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

Population occupancy weights encoded as bond angles
 
AWeights allows optimizing ensemble weights for calculations
including ensWeights.EnsWeights.
 
 
Constructor:
  AWeights(members,
           bondAngles,
           derivedSpecs,
           simulation)   - The members argument is a list of
                           integers which identifies which ensemble
                           members are to have their weights
                           controlled by this object. Multiple
                           AWeights objects can be simultaneously
                           active to describe different
                           subpopulations of ensemble members. The bondAngles
                           argument is a sequence of bondAngle.BondAngle
                           involving pseudoatoms. The size of the bondAngles
                           argument must be len(members)-1. 
 
                           The weights of one or more ensemble
                           members can be dependent on others using the 
                           optional derivedSpecs argument: a list of tuples
                           with three arguments each. For an
                           ensemble with Ne members, Ne_base = Ne -
                           len(derivedSpecs), and the populations of
                           the first Ne_base members are
                           independent. The populations of the
                           dependent (derived) wieghts is
 
                                  w = A * w_b + w_b^T * B * w_b
 
                           The first entry should be a nonnegative integer 
                           less than Ne (this argument may disappear). The 
                           second gives the nonzero members of the A vector 
                           in the equation above in the form [index, value]. 
                           The third entry gives the nonzero values of the B 
                           matrix in the form [index1, index2, value].
 
                           The final Simulation argument is optional.
                             
 
Methods:
 
  simulation()             - return the associated simulation.Simulation.
 
  weights()                - return a map of (member index,weight). 
 
  setWeights(map)          - set ensemble weights to specified values. This
                             will modify pseudoatom coordinates. The map 
                             must have the same keys as specified by the
                             members argument of the constructor which specify 
                             the identities of the ensemble members. The
                             minimum settable weight is 1e-7.
  setWeights(list)         - in this version, the list must be the full size
                             of the ensemble
 
  baseWeights()            - return a sequence of base weights - that is
                             weights not specified by derivedSpecs.
 
  derivedSpecs ()          - return the derivedSpecs argument given in the
                             constructor.
 
  minFrac                  - the fraction of 1/Ne
                             corresponding to the minimal allowed
                             weight. For instance, if minFrac=0.1,
                             wMin would be 0.1/Ne. Default: 0.
  setMinFrac(val)          - set the minFrac value.
 
  members()                - return a list of indices which identify the
                             ensemble members for which this object sets
                             weights.
 
  setAngles(vals);         - pass a list of bondAngle.BondAngle objects
                             which contain the identity of pseudoatoms. The
                             number of angles must be len(baseWeights())-1.
 
  angles()                 - return a list of bondAngle.BondAngle objects
                             which are used to encode ensemble weights.
 
  freedom()                - return the freedom specification.
  setFreedom(string)          - set the freedom specification. This is
                             queried by ensWeightsTools.topologySetup()
                             to correctly handle the IVM setup for
                             pseudoatoms. Valid values are "vary", 
                             "fix", "ignore". This should usually be left
                             at the default value of "vary". The value of
                             "bend" is equivalent to "bend".
 
  computeWeights(modified) - recompute ensemble weights from pseudoatom 
                             positions. Chose a modified  argument value of 
                             True.
 
 
 info()   - return a string describing the current state of the object.
 
 
 
These weights (occupancy fractions) take values between wMin and wMax (which
is 1-wMin), such that their sum is unity. wMin can be given a nonzero value
using the setMinFrac accessor.
 
 
 
# 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
AWeights
CDSList_DerivedSpec
DerivedSpec

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

 
  Methods defined here:
__init__(self, *args)
Initialize self.  See help(type(self)) for accurate signature.
__repr__ = _swig_repr(self)
accumDerivs(self, *args, **kwargs) -> 'void'
angles(self, *args, **kwargs) -> 'CDSList< BondAngle >'
baseWeights(self, *args, **kwargs) -> 'CDSVector< float_type >'
computeWeights(self, *args, **kwargs) -> 'void'
derivedSpecs(self, *args, **kwargs) -> 'CDSList< AWeights::DerivedSpec >'
freedom(self, *args, **kwargs) -> 'String const'
info(self, *args, **kwargs) -> 'String'
members(self, *args, **kwargs) -> 'CDSList< int > const &'
minFrac(self, *args, **kwargs) -> 'float_type const'
pyXplorHelp(self, *args, **kwargs) -> 'String'
setFreedom(self, *args, **kwargs) -> 'void'
setMinFrac(self, val)
setMinFrac_raw(self, *args, **kwargs) -> 'void'
setWeights(self, *args, **kwargs) -> 'void'
setWeights_noBarrier(self, *args, **kwargs) -> 'void'
weights(self, *args, **kwargs) -> 'CDSMap< int,float_type >'
weightsFromAngles(self, *args, **kwargs) -> 'CDSVector< float_type >'
weightsRaw(self, *args, **kwargs) -> 'CDSVector< float_type > const &'

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

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
wMin

 
wScale

 

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

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

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 DerivedSpec(builtins.object)
    DerivedSpec(*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_DerivedSpec(...)

Data descriptors defined here:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

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

 
b

 
c

 
thisown

 
The membership flag

 
Functions
       
pyXplorHelp(*args) -> 'String'