights
VarTensor
rc_EnsemblePot

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

 
  Methods defined here:
__delitem__(self, *args, **kwargs) -> 'void'
__getitem__(self, *args) -> 'CDSList< Pot * >'
__getslice__(self, *args, **kwargs) -> 'CDSList< Pot * >'
__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_Pot(...)
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) -> 'EnsembleSimulationBase 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 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 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 VarTensor_LetterClass(EnsemblePot)
    VarTensor_LetterClass(*args, **kwargs)
 

 
 
Method resolution order:
VarTensor_LetterClass
EnsemblePot
builtins.object
Methods defined here:
Da(self, *args, **kwargs) -> 'double'
DaMax(self, *args, **kwargs) -> 'float_type'
Rh(self, *args, **kwargs) -> 'double'
__init__(self, *args, **kwargs)
Initialize self.  See help(type(self)) for accurate signature.
__repr__ = _swig_repr(self)
accumDerivs(self, *args, **kwargs) -> 'void'
aveDa(self, *args, **kwargs) -> 'double'
aveRh(self, *args, **kwargs) -> 'double'
configTensorAtoms(self, *args, **kwargs) -> 'void'
energyMaybeDerivs0(self, *args, **kwargs) -> 'float_type'
energyMaybeDerivs1(self, *args, **kwargs) -> 'float_type'
ensembleAxis(self, *args, **kwargs) -> 'bool'
ensembleDa(self, *args, **kwargs) -> 'bool'
ensembleRh(self, *args, **kwargs) -> 'bool'
expts(self, *args, **kwargs) -> 'CDSList< Pot * > &'
freedom(self, *args, **kwargs) -> 'String const'
info(self, *args, **kwargs) -> 'String'
initDerivs(self, *args, **kwargs) -> 'void'
numRestraints(self, *args, **kwargs) -> 'int'
o2Atom(self, *args, **kwargs) -> 'Atom const'
o2AtomSel(self, *args, **kwargs) -> 'String const'
oAtom(self, *args, **kwargs) -> 'Atom const'
oAtomSel(self, *args, **kwargs) -> 'String const'
p1Atom(self, *args, **kwargs) -> 'Atom const'
p1AtomSel(self, *args, **kwargs) -> 'String const'
p2Atom(self, *args, **kwargs) -> 'Atom const'
p2AtomSel(self, *args, **kwargs) -> 'String const'
pyXplorHelp(self, *args, **kwargs) -> 'String'
rms(self, *args, **kwargs) -> 'float_type'
scaleDa(self, *args, **kwargs) -> 'float_type const'
scaleRh(self, *args, **kwargs) -> 'float_type const'
setDa(self, *args, **kwargs) -> 'void'
setDaMax(self, *args, **kwargs) -> 'void'
setEnsembleAxis(self, *args, **kwargs) -> 'void'
setEnsembleDa(self, *args, **kwargs) -> 'void'
setEnsembleRh(self, *args, **kwargs) -> 'void'
setExpts(self, *args, **kwargs) -> 'void'
setFreedom(self, *args, **kwargs) -> 'void'
setO2Atom(self, *args, **kwargs) -> 'void'
setO2AtomSel(self, *args, **kwargs) -> 'void'
setOAtom(self, *args, **kwargs) -> 'void'
setOAtomSel(self, *args, **kwargs) -> 'void'
setP1Atom(self, *args, **kwargs) -> 'void'
setP1AtomSel(self, *args, **kwargs) -> 'void'
setP2Atom(self, *args, **kwargs) -> 'void'
setP2AtomSel(self, *args, **kwargs) -> 'void'
setRh(self, *args, **kwargs) -> 'void'
setScaleDa(self, *args, **kwargs) -> 'void'
setScaleRh(self, *args, **kwargs) -> 'void'
setSpreadDa(self, *args, **kwargs) -> 'void'
setSpreadRh(self, *args, **kwargs) -> 'void'
setXAtom(self, *args, **kwargs) -> 'void'
setXAtomSel(self, *args, **kwargs) -> 'void'
setYAtom(self, *args, **kwargs) -> 'void'
setYAtomSel(self, *args, **kwargs) -> 'void'
setZAtom(self, *args, **kwargs) -> 'void'
setZAtomSel(self, *args, **kwargs) -> 'void'
simulation(self, *args, **kwargs) -> 'EnsembleSimulationBase const *'
spreadDa(self, *args, **kwargs) -> 'float_type const'
spreadRh(self, *args, **kwargs) -> 'float_type const'
violations(self, *args, **kwargs) -> 'float_type'
xAtom(self, *args, **kwargs) -> 'Atom const'
xAtomSel(self, *args, **kwargs) -> 'String const'
yAtom(self, *args, **kwargs) -> 'Atom const'
yAtomSel(self, *args, **kwargs) -> 'String const'
zAtom(self, *args, **kwargs) -> 'Atom const'
zAtomSel(self, *args, **kwargs) -> 'String const'
Static methods defined here:
__swig_destroy__ = delete_VarTensor_LetterClass(...)
Data descriptors defined here:
DaMax_

 
U

 
dO

 
dP1

 
dP2

 
dX

 
dY

 
dZ

 
normQ

 
normQp1

 
normQp2

 
qp1

 
qp2

 
sqrtOneMinusZP1Squared

 
thisown

 
The membership flag
xp1hat

 
zp1hat

 
zp2hat

 
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'
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'
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 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

 
realVarTensor = class VarTensor(builtins.object)
    realVarTensor(*args)
 

 
  Methods defined here:
Da(self, *args, **kwargs) -> 'double'
DaMax(self, *args, **kwargs) -> 'float_type'
Rh(self, *args, **kwargs) -> 'double'
__deref__(self, *args, **kwargs) -> 'VarTensor *'
__init__(self, *args)
__oldinit__ = __init__(self, *args, **kwargs)
__ref__(self, *args, **kwargs) -> 'VarTensor &'
__repr__ = _swig_repr(self)
accumDerivs(self, *args, **kwargs) -> 'void'
addEnsWeights(self, *args, **kwargs) -> 'void'
aveDa(self, *args, **kwargs) -> 'double'
aveRh(self, *args, **kwargs) -> 'double'
calcEnergy(self, *args, **kwargs) -> 'float_type'
calcEnergyAndDerivs(self, *args, **kwargs) -> 'float_type'
calcWDerivs(self, *args, **kwargs) -> 'bool const'
clearEnsWeights(self, *args, **kwargs) -> 'void'
configTensorAtoms(self, *args, **kwargs) -> 'void'
decrRefCnt(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'
ensembleAxis(self, *args, **kwargs) -> 'bool'
ensembleDa(self, *args, **kwargs) -> 'bool'
ensembleRh(self, *args, **kwargs) -> 'bool'
expts(self, *args, **kwargs) -> 'CDSList< Pot * > &'
freedom(self, *args, **kwargs) -> 'String const'
getEnsWeights(self, *args, **kwargs) -> 'CDSList< VarEnsWeights > &'
incrRefCnt(self, *args, **kwargs) -> 'void'
info(self, *args, **kwargs) -> 'String'
initDerivs(self, *args, **kwargs) -> 'void'
instanceData(self, *args, **kwargs) -> 'PyObject *'
instanceName(self, *args, **kwargs) -> 'char const *'
numRestraints(self, *args, **kwargs) -> 'int'
o2Atom(self, *args, **kwargs) -> 'Atom const'
o2AtomSel(self, *args, **kwargs) -> 'String const'
oAtom(self, *args, **kwargs) -> 'Atom const'
oAtomSel(self, *args, **kwargs) -> 'String const'
p1Atom(self, *args, **kwargs) -> 'Atom const'
p1AtomSel(self, *args, **kwargs) -> 'String const'
p2Atom(self, *args, **kwargs) -> 'Atom const'
p2AtomSel(self, *args, **kwargs) -> 'String const'
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'
scaleDa(self, *args, **kwargs) -> 'float_type const'
scaleRh(self, *args, **kwargs) -> 'float_type const'
setCalcWDerivs(self, *args, **kwargs) -> 'void'
setDa(self, *args, **kwargs) -> 'void'
setDaMax(self, *args, **kwargs) -> 'void'
setEnsWeights(self, *args, **kwargs) -> 'void'
setEnsembleAxis(self, *args, **kwargs) -> 'void'
setEnsembleDa(self, *args, **kwargs) -> 'void'
setEnsembleRh(self, *args, **kwargs) -> 'void'
setExpts(self, *args, **kwargs) -> 'void'
setFreedom(self, *args, **kwargs) -> 'void'
setO2Atom(self, *args, **kwargs) -> 'void'
setO2AtomSel(self, *args, **kwargs) -> 'void'
setOAtom(self, *args, **kwargs) -> 'void'
setOAtomSel(self, *args, **kwargs) -> 'void'
setP1Atom(self, *args, **kwargs) -> 'void'
setP1AtomSel(self, *args, **kwargs) -> 'void'
setP2Atom(self, *args, **kwargs) -> 'void'
setP2AtomSel(self, *args, **kwargs) -> 'void'
setRh(self, *args, **kwargs) -> 'void'
setScale(self, *args, **kwargs) -> 'void'
setScaleDa(self, *args, **kwargs) -> 'void'
setScaleRh(self, *args, **kwargs) -> 'void'
setSpreadDa(self, *args, **kwargs) -> 'void'
setSpreadRh(self, *args, **kwargs) -> 'void'
setThreshold(self, *args, **kwargs) -> 'void'
setUseSimEnsWeights(self, *args, **kwargs) -> 'void'
setXAtom(self, *args, **kwargs) -> 'void'
setXAtomSel(self, *args, **kwargs) -> 'void'
setYAtom(self, *args, **kwargs) -> 'void'
setYAtomSel(self, *args, **kwargs) -> 'void'
setZAtom(self, *args, **kwargs) -> 'void'
setZAtomSel(self, *args, **kwargs) -> 'void'
simulation(self, *args, **kwargs) -> 'EnsembleSimulationBase const *'
spreadDa(self, *args, **kwargs) -> 'float_type const'
spreadRh(self, *args, **kwargs) -> 'float_type 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'
useSimEnsWeights(self, *args, **kwargs) -> 'bool const'
violations(self, *args, **kwargs) -> 'float_type'
xAtom(self, *args, **kwargs) -> 'Atom const'
xAtomSel(self, *args, **kwargs) -> 'String const'
yAtom(self, *args, **kwargs) -> 'Atom const'
yAtomSel(self, *args, **kwargs) -> 'String const'
zAtom(self, *args, **kwargs) -> 'Atom const'
zAtomSel(self, *args, **kwargs) -> 'String const'
Static methods defined here:
__swig_destroy__ = delete_VarTensor(...)
Data descriptors defined here:
DaMax_

 
U

 
__dict__

 
dictionary for instance variables (if defined)
__weakref__

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

 
dP1

 
dP2

 
dX

 
dY

 
dZ

 
instanceDataCleanup

 
instanceDataCreate

 
instanceData_

 
modified

 
normQ

 
normQp1

 
normQp2

 
qp1

 
qp2

 
registeredSimulations

 
sqrtOneMinusZP1Squared

 
thisown

 
The membership flag
xp1hat

 
zp1hat

 
zp2hat

 

 
Functions
       
VarTensor(*args)
pyXplorHelp(*args) -> 'String'