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


Potential term to restrain a density map computed from atomic position to a
specified target map.
 
constructor: ProbDistPot(instanceName,
                         targetMap,
                         atomSel,
                         atomProb=None)
             - instanceName is an arbitray identifying string.
             - targetMap contains the densityGrid.DensityGrid map to which 
               the structure will be fitted.
             - atomSel specifies the atomSel.AtomSel used to generate a
               map.
             - the atomProb argument is an optional atomProb.AtomProb
               object used to generate a density map from atomic coordinates.
 
 
methods:
  calcEnergy()                 - calc energy, returns the energy value.
  calcEnergyAndDerivs(derivs)  - calc energy, derivs, returns the energy value.
 
  correlation()                - return the normalized cross-correlation between
                                 the map computed from atomic structure and
                                 the target map.
 
  rms()                        - ranges from 0 to 1. 0 means the maps matches 
                                 perfectly. 1 means maps are dissimilar.
 
  simulation()                 - return the simulation.Simulation
                                 associated with this energy term.
 
  targetMap()    - Return the densityGrid.DensityGrid object containing
                   the target map.
 
  atomProb()     - Return the atomProb.AtomProb object which contains the
                   map computed from atomic coordinates.
 
  info()                       - a string containing status information.
 
accessors:
 
   [ can be set using setAccessor( newVal ) ]
 
  scale()                      - force constant for this energy term.
 
  potType()                    - potential type: "diff" (default) or
                                 "cross_correlation"
  oAtom                        - accessors specifying atoms, whose positions
  xAtom                          specify projection orientation. If specified.
  yAtom                          the gradient with respect to projection
  zAtom                          orientation is collected for these atoms.
  tAtom                        - tAtom.pos()-oAtom.pos() specifies translation.
 
 
members:
 
  (direct member access is deprecated)
 
  targetMap_     - densityGrid.DensityGrid object containing the target
                   map.
  prStruct       - atomProb.AtomProb object which contains the
                   map computed from atomSel.
 
 
 
The energy is calculated from rhoObs_i and rhoCalc_i, respectively,
the observed and calculated density at gridpoint i by:
 
[for "cross_correlation" potType]
  E = scale * Natoms * rms 
 
for rms = 1 - C where C is the normalized cross-correlation:
 
              \sum_i rhoObs_i * rhoCalc_i 
   C = -------------------------------------------
       sqrt(\sum_i rhoObs_i^2) sqrt(\sum_i rhoCalc_i^2) 
 
For "correlation" potType, C is calculated as 
  E = scale * Natoms * rms 
 
                 \sum_i rhoObs_i * rhoCalc_i  - <rhoObs> * <rhoCalc>
   C = --------------------------------------------------------------------------
       sqrt(\sum_i rhoObs_i^2 - <rhoObs>^2) sqrt(\sum_i rhoCalc_i^2 - <rhoCalc>^2) 
 
[for "diff" potType]
 
  E = scale * Natoms * delta_x*delta_y*delta_z *
      \sum_i (rhoObs_i - rhoCalc_i)^2
 
where delta_x/y/z correspond to grid spacings, and Natoms is the number of
int the atomSel, specified when this object was created. For 2D maps,
delta_z=1.
 
 
 
 
# 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
ProbDistPot_LetterClass
Modified
ModifiedBase
ProbDistPot
VarEnsWeights
rc_EnsemblePot

 
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

 
class ProbDistPot_LetterClass(EnsemblePot)
    ProbDistPot_LetterClass(*args, **kwargs)
 

 
 
Method resolution order:
ProbDistPot_LetterClass
EnsemblePot
builtins.object

Methods defined here:
__init__(self, *args, **kwargs)
Initialize self.  See help(type(self)) for accurate signature.
__repr__ = _swig_repr(self)
atomProb(self)
calcRadiusGrad(self, *args, **kwargs) -> 'bool const'
correlation(self, *args, **kwargs) -> 'float_type'
energyMaybeDerivs0(self, *args, **kwargs) -> 'float_type'
info(self, *args, **kwargs) -> 'String'
numRestraints(self, *args, **kwargs) -> 'int'
oAtom(self, *args, **kwargs) -> 'Atom const'
potType(self, *args, **kwargs) -> 'ProbDistPot::ProbDist_PotType const'
pyXplorHelp(self, *args, **kwargs) -> 'String'
radiusGrad(self, *args, **kwargs) -> 'CDSVector< float_type >'
renamed_atomProb(self, *args, **kwargs) -> 'AtomProb *'
rms(self, *args, **kwargs) -> 'float_type'
setCalcRadiusGrad(self, *args, **kwargs) -> 'void'
setOAtom(self, *args, **kwargs) -> 'void'
setPotType(self, *args, **kwargs) -> 'void'
setTAtom(self, *args, **kwargs) -> 'void'
setXAtom(self, *args, **kwargs) -> 'void'
setYAtom(self, *args, **kwargs) -> 'void'
setZAtom(self, *args, **kwargs) -> 'void'
simulation(self, *args, **kwargs) -> 'EnsembleSimulation *'
tAtom(self, *args, **kwargs) -> 'Atom const'
targetMap(self, *args, **kwargs) -> 'DensityGrid *'
violations(self, *args, **kwargs) -> 'float_type'
xAtom(self, *args, **kwargs) -> 'Atom const'
yAtom(self, *args, **kwargs) -> 'Atom const'
zAtom(self, *args, **kwargs) -> 'Atom const'

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

Data descriptors defined here:
numAtoms

 
ownAtomProb

 
prStruct

 
rmsval

 
targetMap_

 
thisown

 
The membership flag

Data and other attributes defined here:
CORRELATION = 2
CROSS_CORRELATION = 1
DIFF = 0

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'
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'
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 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

 
realProbDistPot = class ProbDistPot(builtins.object)
    realProbDistPot(*args)
 

 
  Methods defined here:
__deref__(self, *args, **kwargs) -> 'ProbDistPot *'
__init__(self, *args)
__oldinit__ = __init__(self, *args, **kwargs)
__ref__(self, *args, **kwargs) -> 'ProbDistPot &'
__repr__ = _swig_repr(self)
addEnsWeights(self, *args, **kwargs) -> 'void'
atomProb(self)
calcEnergy(self, *args, **kwargs) -> 'float_type'
calcEnergyAndDerivs(self, *args, **kwargs) -> 'float_type'
calcRadiusGrad(self, *args, **kwargs) -> 'bool const'
calcWDerivs(self, *args, **kwargs) -> 'bool const'
clearEnsWeights(self, *args, **kwargs) -> 'void'
correlation(self, *args, **kwargs) -> 'float_type'
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'
getEnsWeights(self, *args, **kwargs) -> 'CDSList< VarEnsWeights > &'
incrRefCnt(self, *args, **kwargs) -> 'void'
info(self, *args, **kwargs) -> 'String'
instanceData(self, *args, **kwargs) -> 'PyObject *'
instanceName(self, *args, **kwargs) -> 'char const *'
numRestraints(self, *args, **kwargs) -> 'int'
oAtom(self, *args, **kwargs) -> 'Atom const'
potName(self, *args, **kwargs) -> 'char const *'
potType(self, *args, **kwargs) -> 'ProbDistPot::ProbDist_PotType const'
pyXplorHelp(self, *args, **kwargs) -> 'String'
radiusGrad(self, *args, **kwargs) -> 'CDSVector< float_type >'
refCnt(self, *args, **kwargs) -> 'int'
registerInstanceData(self, *args, **kwargs) -> 'void'
registerTo(self, *args, **kwargs) -> 'void'
renamed_atomProb(self, *args, **kwargs) -> 'AtomProb *'
resetInstanceName(self, *args, **kwargs) -> 'void'
resetPotName(self, *args, **kwargs) -> 'void'
rms(self, *args, **kwargs) -> 'float_type'
scale(self, *args, **kwargs) -> 'float_type const'
setCalcRadiusGrad(self, *args, **kwargs) -> 'void'
setCalcWDerivs(self, *args, **kwargs) -> 'void'
setEnsWeights(self, *args, **kwargs) -> 'void'
setOAtom(self, *args, **kwargs) -> 'void'
setPotType(self, *args, **kwargs) -> 'void'
setScale(self, *args, **kwargs) -> 'void'
setTAtom(self, *args, **kwargs) -> 'void'
setThreshold(self, *args, **kwargs) -> 'void'
setUseSimEnsWeights(self, *args, **kwargs) -> 'void'
setXAtom(self, *args, **kwargs) -> 'void'
setYAtom(self, *args, **kwargs) -> 'void'
setZAtom(self, *args, **kwargs) -> 'void'
simulation(self, *args, **kwargs) -> 'EnsembleSimulation *'
tAtom(self, *args, **kwargs) -> 'Atom const'
targetMap(self, *args, **kwargs) -> 'DensityGrid *'
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'
yAtom(self, *args, **kwargs) -> 'Atom const'
zAtom(self, *args, **kwargs) -> 'Atom const'

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

Data descriptors defined here:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

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

 
instanceDataCreate

 
instanceData_

 
modified

 
numAtoms

 
ownAtomProb

 
prStruct

 
registeredSimulations

 
rmsval

 
targetMap_

 
thisown

 
The membership flag

 
Functions
       
ProbDistPot(*args)
pyXplorHelp(*args) -> 'String'