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Pydoc: module saTensor

saTensor

index

saTensor steric alignment tensor for use with the sardcPot.SARDCPot potential term See: Jie-rong Huang, Stephan Grzesiek,``Ensemble calculations of unstructured proteins constrained by RDC and PRE data: a case study of urea-denatured ubiquitin'', J. Am. Chem. Soc. 132, 694-705 (2010). constructor: SATensor(instanceName, domainSel) instanceName - a user-specified string identifier. domainSel - atom selection specifying the extend of the full system to treat as being aligned. [not PSEUDO] methods: irredTensor(member=-1) - given a ensemble member index, return the unscaled alignment tensor in irreducible form. If member index = -1, then that of the current ensemble member is returned. domainSel() - atom selection specifying the extend of the full system to treat as being aligned. instanceName() - the name specified when the object is constructed. The following members can be read using the method named member() and set using the method setMember(val) [defaults in square brackets] freeDist - distance between two infinite planes. Parameter L in Eq. 4 of the reference at the top of this page. [1000 angstrom] sphericalN - number of vectors used to represent a (infinite) uniform spherical grid- used to sample particle extrema. [88] sphericalG - factor in the generation of isotropically distributed vectors used in the calculation of the alignment tensor. See Zaremba, Conroy and Wolfsberg, JCP 59, 3992 (1973). [34] public members: esim - the ensembleSimulation.EnsembleSimulation associated with domainSel. # 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

SATensor

VarEnsWeights

rc_EnsemblePot

rc_SATensor

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

SATensor = class rc_SATensor(builtins.object)

SATensor(*args)

Methods defined here:

__deref__(self, *args, **kwargs) -> 'SATensor *'

__init__ = newinit(self, *args)

__ref__(self, *args, **kwargs) -> 'SATensor &'

__repr__ = _swig_repr(self)

accumDerivs(self, *args, **kwargs) -> 'void'

c2_real(self, *args, **kwargs) -> 'SATensor::Vec5'

c2_real_deriv(self, *args, **kwargs) -> 'SATensor::Vec5Vec3'

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

decr(self, *args, **kwargs) -> 'void'

domainSel(self, *args, **kwargs) -> 'AtomSel const'

forceDelete(self, *args, **kwargs) -> 'void'

freeDist(self, *args, **kwargs) -> 'float_type const'

incr(self, *args, **kwargs) -> 'void'

instanceName(self, *args, **kwargs) -> 'String const'

irredTensor(self, *args, **kwargs) -> 'SATensor::Vec5'

oritensor_irred_get(self, *args, **kwargs) -> 'SATensor::Vec5'

ptr(self, *args, **kwargs) -> 'SATensor *'

registerTo(self, *args, **kwargs) -> 'void'

release(self, *args, **kwargs) -> 'SATensor *'

reset(self, *args, **kwargs) -> 'void'

setDomainSel(self, *args, **kwargs) -> 'void'

setFreeDist(self, *args, **kwargs) -> 'void'

setInstanceName(self, *args, **kwargs) -> 'void'

setSphericalG(self, *args, **kwargs) -> 'void'

setSphericalN(self, *args, **kwargs) -> 'void'

sphericalG(self, *args, **kwargs) -> 'float_type const'

sphericalN(self, *args, **kwargs) -> 'int const'

spherical_probability_get(self, *args, **kwargs) -> 'void'

spherical_sampling_init(self, *args, **kwargs) -> 'void'

unRegister(self, *args, **kwargs) -> 'void'

updateValues(self, *args, **kwargs) -> 'void'

Static methods defined here:

__swig_destroy__ = delete_rc_SATensor(...)

Data descriptors defined here:

__dict__: dictionary for instance variables (if defined)

__weakref__: list of weak references to the object (if defined)

avector_real

esim

modified

probSum

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 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_SATensor(builtins.object)

rc_SATensor(*args)

Methods defined here:

__deref__(self, *args, **kwargs) -> 'SATensor *'

__init__ = newinit(self, *args)

__ref__(self, *args, **kwargs) -> 'SATensor &'

__repr__ = _swig_repr(self)

accumDerivs(self, *args, **kwargs) -> 'void'

c2_real(self, *args, **kwargs) -> 'SATensor::Vec5'

c2_real_deriv(self, *args, **kwargs) -> 'SATensor::Vec5Vec3'

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

decr(self, *args, **kwargs) -> 'void'

domainSel(self, *args, **kwargs) -> 'AtomSel const'

forceDelete(self, *args, **kwargs) -> 'void'

freeDist(self, *args, **kwargs) -> 'float_type const'

incr(self, *args, **kwargs) -> 'void'

instanceName(self, *args, **kwargs) -> 'String const'

irredTensor(self, *args, **kwargs) -> 'SATensor::Vec5'

oritensor_irred_get(self, *args, **kwargs) -> 'SATensor::Vec5'

ptr(self, *args, **kwargs) -> 'SATensor *'

registerTo(self, *args, **kwargs) -> 'void'

release(self, *args, **kwargs) -> 'SATensor *'

reset(self, *args, **kwargs) -> 'void'

setDomainSel(self, *args, **kwargs) -> 'void'

setFreeDist(self, *args, **kwargs) -> 'void'

setInstanceName(self, *args, **kwargs) -> 'void'

setSphericalG(self, *args, **kwargs) -> 'void'

setSphericalN(self, *args, **kwargs) -> 'void'

sphericalG(self, *args, **kwargs) -> 'float_type const'

sphericalN(self, *args, **kwargs) -> 'int const'

spherical_probability_get(self, *args, **kwargs) -> 'void'

spherical_sampling_init(self, *args, **kwargs) -> 'void'

unRegister(self, *args, **kwargs) -> 'void'

updateValues(self, *args, **kwargs) -> 'void'

Static methods defined here:

__swig_destroy__ = delete_rc_SATensor(...)

Data descriptors defined here:

__dict__: dictionary for instance variables (if defined)

__weakref__: list of weak references to the object (if defined)

avector_real

esim

modified

probSum

registeredSimulations

thisown: The membership flag

wrapped_SATensor = class SATensor(ModifiedBase)

wrapped_SATensor(*args, **kwargs)

Method resolution order:: SATensor; ModifiedBase; builtins.object

Methods defined here:

__init__(self, *args, **kwargs)

__repr__ = _swig_repr(self)

accumDerivs(self, *args, **kwargs) -> 'void'

domainSel(self, *args, **kwargs) -> 'AtomSel const'

freeDist(self, *args, **kwargs) -> 'float_type const'

instanceName(self, *args, **kwargs) -> 'String const'

irredTensor(self, *args, **kwargs) -> 'SATensor::Vec5'

oritensor_irred_get(self, *args, **kwargs) -> 'SATensor::Vec5'

setDomainSel(self, *args, **kwargs) -> 'void'

setFreeDist(self, *args, **kwargs) -> 'void'

setInstanceName(self, *args, **kwargs) -> 'void'

setSphericalG(self, *args, **kwargs) -> 'void'

setSphericalN(self, *args, **kwargs) -> 'void'

sphericalG(self, *args, **kwargs) -> 'float_type const'

sphericalN(self, *args, **kwargs) -> 'int const'

spherical_probability_get(self, *args, **kwargs) -> 'void'

spherical_sampling_init(self, *args, **kwargs) -> 'void'

updateValues(self, *args, **kwargs) -> 'void'

Static methods defined here:

__swig_destroy__ = delete_SATensor(...)

c2_real(*args, **kwargs) -> 'SATensor::Vec5'

c2_real_deriv(*args, **kwargs) -> 'SATensor::Vec5Vec3'

Data descriptors defined here:

avector_real

esim

probSum

thisown: The membership flag

Methods inherited from ModifiedBase:

registerTo(self, *args, **kwargs) -> 'void'

unRegister(self, *args, **kwargs) -> 'void'

Data descriptors inherited from ModifiedBase:

__dict__: dictionary for instance variables (if defined)

__weakref__: list of weak references to the object (if defined)

modified

registeredSimulations

Functions

SATensor_c2_real(*args, **kwargs) -> 'SATensor::Vec5'

SATensor_c2_real_deriv(*args, **kwargs) -> 'SATensor::Vec5Vec3'

__oldinit__ = __init__(self, *args)

newinit(self, *args)

pyXplorHelp(*args) -> 'String'