solnScatPot
index
solnScatPot.py

potential term for solution-phase scattering experiments, including 
SAXS and SANS
 
 One normally creates SolnScatPot objects using 
solnXRayPotTools.create_XRayScatPot or sansPotTools.create_SANSPot.
 
constructor:
 
  SolnScatPot(instanceName,
              sel         ,
              qValues     ,
              groupMap    ,
              formFactors ,
              iFormFactors,
              globDefs    ,
              experiment  ,
              simulation  )
 
  where:
    instanceName  user-specified identifier.
    sel           atomSel.AtomSel which specifies atoms to use in 
                  the scattering calculation (frequently all heavy atoms).
    qValues       a sequence of values of scattering vector at which
                  to perform refinement. q=4 PI sin(theta) / lambda,
                  where 2 theta is the scattering angle, and lambda is
                  the wavelength of the incident beam. These should usually
                  be specified at uniform values of q.
    groupMap      a sequence of group names to use in the scattering calc.
    formFactors   a sequence of maps of group name to effective form factor,
                  one for each value of scattering vector- in the same order
    iFormFactors  a sequence of maps of atom index to effective form factor,
                  one for each value of scattering vector- in the same order.
                  Generally, individual atoms need not be specified-
                  but are rather specified by group name. This is for 
                  exceptions, and will override any group entry.
    globDefs      a sequence of glob definitions. Each definition is a 
                  sequence of tuples (w,index), where w is a weight and index
                  is an atom index.
    experiment    solvent-corrected experimental scattering intensity values-
                  one for each value of q.
    simulation    optional simulation.Simulation object.
  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.
 
members:
 The following parameters can be set [defaults in square brackets]
 
  scale            - scale factor (force constant) [1]
 
  weights   - sequence of factors to weight calculated scattering intensity
              to its corresponding experimental value. Used for rms, energy 
              calculation. See below. Default is a value of 1 for all.
 
  calcType  - specifies how I(q) is to be calculated. Valid values are
                "n2"  - use the exact, but slow Debye formula.
                "n"   - numerically integrate over surface of constant
                        q, using theta, phi values determined by angleType
                 "uniform" - a faster version of the n algorithm which
                             can be used if q values are equally spaced.
                 "multipole" - Use the spherical harmonic expansion of
                                 Svergun, Barberato and Koch, 
                                 J. Appl. Cryt. 28, 768 (1995)
                               Note: at this time it is not possible
                               to refine using the calcType, as the 
                               derivatives are not yet coded.
 
 
  numAngles - for calcTypes n and uniform, the number of (theta,phi)
              pairs to use in the evaluation of I(q).
 
  qValues   - return the values of scattering vector amplitude q.
 
  formFactors  - specified the formFactor map.
 
  iFormFactors - specify the atom-indexed formFactor map.
 
  angleType - specifies how (theta,phi) angle pairs are chosen over
              the surface of a sphere. Choices are:
                "random"    - choose randomly- not recommended.
                "fibonacci" - method based on Fibonacci numbers.
                                D. Svergun, Acta Cryst. A50, 391 (1994).
                "spiral"    - spiral algorithm from 
                                E.B. Saff and A.B.J. Kuijlaars, 
                                Distributing Many Points on a Sphere,
                                The Mathematical Intelligencer, 19(1), 
                                Winter (1997).
                              This is the preferred algorithm.
 
  lMax      - for calcType multipole, the maximum value of l to use in
              the spherical harmonic expansion.
 
  cmpType   - should be "plain" or "log." This controls whether the
              logarithm is taken before the energy is evaluated. See below.
              [Default: plain]
 
  globs     - sequence of glob definitions - see description above.
 
  normalizeIndex - if greater than or equal to zero, specifies which
                   value of q at which to consider Icalc and Iobs to be
                   equal. If the value is -2, the normalization is taken
                   as the average of the Icalc or Iobs values weighted by
                   weights. If the value of normalizeIndex lies outside 
                   the above values, no normalization is performed. If the
                   value -3 is specified, the normalization will instead 
                   minimize chi^2. 
                   [default: -2]
 
  radiusScale - scale factor used in the calculation of the displaced
                solvent scattering contribution. See below.
 
  volumeScale - scale factor used in the calculation of the displaced
                solvent scattering contribution. See below.
 
  radiusType  - "radius" or "volume" - specifies the method used for 
                computing atomic radii. See below.
 
  rho0        - excluded solvent electron density.
 
  calcBoundary         - boolean - whether to calculate boundary layer 
                         scattering contribution [default: False]
 
  rhob                 - boundary layer electron density [default: 0.03]
 
  boundaryPointsPerAtom- how many samples of the boundary layer to make
                         (per atom) [default: 0.5].
 
  boundaryThickness    - the thickness of the boundary layer [default: 2.88].
 
  solventRadius        - radius used in the surface computation 
                         [default: 1.44]. 
 
  formScale   - overall scale factor for vacuum atomic form factors.
 
  useGlobs  - whether or not to use globs in the scattering calculation.
 
  verbose   - if true, produce more detailed output [False]
 
  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).
 
 
  QValues - a plain member containing values of (x,y,z) on a r=1
            sphere used for numerical integration of I(q).
 
 
methods:
  
  calcEnergy()                 - calc energy, returns the energy value.
  calcEnergyAndDerivs(derivs)  - calc energy, derivs, returns the energy value.
 
  calcGlobCorrect(val) - calculate the globic correction factor. The argument
                         val can be calcType (e.g. 'n2'), in which case 
                         the globic correction factor will be calculated by
                         using the specified calcType. val can alternatively
                         be a raw array of I(q) values which are used to
                         generate g(q). val defaults to the current calcType.
 
  globCorrect() - return the current globic correction factor.
 
  getF()        - return a matrix of scattering amplitudes at each angle
                  and q value.
 
  rms()         - return the rms of calcedShift - effShift
 
  info()       - string with current info about the state of this instance
  simulation() - return the associated simulation.Simulation.
 
  expt()    - return the observed values of I(q) (as set in the constructor).
  calcd()   - return the calculated values of I(q).
 
  exptScale()  Iobs(qn), for n=normalizeIndex, if normalizeIndex>-1, 
               1 otherwise.
  calcScale()  Icalc(qn), for n=normalizeIndex, if normalizeIndex>-1, 
               1 otherwise.
 
  I_contrib(memberIndex) - the scatter intensity from the specified ensemble
                           member structure, or the local member if the
                           index is omitted.
  boundaryI()            - scattering intensity contribution from the boundary
                           layer.
  selection()            - return the atom selection specified in the 
                           constructor.
  radii()                - return array of atomic radii
  aveRadius()            - average atomic radius.
  aveVolume()            - average atomic volume.
 
  boundaryVol()          - volume of the boundary layer.
  
  calcBoundaryPoints()   - calculate new points used to compute the 
                           boundary layer scattering contribution.
 
 
Energy is calculated as
 
  scale * rms^2
 
where
 
   rms^2 = sum_i w_i (Icalc_i - Iobs_i)^2 / (Nq),
 
in which Nq is the total number of values of q at which Iobs is
specified, and w_i is the corresponding weight. Typically, we choose
w_i = (sigma_i)^(-2), where sigma_i is the error in I(q) at q=q_i.
 
Given a set of atomic coordinates the scattering intensity is
calculated from the following expression: 
 
    I(q) = <| A(Q) |^2>_q
 
where <>_q denotes average over solid angle at constant amplitude of
the scattering vector.
 
The scattering amplitude A(Q) consists of a sum of contributions from
each atom (usually only heavy atoms are included)
 
  A(Q) = sum_j f_j(q) exp(i dot(Q,r_j)) + 
         sum_j2 rhob(r_j2) exp(i dot(Q,r_j2))
 
where f_j(q) is the total effective scattering amplitude of atom j
(including excluded solvent effects), and r_j is atom j's position. The
second contribution is due to boundary-layer scattering, and the sum
over j2 is, in principle an integral over the region in which rhob,
the boundary layer density is nonzero.
 
For rhob=0, the integral over solid angle can be carried out
analytically, resulting in the Debye formula calcType=n2:
 
  I(q) = sum_j1 sum_j2 f_j1(q) f_j2(q) sinc(q |r_j1-r_j2|)
 
where sinc(x) = sin(x) / x.
 
This expression is quite expensive for biological systems due to the
double sum.
 
One alternative is to express A(Q) as an expansion in terms of
spherical harmonic functions (calcType=multipole), and approximate
I(q) by truncating the expansion. This is works well (is efficient)
for small scattering angles - like those used in most SAXS
experiments. For larger angles, the expansion fails spectacularly.
 
One can also evaluate the integral over solid angle by simple grid
integration (calcTypes=n, uniform). This works well for all moderate
values of q.
 
Excluded Solvent Treatment:
 
  The total atomic effective scattering amplitude is
 
   f_j(q) = fv_j(q) - g_j(q),
 
where fv_j(q) is the vacuum atomic form factor, and g_j is an excluded
solvent contribution
 
  g_j(q) = rho0 * V_j * exp(-s**2 * PI * V_j**(2./3)) *
           volumeScale * exp(-q**2 * PI * (4PI/3)^{1/3} * (r0^2 - rm^2)),
 
which depends on atomic volume V_j and scaled scattering vector
amplitude s=q/(2PI). rm is aveRadius() and r0 is a scaled radius
 
   r0= radiusScale() * rm
 
If radiusType=="volume" (the default), rm actually is computed as the
radius corresoponding to aveVolume() [i.e. (3 Vm / (4 PI))^(1/3) ]
 
Boundary Layer Treatment:
 
The boundary layer contribution is computed based on a molecular
surface generated using surfD. The molecular surface is generated
based on atomic radii and solventRadius(). For each atom,
boundaryPointsPerAtom() points are randomly placed in a section of a
sphere of each convex face extending from the surface out a distance
boundaryThickness(). The contribution is appropriately weighted by
volume of the section. Because of the random placement, repeated calls
to the same surface will yield slightly different values scattering
intensity. 
 
Ensemble Calculations
 
When calculated in the context of an ensembleSimulation.EnsembleSimulation
the scattering intensity becomes:
 
   I(q) = sum_n W_n I_n(q)
 
where the sum is over all members of an ensemble, w_n is the weight
for ensemble member n, and I_n(q) is the scattering intensity from
ensemble member n, calculated as above.
 
One should note that the approximate methods of calculating I(q)
introduce a rotational dependence: the grid on which the scattering
amplitude is calculated is fixed in space. This rotational dependence
implies that the potential energy term is not constant upon overall
rotation. The amount of the rotational dependence decreases with
increased numAngles. A future enhancement may have the grid rotate
along with the rest of the system.
 
 
 
# This file was created automatically by SWIG.
# Don't modify this file, modify the SWIG interface instead.
# This file is compatible with both classic and new-style classes.

 
Classes
       
__builtin__.object
CDSList_FloatPair
CDSList_FloatPairPtr
CDSVector_CDSVector_Complex
CDSVector_CDSVector_ComplexPtr
Modified
ModifiedPtr
ModifiedBase
ModifiedBasePtr
SolnScatPot_FracElec_SelIndex
SolnScatPot_FracElec_SelIndexPtr
SolnScatPot_real
SolnScatPot_realPtr
SolnScattBase
SolnScatPot_real_LetterClass
SolnScatPot_real_LetterClassPtr
SolnScattBasePtr

 
class CDSList_FloatPair(__builtin__.object)
   
 

 
  Methods defined here:
__del__(self, destroy=<built-in function delete_CDSList_FloatPair>)

 
__delitem__(*args)

 
__getattr__ lambda self, name

 
__getitem__(*args)

 
__getslice__(*args)

 
__init__(self, *args)

 
__len__(*args)

 
__repr__(self)

 
__setattr__ lambda self, name, value

 
__setitem__(*args)

 
help(*args)

 

Data and other attributes defined here:
__dict__ = <dictproxy object at 0x290ea28>

 
dictionary for instance variables (if defined)
__swig_getmethods__ = {}
__swig_setmethods__ = {}
__weakref__ = <attribute '__weakref__' of 'CDSList_FloatPair' objects>

 
list of weak references to the object (if defined)

 
class CDSList_FloatPairPtr(CDSList_FloatPair)
   
 

 
 
Method resolution order:
CDSList_FloatPairPtr
CDSList_FloatPair
__builtin__.object

Methods defined here:
__init__(self, this)

 

Methods inherited from CDSList_FloatPair:
__del__(self, destroy=<built-in function delete_CDSList_FloatPair>)

 
__delitem__(*args)

 
__getattr__ lambda self, name

 
__getitem__(*args)

 
__getslice__(*args)

 
__len__(*args)

 
__repr__(self)

 
__setattr__ lambda self, name, value

 
__setitem__(*args)

 
help(*args)

 

Data and other attributes inherited from CDSList_FloatPair:
__dict__ = <dictproxy object at 0x290ea98>

 
dictionary for instance variables (if defined)
__swig_getmethods__ = {}
__swig_setmethods__ = {}
__weakref__ = <attribute '__weakref__' of 'CDSList_FloatPair' objects>

 
list of weak references to the object (if defined)

 
class CDSVector_CDSVector_Complex(__builtin__.object)
   
 

 
  Methods defined here:
__add__(*args)

 
__del__(self, destroy=<built-in function delete_CDSVector_CDSVector_Complex>)

 
__div__(*args)

 
__getattr__ lambda self, name

 
__getitem__(*args)

 
__getslice__(*args)

 
__iadd__(*args)

 
__idiv__(*args)

 
__imul__(*args)

 
__init__(self, *args)

 
__isub__(*args)

 
__len__(*args)

 
__mul__(*args)

 
__neg__(*args)

 
__pow__(*args)

 
__repr__(self)

 
__rmul__(*args)

 
__setattr__ lambda self, name, value

 
__setitem__(*args)

 
__str__(*args)

 
__sub__(*args)

 
fromList(s, l)

 
help(*args)

 
resize(*args)

 
scale(*args)

 
set(*args)

 

Data and other attributes defined here:
__dict__ = <dictproxy object at 0x290ea28>

 
dictionary for instance variables (if defined)
__swig_getmethods__ = {}
__swig_setmethods__ = {}
__weakref__ = <attribute '__weakref__' of 'CDSVector_CDSVector_Complex' objects>

 
list of weak references to the object (if defined)

 
class CDSVector_CDSVector_ComplexPtr(CDSVector_CDSVector_Complex)
   
 

 
 
Method resolution order:
CDSVector_CDSVector_ComplexPtr
CDSVector_CDSVector_Complex
__builtin__.object

Methods defined here:
__init__(self, this)

 

Methods inherited from CDSVector_CDSVector_Complex:
__add__(*args)

 
__del__(self, destroy=<built-in function delete_CDSVector_CDSVector_Complex>)

 
__div__(*args)

 
__getattr__ lambda self, name

 
__getitem__(*args)

 
__getslice__(*args)

 
__iadd__(*args)

 
__idiv__(*args)

 
__imul__(*args)

 
__isub__(*args)

 
__len__(*args)

 
__mul__(*args)

 
__neg__(*args)

 
__pow__(*args)

 
__repr__(self)

 
__rmul__(*args)

 
__setattr__ lambda self, name, value

 
__setitem__(*args)

 
__str__(*args)

 
__sub__(*args)

 
fromList(s, l)

 
help(*args)

 
resize(*args)

 
scale(*args)

 
set(*args)

 

Data and other attributes inherited from CDSVector_CDSVector_Complex:
__dict__ = <dictproxy object at 0x290e8a0>

 
dictionary for instance variables (if defined)
__swig_getmethods__ = {}
__swig_setmethods__ = {}
__weakref__ = <attribute '__weakref__' of 'CDSVector_CDSVector_Complex' objects>

 
list of weak references to the object (if defined)

 
class Modified(__builtin__.object)
   
 

 
  Methods defined here:
__call__(*args)

 
__del__(self, destroy=<built-in function delete_Modified>)

 
__getattr__ lambda self, name

 
__init__(self, *args)

 
__repr__(self)

 
__setattr__ lambda self, name, value

 
clear(*args)

 
set(*args)

 
update(*args)

 
value(*args)

 

Data and other attributes defined here:
MOD_SELF = 1
MOD_SIMULATION = 2
__dict__ = <dictproxy object at 0x290ead0>

 
dictionary for instance variables (if defined)
__swig_getmethods__ = {}
__swig_setmethods__ = {}
__weakref__ = <attribute '__weakref__' of 'Modified' objects>

 
list of weak references to the object (if defined)

 
class ModifiedBase(__builtin__.object)
   
 

 
  Methods defined here:
__del__(self, destroy=<built-in function delete_ModifiedBase>)

 
__getattr__ lambda self, name

 
__init__(self)

 
__repr__(self)

 
__setattr__ lambda self, name, value

 
registerTo(*args)

 
unRegister(*args)

 
updateValues(*args)

 

Properties defined here:
modified

 
get = ModifiedBase_modified_get(...)

 
set = ModifiedBase_modified_set(...)

 
registeredSimulations

 
get = ModifiedBase_registeredSimulations_get(...)

 
set = ModifiedBase_registeredSimulations_set(...)

 

Data and other attributes defined here:
__dict__ = <dictproxy object at 0x290ead0>

 
dictionary for instance variables (if defined)
__swig_getmethods__ = {'modified': <built-in function ModifiedBase_modified_get>, 'registeredSimulations': <built-in function ModifiedBase_registeredSimulations_get>}
__swig_setmethods__ = {'modified': <built-in function ModifiedBase_modified_set>, 'registeredSimulations': <built-in function ModifiedBase_registeredSimulations_set>}
__weakref__ = <attribute '__weakref__' of 'ModifiedBase' objects>

 
list of weak references to the object (if defined)

 
class ModifiedBasePtr(ModifiedBase)
   
 

 
 
Method resolution order:
ModifiedBasePtr
ModifiedBase
__builtin__.object

Methods defined here:
__init__(self, this)

 

Methods inherited from ModifiedBase:
__del__(self, destroy=<built-in function delete_ModifiedBase>)

 
__getattr__ lambda self, name

 
__repr__(self)

 
__setattr__ lambda self, name, value

 
registerTo(*args)

 
unRegister(*args)

 
updateValues(*args)

 

Properties inherited from ModifiedBase:
modified

 
get = ModifiedBase_modified_get(...)

 
set = ModifiedBase_modified_set(...)

 
registeredSimulations

 
get = ModifiedBase_registeredSimulations_get(...)

 
set = ModifiedBase_registeredSimulations_set(...)

 

Data and other attributes inherited from ModifiedBase:
__dict__ = <dictproxy object at 0x290e8a0>

 
dictionary for instance variables (if defined)
__swig_getmethods__ = {'modified': <built-in function ModifiedBase_modified_get>, 'registeredSimulations': <built-in function ModifiedBase_registeredSimulations_get>}
__swig_setmethods__ = {'modified': <built-in function ModifiedBase_modified_set>, 'registeredSimulations': <built-in function ModifiedBase_registeredSimulations_set>}
__weakref__ = <attribute '__weakref__' of 'ModifiedBase' objects>

 
list of weak references to the object (if defined)

 
class ModifiedPtr(Modified)
   
 

 
 
Method resolution order:
ModifiedPtr
Modified
__builtin__.object

Methods defined here:
__init__(self, this)

 

Methods inherited from Modified:
__call__(*args)

 
__del__(self, destroy=<built-in function delete_Modified>)

 
__getattr__ lambda self, name

 
__repr__(self)

 
__setattr__ lambda self, name, value

 
clear(*args)

 
set(*args)

 
update(*args)

 
value(*args)

 

Data and other attributes inherited from Modified:
MOD_SELF = 1
MOD_SIMULATION = 2
__dict__ = <dictproxy object at 0x290e718>

 
dictionary for instance variables (if defined)
__swig_getmethods__ = {}
__swig_setmethods__ = {}
__weakref__ = <attribute '__weakref__' of 'Modified' objects>

 
list of weak references to the object (if defined)

 
class SolnScatPot_FracElec_SelIndex(__builtin__.object)
   
 

 
  Methods defined here:
__del__(self, destroy=<built-in function delete_SolnScatPot_FracElec_SelIndex>)

 
__getattr__ lambda self, name

 
__init__(self, *args)

 
__repr__(self)

 
__setattr__ lambda self, name, value

 

Properties defined here:
fracElec

 
get = SolnScatPot_FracElec_SelIndex_fracElec_get(...)

 
set = SolnScatPot_FracElec_SelIndex_fracElec_set(...)

 
selIndex

 
get = SolnScatPot_FracElec_SelIndex_selIndex_get(...)

 
set = SolnScatPot_FracElec_SelIndex_selIndex_set(...)

 

Data and other attributes defined here:
__dict__ = <dictproxy object at 0x290e868>

 
dictionary for instance variables (if defined)
__swig_getmethods__ = {'fracElec': <built-in function SolnScatPot_FracElec_SelIndex_fracElec_get>, 'selIndex': <built-in function SolnScatPot_FracElec_SelIndex_selIndex_get>}
__swig_setmethods__ = {'fracElec': <built-in function SolnScatPot_FracElec_SelIndex_fracElec_set>, 'selIndex': <built-in function SolnScatPot_FracElec_SelIndex_selIndex_set>}
__weakref__ = <attribute '__weakref__' of 'SolnScatPot_FracElec_SelIndex' objects>

 
list of weak references to the object (if defined)

 
class SolnScatPot_FracElec_SelIndexPtr(SolnScatPot_FracElec_SelIndex)
   
 

 
 
Method resolution order:
SolnScatPot_FracElec_SelIndexPtr
SolnScatPot_FracElec_SelIndex
__builtin__.object

Methods defined here:
__init__(self, this)

 

Methods inherited from SolnScatPot_FracElec_SelIndex:
__del__(self, destroy=<built-in function delete_SolnScatPot_FracElec_SelIndex>)

 
__getattr__ lambda self, name

 
__repr__(self)

 
__setattr__ lambda self, name, value

 

Properties inherited from SolnScatPot_FracElec_SelIndex:
fracElec

 
get = SolnScatPot_FracElec_SelIndex_fracElec_get(...)

 
set = SolnScatPot_FracElec_SelIndex_fracElec_set(...)

 
selIndex

 
get = SolnScatPot_FracElec_SelIndex_selIndex_get(...)

 
set = SolnScatPot_FracElec_SelIndex_selIndex_set(...)

 

Data and other attributes inherited from SolnScatPot_FracElec_SelIndex:
__dict__ = <dictproxy object at 0x290ea98>

 
dictionary for instance variables (if defined)
__swig_getmethods__ = {'fracElec': <built-in function SolnScatPot_FracElec_SelIndex_fracElec_get>, 'selIndex': <built-in function SolnScatPot_FracElec_SelIndex_selIndex_get>}
__swig_setmethods__ = {'fracElec': <built-in function SolnScatPot_FracElec_SelIndex_fracElec_set>, 'selIndex': <built-in function SolnScatPot_FracElec_SelIndex_selIndex_set>}
__weakref__ = <attribute '__weakref__' of 'SolnScatPot_FracElec_SelIndex' objects>

 
list of weak references to the object (if defined)

 
class SolnScatPot_real(__builtin__.object)
   
 

 
  Methods defined here:
I_contrib(*args)

 
__del__(self, destroy=<built-in function delete_SolnScatPot_real>)

 
__deref__(*args)

 
__getattr__ lambda self, name

 
__init__(self, *args)

 
__mul__(*args)

 
__oldinit__ = __init__(self, *args)

 
__repr__(self)

 
__setattr__ lambda self, name, value

 
angleType(*args)

 
aveRadius(*args)

 
aveVolume(*args)

 
boundaryI(*args)

 
boundaryPointsPerAtom(*args)

 
boundaryThickness(*args)

 
boundaryVol(*args)

 
calcBoundary(*args)

 
calcBoundaryPoints(*args)

 
calcDeriv_N(*args)

 
calcDeriv_N2(*args)

 
calcDeriv_uniform(*args)

 
calcEnergy(*args)

 
calcEnergyAndDerivs(*args)

 
calcFGlob(*args)

 
calcGlobCorrect_calcType(*args)

 
calcGlobCorrect_new(s, arg='current')

 
swig can't handle the enumtypemap with this overridden method:
we must do it manually
calcGlobCorrect_vec(*args)

 
calcI_N(*args)

 
calcI_N2(*args)

 
calcI_multipole(*args)

 
calcI_uniform(*args)

 
calcPosGlob(*args)

 
calcType(*args)

 
calc_g(*args)

 
calcd(*args)

 
calcdScale(*args)

 
cmpType(*args)

 
convertFormFactors(*args)

 
energyMaybeDerivs0(*args)

 
energyMaybeDerivs1(*args)

 
energyMaybeDerivs2(*args)

 
energyMaybeDerivs3(*args)

 
energyMaybeDerivs4(*args)

 
ensWeight(*args)

 
expt(*args)

 
exptScale(*args)

 
formFactors(*args)

 
formScale(*args)

 
getF(*args)

 
globCorrectCalcType(*args)

 
globCorrectMovement(*args)

 
globCorrectReference(*args)

 
globCorrectSteps(*args)

 
globs(*args)

 
iFormFactors(*args)

 
incrRefCount(*args)

 
info(*args)

 
instanceData(*args)

 
instanceName(*args)

 
lMax(*args)

 
normalizeIndex(*args)

 
numAngles(*args)

 
numRestraints(*args)

 
pointer(*args)

 
potName(*args)

 
qValues(*args)

 
radii(*args)

 
radiusScale(*args)

 
radiusType(*args)

 
registerInstanceData(*args)

 
registerTo(*args)

 
resetPotName(*args)

 
rho0(*args)

 
rhob(*args)

 
rms(*args)

 
scale(*args)

 
selection(*args)

 
setAngleType(*args)

 
setBoundaryPointsPerAtom(*args)

 
setBoundaryThickness(*args)

 
setCalcBoundary(*args)

 
setCalcType(*args)

 
setCmpType(*args)

 
setEnsWeights(*args)

 
setFormFactors(*args)

 
setFormScale(*args)

 
setGlobCorrectCalcType(*args)

 
setGlobCorrectMovement(*args)

 
setGlobCorrectReference(*args)

 
setGlobCorrectSteps(*args)

 
setGlobs(*args)

 
setIFormFactors(*args)

 
setLMax(*args)

 
setNormalizeIndex(*args)

 
setNumAngles(*args)

 
setQValues(*args)

 
setRadiusScale(*args)

 
setRadiusType(*args)

 
setRho0(*args)

 
setRhob(*args)

 
setScale(*args)

 
setSolventRadius(*args)

 
setThreshold(*args)

 
setUseGlobs(*args)

 
setUseSimEnsWeights(*args)

 
setVerbose(*args)

 
setVolumeScale(*args)

 
setWeights(*args)

 
simulation(*args)

 
solventRadius(*args)

 
threshold(*args)

 
unRegister(*args)

 
updateDelta(*args)

 
updateGlobCorrect(*args)

 
updateValues(*args)

 
useGlobs(*args)

 
useSimEnsWeights(*args)

 
verbose(*args)

 
violations(*args)

 
volumeScale(*args)

 
weights(*args)

 

Properties defined here:
QValues

 
get = SolnScatPot_real_QValues_get(...)

 
set = SolnScatPot_real_QValues_set(...)

 
boundaryF

 
get = SolnScatPot_real_boundaryF_get(...)

 
set = SolnScatPot_real_boundaryF_set(...)

 
boundaryI_

 
get = SolnScatPot_real_boundaryI__get(...)

 
set = SolnScatPot_real_boundaryI__set(...)

 
boundaryPoints

 
get = SolnScatPot_real_boundaryPoints_get(...)

 
set = SolnScatPot_real_boundaryPoints_set(...)

 
fGlob

 
get = SolnScatPot_real_fGlob_get(...)

 
set = SolnScatPot_real_fGlob_set(...)

 
fValues

 
get = SolnScatPot_real_fValues_get(...)

 
set = SolnScatPot_real_fValues_set(...)

 
globCorrect

 
get = SolnScatPot_real_globCorrect_get(...)

 
set = SolnScatPot_real_globCorrect_set(...)

 
instanceData_

 
get = SolnScatPot_real_instanceData__get(...)

 
set = SolnScatPot_real_instanceData__set(...)

 
modified

 
get = SolnScatPot_real_modified_get(...)

 
set = SolnScatPot_real_modified_set(...)

 
posCenter

 
get = SolnScatPot_real_posCenter_get(...)

 
set = SolnScatPot_real_posCenter_set(...)

 
posGlob

 
get = SolnScatPot_real_posGlob_get(...)

 
set = SolnScatPot_real_posGlob_set(...)

 
registeredSimulations

 
get = SolnScatPot_real_registeredSimulations_get(...)

 
set = SolnScatPot_real_registeredSimulations_set(...)

 
surfaceAreaFraction

 
get = SolnScatPot_real_surfaceAreaFraction_get(...)

 
set = SolnScatPot_real_surfaceAreaFraction_set(...)

 

Data and other attributes defined here:
__dict__ = <dictproxy object at 0x290e8d8>

 
dictionary for instance variables (if defined)
__swig_getmethods__ = {'QValues': <built-in function SolnScatPot_real_QValues_get>, 'boundaryF': <built-in function SolnScatPot_real_boundaryF_get>, 'boundaryI_': <built-in function SolnScatPot_real_boundaryI__get>, 'boundaryPoints': <built-in function SolnScatPot_real_boundaryPoints_get>, 'fGlob': <built-in function SolnScatPot_real_fGlob_get>, 'fValues': <built-in function SolnScatPot_real_fValues_get>, 'globCorrect': <built-in function SolnScatPot_real_globCorrect_get>, 'instanceData_': <built-in function SolnScatPot_real_instanceData__get>, 'modified': <built-in function SolnScatPot_real_modified_get>, 'posCenter': <built-in function SolnScatPot_real_posCenter_get>, ...}
__swig_setmethods__ = {'QValues': <built-in function SolnScatPot_real_QValues_set>, 'boundaryF': <built-in function SolnScatPot_real_boundaryF_set>, 'boundaryI_': <built-in function SolnScatPot_real_boundaryI__set>, 'boundaryPoints': <built-in function SolnScatPot_real_boundaryPoints_set>, 'fGlob': <built-in function SolnScatPot_real_fGlob_set>, 'fValues': <built-in function SolnScatPot_real_fValues_set>, 'globCorrect': <built-in function SolnScatPot_real_globCorrect_set>, 'instanceData_': <built-in function SolnScatPot_real_instanceData__set>, 'modified': <built-in function SolnScatPot_real_modified_set>, 'posCenter': <built-in function SolnScatPot_real_posCenter_set>, ...}
__weakref__ = <attribute '__weakref__' of 'SolnScatPot_real' objects>

 
list of weak references to the object (if defined)
cdsMatrix = <module 'cdsMatrix' from '/home/schwitrs/xplor-bzr/bin.Linux_2.6_x86_64/cdsMatrix.pyo'>

 
class SolnScatPot_realPtr(SolnScatPot_real)
   
 

 
 
Method resolution order:
SolnScatPot_realPtr
SolnScatPot_real
__builtin__.object

Methods defined here:
__init__(self, this)

 

Methods inherited from SolnScatPot_real:
I_contrib(*args)

 
__del__(self, destroy=<built-in function delete_SolnScatPot_real>)

 
__deref__(*args)

 
__getattr__ lambda self, name

 
__mul__(*args)

 
__oldinit__ = __init__(self, *args)

 
__repr__(self)

 
__setattr__ lambda self, name, value

 
angleType(*args)

 
aveRadius(*args)

 
aveVolume(*args)

 
boundaryI(*args)

 
boundaryPointsPerAtom(*args)

 
boundaryThickness(*args)

 
boundaryVol(*args)

 
calcBoundary(*args)

 
calcBoundaryPoints(*args)

 
calcDeriv_N(*args)

 
calcDeriv_N2(*args)

 
calcDeriv_uniform(*args)

 
calcEnergy(*args)

 
calcEnergyAndDerivs(*args)

 
calcFGlob(*args)

 
calcGlobCorrect_calcType(*args)

 
calcGlobCorrect_new(s, arg='current')

 
swig can't handle the enumtypemap with this overridden method:
we must do it manually
calcGlobCorrect_vec(*args)

 
calcI_N(*args)

 
calcI_N2(*args)

 
calcI_multipole(*args)

 
calcI_uniform(*args)

 
calcPosGlob(*args)

 
calcType(*args)

 
calc_g(*args)

 
calcd(*args)

 
calcdScale(*args)

 
cmpType(*args)

 
convertFormFactors(*args)

 
energyMaybeDerivs0(*args)

 
energyMaybeDerivs1(*args)

 
energyMaybeDerivs2(*args)

 
energyMaybeDerivs3(*args)

 
energyMaybeDerivs4(*args)

 
ensWeight(*args)

 
expt(*args)

 
exptScale(*args)

 
formFactors(*args)

 
formScale(*args)

 
getF(*args)

 
globCorrectCalcType(*args)

 
globCorrectMovement(*args)

 
globCorrectReference(*args)

 
globCorrectSteps(*args)

 
globs(*args)

 
iFormFactors(*args)

 
incrRefCount(*args)

 
info(*args)

 
instanceData(*args)

 
instanceName(*args)

 
lMax(*args)

 
normalizeIndex(*args)

 
numAngles(*args)

 
numRestraints(*args)

 
pointer(*args)

 
potName(*args)

 
qValues(*args)

 
radii(*args)

 
radiusScale(*args)

 
radiusType(*args)

 
registerInstanceData(*args)

 
registerTo(*args)

 
resetPotName(*args)

 
rho0(*args)

 
rhob(*args)

 
rms(*args)

 
scale(*args)

 
selection(*args)

 
setAngleType(*args)

 
setBoundaryPointsPerAtom(*args)

 
setBoundaryThickness(*args)

 
setCalcBoundary(*args)

 
setCalcType(*args)

 
setCmpType(*args)

 
setEnsWeights(*args)

 
setFormFactors(*args)

 
setFormScale(*args)

 
setGlobCorrectCalcType(*args)

 
setGlobCorrectMovement(*args)

 
setGlobCorrectReference(*args)

 
setGlobCorrectSteps(*args)

 
setGlobs(*args)

 
setIFormFactors(*args)

 
setLMax(*args)

 
setNormalizeIndex(*args)

 
setNumAngles(*args)

 
setQValues(*args)

 
setRadiusScale(*args)

 
setRadiusType(*args)

 
setRho0(*args)

 
setRhob(*args)

 
setScale(*args)

 
setSolventRadius(*args)

 
setThreshold(*args)

 
setUseGlobs(*args)

 
setUseSimEnsWeights(*args)

 
setVerbose(*args)

 
setVolumeScale(*args)

 
setWeights(*args)

 
simulation(*args)

 
solventRadius(*args)

 
threshold(*args)

 
unRegister(*args)

 
updateDelta(*args)

 
updateGlobCorrect(*args)

 
updateValues(*args)

 
useGlobs(*args)

 
useSimEnsWeights(*args)

 
verbose(*args)

 
violations(*args)

 
volumeScale(*args)

 
weights(*args)

 

Properties inherited from SolnScatPot_real:
QValues

 
get = SolnScatPot_real_QValues_get(...)

 
set = SolnScatPot_real_QValues_set(...)

 
boundaryF

 
get = SolnScatPot_real_boundaryF_get(...)

 
set = SolnScatPot_real_boundaryF_set(...)

 
boundaryI_

 
get = SolnScatPot_real_boundaryI__get(...)

 
set = SolnScatPot_real_boundaryI__set(...)

 
boundaryPoints

 
get = SolnScatPot_real_boundaryPoints_get(...)

 
set = SolnScatPot_real_boundaryPoints_set(...)

 
fGlob

 
get = SolnScatPot_real_fGlob_get(...)

 
set = SolnScatPot_real_fGlob_set(...)

 
fValues

 
get = SolnScatPot_real_fValues_get(...)

 
set = SolnScatPot_real_fValues_set(...)

 
globCorrect

 
get = SolnScatPot_real_globCorrect_get(...)

 
set = SolnScatPot_real_globCorrect_set(...)

 
instanceData_

 
get = SolnScatPot_real_instanceData__get(...)

 
set = SolnScatPot_real_instanceData__set(...)

 
modified

 
get = SolnScatPot_real_modified_get(...)

 
set = SolnScatPot_real_modified_set(...)

 
posCenter

 
get = SolnScatPot_real_posCenter_get(...)

 
set = SolnScatPot_real_posCenter_set(...)

 
posGlob

 
get = SolnScatPot_real_posGlob_get(...)

 
set = SolnScatPot_real_posGlob_set(...)

 
registeredSimulations

 
get = SolnScatPot_real_registeredSimulations_get(...)

 
set = SolnScatPot_real_registeredSimulations_set(...)

 
surfaceAreaFraction

 
get = SolnScatPot_real_surfaceAreaFraction_get(...)

 
set = SolnScatPot_real_surfaceAreaFraction_set(...)

 

Data and other attributes inherited from SolnScatPot_real:
__dict__ = <dictproxy object at 0x290e868>

 
dictionary for instance variables (if defined)
__swig_getmethods__ = {'QValues': <built-in function SolnScatPot_real_QValues_get>, 'boundaryF': <built-in function SolnScatPot_real_boundaryF_get>, 'boundaryI_': <built-in function SolnScatPot_real_boundaryI__get>, 'boundaryPoints': <built-in function SolnScatPot_real_boundaryPoints_get>, 'fGlob': <built-in function SolnScatPot_real_fGlob_get>, 'fValues': <built-in function SolnScatPot_real_fValues_get>, 'globCorrect': <built-in function SolnScatPot_real_globCorrect_get>, 'instanceData_': <built-in function SolnScatPot_real_instanceData__get>, 'modified': <built-in function SolnScatPot_real_modified_get>, 'posCenter': <built-in function SolnScatPot_real_posCenter_get>, ...}
__swig_setmethods__ = {'QValues': <built-in function SolnScatPot_real_QValues_set>, 'boundaryF': <built-in function SolnScatPot_real_boundaryF_set>, 'boundaryI_': <built-in function SolnScatPot_real_boundaryI__set>, 'boundaryPoints': <built-in function SolnScatPot_real_boundaryPoints_set>, 'fGlob': <built-in function SolnScatPot_real_fGlob_set>, 'fValues': <built-in function SolnScatPot_real_fValues_set>, 'globCorrect': <built-in function SolnScatPot_real_globCorrect_set>, 'instanceData_': <built-in function SolnScatPot_real_instanceData__set>, 'modified': <built-in function SolnScatPot_real_modified_set>, 'posCenter': <built-in function SolnScatPot_real_posCenter_set>, ...}
__weakref__ = <attribute '__weakref__' of 'SolnScatPot_real' objects>

 
list of weak references to the object (if defined)
cdsMatrix = <module 'cdsMatrix' from '/home/schwitrs/xplor-bzr/bin.Linux_2.6_x86_64/cdsMatrix.pyo'>

 
class SolnScatPot_real_LetterClass(SolnScattBase)
   
 

 
 
Method resolution order:
SolnScatPot_real_LetterClass
SolnScattBase
__builtin__.object

Methods defined here:
I_contrib(*args)

 
__del__(self, destroy=<built-in function delete_SolnScatPot_real_LetterClass>)

 
__getattr__ lambda self, name

 
__init__(self, *args)

 
__repr__(self)

 
__setattr__ lambda self, name, value

 
angleType(*args)

 
aveRadius(*args)

 
aveVolume(*args)

 
boundaryI(*args)

 
boundaryPointsPerAtom(*args)

 
boundaryThickness(*args)

 
boundaryVol(*args)

 
calcBoundary(*args)

 
calcBoundaryPoints(*args)

 
calcDeriv_N(*args)

 
calcDeriv_N2(*args)

 
calcDeriv_uniform(*args)

 
calcFGlob(*args)

 
calcGlobCorrect_calcType(*args)

 
calcGlobCorrect_vec(*args)

 
calcI_N(*args)

 
calcI_N2(*args)

 
calcI_multipole(*args)

 
calcI_uniform(*args)

 
calcPosGlob(*args)

 
calcType(*args)

 
calc_g(*args)

 
calcd(*args)

 
calcdScale(*args)

 
cmpType(*args)

 
convertFormFactors(*args)

 
energyMaybeDerivs0(*args)

 
energyMaybeDerivs1(*args)

 
energyMaybeDerivs2(*args)

 
expt(*args)

 
exptScale(*args)

 
formFactors(*args)

 
formScale(*args)

 
getF(*args)

 
globCorrectCalcType(*args)

 
globCorrectMovement(*args)

 
globCorrectReference(*args)

 
globCorrectSteps(*args)

 
globs(*args)

 
help(*args)

 
iFormFactors(*args)

 
info(*args)

 
lMax(*args)

 
normalizeIndex(*args)

 
numAngles(*args)

 
numRestraints(*args)

 
qValues(*args)

 
radii(*args)

 
radiusScale(*args)

 
radiusType(*args)

 
rho0(*args)

 
rhob(*args)

 
rms(*args)

 
selection(*args)

 
setAngleType(*args)

 
setBoundaryPointsPerAtom(*args)

 
setBoundaryThickness(*args)

 
setCalcBoundary(*args)

 
setCalcType(*args)

 
setCmpType(*args)

 
setFormFactors(*args)

 
setFormScale(*args)

 
setGlobCorrectCalcType(*args)

 
setGlobCorrectMovement(*args)

 
setGlobCorrectReference(*args)

 
setGlobCorrectSteps(*args)

 
setGlobs(*args)

 
setIFormFactors(*args)

 
setLMax(*args)

 
setNormalizeIndex(*args)

 
setNumAngles(*args)

 
setQValues(*args)

 
setRadiusScale(*args)

 
setRadiusType(*args)

 
setRho0(*args)

 
setRhob(*args)

 
setSolventRadius(*args)

 
setUseGlobs(*args)

 
setVerbose(*args)

 
setVolumeScale(*args)

 
setWeights(*args)

 
simulation(*args)

 
solventRadius(*args)

 
updateDelta(*args)

 
updateGlobCorrect(*args)

 
useGlobs(*args)

 
verbose(*args)

 
violations(*args)

 
volumeScale(*args)

 
weights(*args)

 

Properties defined here:
QValues

 
get = SolnScatPot_real_LetterClass_QValues_get(...)

 
set = SolnScatPot_real_LetterClass_QValues_set(...)

 
boundaryF

 
get = SolnScatPot_real_LetterClass_boundaryF_get(...)

 
set = SolnScatPot_real_LetterClass_boundaryF_set(...)

 
boundaryI_

 
get = SolnScatPot_real_LetterClass_boundaryI__get(...)

 
set = SolnScatPot_real_LetterClass_boundaryI__set(...)

 
boundaryPoints

 
get = SolnScatPot_real_LetterClass_boundaryPoints_get(...)

 
set = SolnScatPot_real_LetterClass_boundaryPoints_set(...)

 
fGlob

 
get = SolnScatPot_real_LetterClass_fGlob_get(...)

 
set = SolnScatPot_real_LetterClass_fGlob_set(...)

 
fValues

 
get = SolnScatPot_real_LetterClass_fValues_get(...)

 
set = SolnScatPot_real_LetterClass_fValues_set(...)

 
globCorrect

 
get = SolnScatPot_real_LetterClass_globCorrect_get(...)

 
set = SolnScatPot_real_LetterClass_globCorrect_set(...)

 
posCenter

 
get = SolnScatPot_real_LetterClass_posCenter_get(...)

 
set = SolnScatPot_real_LetterClass_posCenter_set(...)

 
posGlob

 
get = SolnScatPot_real_LetterClass_posGlob_get(...)

 
set = SolnScatPot_real_LetterClass_posGlob_set(...)

 
surfaceAreaFraction

 
get = SolnScatPot_real_LetterClass_surfaceAreaFraction_get(...)

 
set = SolnScatPot_real_LetterClass_surfaceAreaFraction_set(...)

 

Data and other attributes defined here:
__swig_getmethods__ = {'QValues': <built-in function SolnScatPot_real_LetterClass_QValues_get>, 'boundaryF': <built-in function SolnScatPot_real_LetterClass_boundaryF_get>, 'boundaryI_': <built-in function SolnScatPot_real_LetterClass_boundaryI__get>, 'boundaryPoints': <built-in function SolnScatPot_real_LetterClass_boundaryPoints_get>, 'fGlob': <built-in function SolnScatPot_real_LetterClass_fGlob_get>, 'fValues': <built-in function SolnScatPot_real_LetterClass_fValues_get>, 'globCorrect': <built-in function SolnScatPot_real_LetterClass_globCorrect_get>, 'posCenter': <built-in function SolnScatPot_real_LetterClass_posCenter_get>, 'posGlob': <built-in function SolnScatPot_real_LetterClass_posGlob_get>, 'surfaceAreaFraction': <built-in function SolnScatPot_real_LetterClass_surfaceAreaFraction_get>}
__swig_setmethods__ = {'QValues': <built-in function SolnScatPot_real_LetterClass_QValues_set>, 'boundaryF': <built-in function SolnScatPot_real_LetterClass_boundaryF_set>, 'boundaryI_': <built-in function SolnScatPot_real_LetterClass_boundaryI__set>, 'boundaryPoints': <built-in function SolnScatPot_real_LetterClass_boundaryPoints_set>, 'fGlob': <built-in function SolnScatPot_real_LetterClass_fGlob_set>, 'fValues': <built-in function SolnScatPot_real_LetterClass_fValues_set>, 'globCorrect': <built-in function SolnScatPot_real_LetterClass_globCorrect_set>, 'posCenter': <built-in function SolnScatPot_real_LetterClass_posCenter_set>, 'posGlob': <built-in function SolnScatPot_real_LetterClass_posGlob_set>, 'surfaceAreaFraction': <built-in function SolnScatPot_real_LetterClass_surfaceAreaFraction_set>}

Data and other attributes inherited from SolnScattBase:
ANGLE_FIBONACCI = 1
ANGLE_RANDOM = 0
ANGLE_SPIRAL = 2
CALC_CURRENT = 4
CALC_MULTIPOLE = 3
CALC_N = 1
CALC_N2 = 0
CALC_NONE = 6
CALC_REFERENCE = 5
CALC_UNIFORM = 2
CMP_LOG = 0
CMP_PLAIN = 1
RADIUS = 0
VOLUME = 1
__dict__ = <dictproxy object at 0x290e868>

 
dictionary for instance variables (if defined)
__weakref__ = <attribute '__weakref__' of 'SolnScattBase' objects>

 
list of weak references to the object (if defined)

 
class SolnScatPot_real_LetterClassPtr(SolnScatPot_real_LetterClass)
   
 

 
 
Method resolution order:
SolnScatPot_real_LetterClassPtr
SolnScatPot_real_LetterClass
SolnScattBase
__builtin__.object

Methods defined here:
__init__(self, this)

 

Methods inherited from SolnScatPot_real_LetterClass:
I_contrib(*args)

 
__del__(self, destroy=<built-in function delete_SolnScatPot_real_LetterClass>)

 
__getattr__ lambda self, name

 
__repr__(self)

 
__setattr__ lambda self, name, value

 
angleType(*args)

 
aveRadius(*args)

 
aveVolume(*args)

 
boundaryI(*args)

 
boundaryPointsPerAtom(*args)

 
boundaryThickness(*args)

 
boundaryVol(*args)

 
calcBoundary(*args)

 
calcBoundaryPoints(*args)

 
calcDeriv_N(*args)

 
calcDeriv_N2(*args)

 
calcDeriv_uniform(*args)

 
calcFGlob(*args)

 
calcGlobCorrect_calcType(*args)

 
calcGlobCorrect_vec(*args)

 
calcI_N(*args)

 
calcI_N2(*args)

 
calcI_multipole(*args)

 
calcI_uniform(*args)

 
calcPosGlob(*args)

 
calcType(*args)

 
calc_g(*args)

 
calcd(*args)

 
calcdScale(*args)

 
cmpType(*args)

 
convertFormFactors(*args)

 
energyMaybeDerivs0(*args)

 
energyMaybeDerivs1(*args)

 
energyMaybeDerivs2(*args)

 
expt(*args)

 
exptScale(*args)

 
formFactors(*args)

 
formScale(*args)

 
getF(*args)

 
globCorrectCalcType(*args)

 
globCorrectMovement(*args)

 
globCorrectReference(*args)

 
globCorrectSteps(*args)

 
globs(*args)

 
help(*args)

 
iFormFactors(*args)

 
info(*args)

 
lMax(*args)

 
normalizeIndex(*args)

 
numAngles(*args)

 
numRestraints(*args)

 
qValues(*args)

 
radii(*args)

 
radiusScale(*args)

 
radiusType(*args)

 
rho0(*args)

 
rhob(*args)

 
rms(*args)

 
selection(*args)

 
setAngleType(*args)

 
setBoundaryPointsPerAtom(*args)

 
setBoundaryThickness(*args)

 
setCalcBoundary(*args)

 
setCalcType(*args)

 
setCmpType(*args)

 
setFormFactors(*args)

 
setFormScale(*args)

 
setGlobCorrectCalcType(*args)

 
setGlobCorrectMovement(*args)

 
setGlobCorrectReference(*args)

 
setGlobCorrectSteps(*args)

 
setGlobs(*args)

 
setIFormFactors(*args)

 
setLMax(*args)

 
setNormalizeIndex(*args)

 
setNumAngles(*args)

 
setQValues(*args)

 
setRadiusScale(*args)

 
setRadiusType(*args)

 
setRho0(*args)

 
setRhob(*args)

 
setSolventRadius(*args)

 
setUseGlobs(*args)

 
setVerbose(*args)

 
setVolumeScale(*args)

 
setWeights(*args)

 
simulation(*args)

 
solventRadius(*args)

 
updateDelta(*args)

 
updateGlobCorrect(*args)

 
useGlobs(*args)

 
verbose(*args)

 
violations(*args)

 
volumeScale(*args)

 
weights(*args)

 

Properties inherited from SolnScatPot_real_LetterClass:
QValues

 
get = SolnScatPot_real_LetterClass_QValues_get(...)

 
set = SolnScatPot_real_LetterClass_QValues_set(...)

 
boundaryF

 
get = SolnScatPot_real_LetterClass_boundaryF_get(...)

 
set = SolnScatPot_real_LetterClass_boundaryF_set(...)

 
boundaryI_

 
get = SolnScatPot_real_LetterClass_boundaryI__get(...)

 
set = SolnScatPot_real_LetterClass_boundaryI__set(...)

 
boundaryPoints

 
get = SolnScatPot_real_LetterClass_boundaryPoints_get(...)

 
set = SolnScatPot_real_LetterClass_boundaryPoints_set(...)

 
fGlob

 
get = SolnScatPot_real_LetterClass_fGlob_get(...)

 
set = SolnScatPot_real_LetterClass_fGlob_set(...)

 
fValues

 
get = SolnScatPot_real_LetterClass_fValues_get(...)

 
set = SolnScatPot_real_LetterClass_fValues_set(...)

 
globCorrect

 
get = SolnScatPot_real_LetterClass_globCorrect_get(...)

 
set = SolnScatPot_real_LetterClass_globCorrect_set(...)

 
posCenter

 
get = SolnScatPot_real_LetterClass_posCenter_get(...)

 
set = SolnScatPot_real_LetterClass_posCenter_set(...)

 
posGlob

 
get = SolnScatPot_real_LetterClass_posGlob_get(...)

 
set = SolnScatPot_real_LetterClass_posGlob_set(...)

 
surfaceAreaFraction

 
get = SolnScatPot_real_LetterClass_surfaceAreaFraction_get(...)

 
set = SolnScatPot_real_LetterClass_surfaceAreaFraction_set(...)

 

Data and other attributes inherited from SolnScatPot_real_LetterClass:
__swig_getmethods__ = {'QValues': <built-in function SolnScatPot_real_LetterClass_QValues_get>, 'boundaryF': <built-in function SolnScatPot_real_LetterClass_boundaryF_get>, 'boundaryI_': <built-in function SolnScatPot_real_LetterClass_boundaryI__get>, 'boundaryPoints': <built-in function SolnScatPot_real_LetterClass_boundaryPoints_get>, 'fGlob': <built-in function SolnScatPot_real_LetterClass_fGlob_get>, 'fValues': <built-in function SolnScatPot_real_LetterClass_fValues_get>, 'globCorrect': <built-in function SolnScatPot_real_LetterClass_globCorrect_get>, 'posCenter': <built-in function SolnScatPot_real_LetterClass_posCenter_get>, 'posGlob': <built-in function SolnScatPot_real_LetterClass_posGlob_get>, 'surfaceAreaFraction': <built-in function SolnScatPot_real_LetterClass_surfaceAreaFraction_get>}
__swig_setmethods__ = {'QValues': <built-in function SolnScatPot_real_LetterClass_QValues_set>, 'boundaryF': <built-in function SolnScatPot_real_LetterClass_boundaryF_set>, 'boundaryI_': <built-in function SolnScatPot_real_LetterClass_boundaryI__set>, 'boundaryPoints': <built-in function SolnScatPot_real_LetterClass_boundaryPoints_set>, 'fGlob': <built-in function SolnScatPot_real_LetterClass_fGlob_set>, 'fValues': <built-in function SolnScatPot_real_LetterClass_fValues_set>, 'globCorrect': <built-in function SolnScatPot_real_LetterClass_globCorrect_set>, 'posCenter': <built-in function SolnScatPot_real_LetterClass_posCenter_set>, 'posGlob': <built-in function SolnScatPot_real_LetterClass_posGlob_set>, 'surfaceAreaFraction': <built-in function SolnScatPot_real_LetterClass_surfaceAreaFraction_set>}

Data and other attributes inherited from SolnScattBase:
ANGLE_FIBONACCI = 1
ANGLE_RANDOM = 0
ANGLE_SPIRAL = 2
CALC_CURRENT = 4
CALC_MULTIPOLE = 3
CALC_N = 1
CALC_N2 = 0
CALC_NONE = 6
CALC_REFERENCE = 5
CALC_UNIFORM = 2
CMP_LOG = 0
CMP_PLAIN = 1
RADIUS = 0
VOLUME = 1
__dict__ = <dictproxy object at 0x290e868>

 
dictionary for instance variables (if defined)
__weakref__ = <attribute '__weakref__' of 'SolnScattBase' objects>

 
list of weak references to the object (if defined)

 
class SolnScattBase(__builtin__.object)
   
 

 
  Methods defined here:
__del__(self, destroy=<built-in function delete_SolnScattBase>)

 
__getattr__ lambda self, name

 
__init__(self, *args)

 
__repr__(self)

 
__setattr__ lambda self, name, value

 

Data and other attributes defined here:
ANGLE_FIBONACCI = 1
ANGLE_RANDOM = 0
ANGLE_SPIRAL = 2
CALC_CURRENT = 4
CALC_MULTIPOLE = 3
CALC_N = 1
CALC_N2 = 0
CALC_NONE = 6
CALC_REFERENCE = 5
CALC_UNIFORM = 2
CMP_LOG = 0
CMP_PLAIN = 1
RADIUS = 0
VOLUME = 1
__dict__ = <dictproxy object at 0x290e8d8>

 
dictionary for instance variables (if defined)
__swig_getmethods__ = {}
__swig_setmethods__ = {}
__weakref__ = <attribute '__weakref__' of 'SolnScattBase' objects>

 
list of weak references to the object (if defined)

 
class SolnScattBasePtr(SolnScattBase)
   
 

 
 
Method resolution order:
SolnScattBasePtr
SolnScattBase
__builtin__.object

Methods defined here:
__init__(self, this)

 

Methods inherited from SolnScattBase:
__del__(self, destroy=<built-in function delete_SolnScattBase>)

 
__getattr__ lambda self, name

 
__repr__(self)

 
__setattr__ lambda self, name, value

 

Data and other attributes inherited from SolnScattBase:
ANGLE_FIBONACCI = 1
ANGLE_RANDOM = 0
ANGLE_SPIRAL = 2
CALC_CURRENT = 4
CALC_MULTIPOLE = 3
CALC_N = 1
CALC_N2 = 0
CALC_NONE = 6
CALC_REFERENCE = 5
CALC_UNIFORM = 2
CMP_LOG = 0
CMP_PLAIN = 1
RADIUS = 0
VOLUME = 1
__dict__ = <dictproxy object at 0x290ea98>

 
dictionary for instance variables (if defined)
__swig_getmethods__ = {}
__swig_setmethods__ = {}
__weakref__ = <attribute '__weakref__' of 'SolnScattBase' objects>

 
list of weak references to the object (if defined)

 
Functions
       
calcIfromF(...)

 
fromPy(...)

 
help(...)

 
pairDistribution(...)

 
volContrib(...)

 

 
Data
        __package__ = None
pyXplorHelp = Type help() for interactive help, or help(object) for help about object.