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

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
       
builtins.object
EnsemblePot
Modified
ModifiedBase
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) -> '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 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

 
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'