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Pydoc: 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

VarTensor

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'

calcTensorOrientation(self, *args, **kwargs) -> 'int'

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 * > &'

exptsdiff(self, *args, **kwargs) -> 'CDSVector< float_type >'

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, **kwargs)

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, **kwargs)

__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'

calcTensorOrientation(self, *args, **kwargs) -> 'int'

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 * > &'

exptsdiff(self, *args, **kwargs) -> 'CDSVector< float_type >'

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, **kwargs)

pyXplorHelp(*args) -> 'String'