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


Potential term to restrain the volume associated with the gyration
tensor. This is used as an alternative to a radius of gyration
resrtaint- to allow elongated structures.  The target value is set in
gyrPotTools.create_GyrPot based on values observed in the
PDB. This term can also be used to restrain Rg values, including those
due to ensembles. The Rg term can be conveniently set up using 
gyrPotTools.create_RgyrPot.
 
 
constructor: GyrPot(instanceName,
                    selection   )
 
  instanceName is a user-specified identifier
  selection is a atomSel.AtomSel object specifying the atoms to include
  when calculating the gyration tensor.
 
methods
  calcEnergy()                 - calc energy, returns the energy value.
  calcEnergyAndDerivs(derivs)  - calc energy, derivs, returns the energy value.
 
  rms()                        - return the magnitude of violation of this
                                 term -- abs(diff).
  scale()                      - scale factor for this energy term.
 
  selection()                  - return the atom selection specified in
                                 the constructor.
 
  info()                    - current info about the state of this instance
 
  qc()             - The calculated centroid of selection().
  gyrTensor()      - The calculated gyration tensor.
  Rg()             - The calculated radius of gyration ( sqrt(Tr G) )
  volume()         - The calculated gyration volume.
  eigenPairs()     - The three principal moments and directions of the 
                     gyration tensor.
 
 The following parameters can be set [defaults in square brackets]
 
  targetType()   - "volume" or "radius"
  volTarget      -   The target gyration volume.
  volRange       -   The +/- range about the target volume about which to
                     evaluate zero energy (see below).
  rTarget        -   The target Rg.
  rRange         -   The +/- range about the target Rg about which to
                     evaluate zero energy (see below).
  gyrWeights     -   a sequence specifying the relative weight to give
                     an ensemble member's Rg. For instance, for a
                     SAXS-derived Rg, the entries are proportional to
                     the number of electrons of a species. For
                     instance, [1,2] would describe a mixture of
                     monomer and dimer. By default it is [1,1].
 
 the above quantities may be retrieved using the member function form
 quantity(), while they are set using the form setQuantity(value).
 
 
The gyration tensor is defined as 
 
              
     G = 1/N sum_i  (q_i - qc ) X (q_i - qc)
 
where N is the number of selected atoms, q_i is atom i's position and qc is 
the centroid of the selected atoms. The ``X'' denotes outer product.
 
The gyration volume is
 
     Vg =  4/3 pi sqrt(det G)
              
The energy function is defined as 
 
      V = scale * diff^2
 
  where 
 
             Vg - targetVol - rangeVol       if Vg>targetVol+rangeVol
     diff =  targetVol - rangeVol - Vg       if Vg<targetVol-rangeVol
             0                               otherwise
 
For Rg target type, Rg = sqrt( Trace G), and energy is defined as
above. For an ensemble, the observed Rg is defined as
 
   
    Rg^2 = \sum_i w_i wg_i RG_i^2 / \sum_j w_j wg_j
 
where w_i are ensemble weights (populations), and wg_i are specified
by gyrWeights (see above). Ensemble weight gradient optimization is
supported for this term.
 
 
 
# 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
GyrPot_LetterClass
GyrPot
GyrPot_EigenPair
Modified
ModifiedBase
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 GyrPot_EigenPair(builtins.object)
    GyrPot_EigenPair(*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_GyrPot_EigenPair(...)

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
value

 
vector

 

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

 
 
Method resolution order:
GyrPot_LetterClass
EnsemblePot
builtins.object

Methods defined here:
Rg(self, *args, **kwargs) -> 'float_type'
__init__(self, *args, **kwargs)
Initialize self.  See help(type(self)) for accurate signature.
__repr__ = _swig_repr(self)
energyMaybeDerivs0(self, *args, **kwargs) -> 'float_type'
energyMaybeDerivs1(self, *args, **kwargs) -> 'float_type'
gyrTensor(self, *args, **kwargs) -> 'SymMat3'
gyrWeights(self, *args, **kwargs) -> 'CDSVector< float_type > const'
info(self, *args, **kwargs) -> 'String'
numRestraints(self, *args, **kwargs) -> 'int'
pyXplorHelp(self, *args, **kwargs) -> 'String'
qc(self, *args, **kwargs) -> 'Vec3'
rRange(self, *args, **kwargs) -> 'float_type const'
rTarget(self, *args, **kwargs) -> 'float_type const'
renamed_eigenPairs(self, *args, **kwargs) -> 'FixedVector< GyrPot_EigenPair,3 >'
rms(self, *args, **kwargs) -> 'float_type'
selection(self, *args, **kwargs) -> 'AtomSel'
setGyrWeights(self, *args, **kwargs) -> 'void'
setRRange(self, *args, **kwargs) -> 'void'
setRTarget(self, *args, **kwargs) -> 'void'
setTargetType(self, *args, **kwargs) -> 'void'
setVerbose(self, *args, **kwargs) -> 'void'
setVolRange(self, *args, **kwargs) -> 'void'
setVolTarget(self, *args, **kwargs) -> 'void'
targetType(self, *args, **kwargs) -> 'GyrPot::GyrTargetType const'
updateValues(self, *args, **kwargs) -> 'void'
verbose(self, *args, **kwargs) -> 'bool const'
violations(self, *args, **kwargs) -> 'float_type'
volRange(self, *args, **kwargs) -> 'float_type const'
volTarget(self, *args, **kwargs) -> 'float_type const'
volume(self, *args, **kwargs) -> 'float_type'

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

Data descriptors defined here:
thisown

 
The membership flag

Data and other attributes defined here:
RADIUS = 0
VOLUME = 1

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'
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'

Data descriptors inherited from EnsemblePot:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

 
list of weak references to the object (if defined)

 
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 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

 
realGyrPot = class GyrPot(builtins.object)
    realGyrPot(*args)
 

 
  Methods defined here:
Rg(self, *args, **kwargs) -> 'float_type'
__deref__(self, *args, **kwargs) -> 'GyrPot *'
__init__(self, *args)
__oldinit__ = __init__(self, *args, **kwargs)
__ref__(self, *args, **kwargs) -> 'GyrPot &'
__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'
decrRefCnt(self, *args, **kwargs) -> 'void'
eigenPairs(self, memberIndex=-1)
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 > &'
gyrTensor(self, *args, **kwargs) -> 'SymMat3'
gyrWeights(self, *args, **kwargs) -> 'CDSVector< float_type > const'
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'
potName(self, *args, **kwargs) -> 'char const *'
pyXplorHelp(self, *args, **kwargs) -> 'String'
qc(self, *args, **kwargs) -> 'Vec3'
rRange(self, *args, **kwargs) -> 'float_type const'
rTarget(self, *args, **kwargs) -> 'float_type const'
refCnt(self, *args, **kwargs) -> 'int'
registerInstanceData(self, *args, **kwargs) -> 'void'
registerTo(self, *args, **kwargs) -> 'void'
renamed_eigenPairs(self, *args, **kwargs) -> 'FixedVector< GyrPot_EigenPair,3 >'
resetInstanceName(self, *args, **kwargs) -> 'void'
resetPotName(self, *args, **kwargs) -> 'void'
rms(self, *args, **kwargs) -> 'float_type'
scale(self, *args, **kwargs) -> 'float_type const'
selection(self, *args, **kwargs) -> 'AtomSel'
setCalcWDerivs(self, *args, **kwargs) -> 'void'
setEnsWeights(self, *args, **kwargs) -> 'void'
setGyrWeights(self, *args, **kwargs) -> 'void'
setRRange(self, *args, **kwargs) -> 'void'
setRTarget(self, *args, **kwargs) -> 'void'
setScale(self, *args, **kwargs) -> 'void'
setTargetType(self, *args, **kwargs) -> 'void'
setThreshold(self, *args, **kwargs) -> 'void'
setUseSimEnsWeights(self, *args, **kwargs) -> 'void'
setVerbose(self, *args, **kwargs) -> 'void'
setVolRange(self, *args, **kwargs) -> 'void'
setVolTarget(self, *args, **kwargs) -> 'void'
simulation(self, *args) -> 'EnsembleSimulation const *'
targetType(self, *args, **kwargs) -> 'GyrPot::GyrTargetType const'
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'
verbose(self, *args, **kwargs) -> 'bool const'
violations(self, *args, **kwargs) -> 'float_type'
volRange(self, *args, **kwargs) -> 'float_type const'
volTarget(self, *args, **kwargs) -> 'float_type const'
volume(self, *args, **kwargs) -> 'float_type'

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

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

 
registeredSimulations

 
thisown

 
The membership flag

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