avePot
index
avePot.py

ensemble average a potential term
 
Used with an ensembleSimulation.EnsembleSimulation for an energy
term which is a simple ensemble average of an energy term. i.e. the
potential is 
 
      E = sum_i w_i E_i
 
where the sum is over all members of an ensemble, w_i is the weight
for ensemble member i, and E_i is the averaged energy.
 
Constructors:
 
   AvePot( otherPotentialName, args )
 
otherPotentialName could be e.g. xplorPot.XplorPot, noePot.NOEPot, etc. args are the arguments which these other terms
take. 
 
*or*
 
   AvePot( pot )
 
where pot is a previously defined potential term.
 
Methods:
 
  calcEnergy()
  calcEnergyAndDerivs()
 
  potName()
  instanceName()
 
  subPot() - return pot.Pot object which is averaged over.
 
Accessors (read/write)
  scale - scale factor for the term. Overall scale is product of this value
          and subPot->scale().
 
Additionally, all of the methods of the underlying class can be accessed as if
the AvePot object was actually the sub-potential type.

 
Classes
       
avePot1.AvePot(__builtin__.object)
AvePot
avePot1.AvePotPtr(avePot1.AvePot)
AvePotPtr

 
class AvePot(avePot1.AvePot)
   
    wrapper around avePot1.AvePot:
      construct from either an already created Pot:
        pot = XplorPot("BOND")
        AvePot(pot)
      or internally call the averaged pot's constructor
        AvePot(XplorPot,"BOND")
      where the first argument is the class constructor and the remaining
      are parameters for that constructor.
 
      __getattr__ is defined such that first the avePot1.AvePot attributes are
      used, and then those of the subPot are attempted.
    
 
 
Method resolution order:
AvePot
avePot1.AvePot
__builtin__.object

Methods defined here:
__getattr__(self, name)
__init__(self, *args)

Methods inherited from avePot1.AvePot:
__del__(self, destroy=<built-in function delete_AvePot>)
__deref__(*args)
__mul__(*args)
__oldinit__ = __init__(self, *args)
__repr__(self)
__setattr__ lambda self, name, value
calcEnergy(*args)
calcEnergyAndDerivs(*args)
energyMaybeDerivs0(*args)
energyMaybeDerivs1(*args)
energyMaybeDerivs2(*args)
energyMaybeDerivs3(*args)
energyMaybeDerivs4(*args)
help(*args)
incrRefCount(*args)
instanceData(*args)
instanceName(*args)
numRestraints(*args)
pointer(*args)
potName(*args)
rcPot(*args)
registerInstanceData(*args)
registerTo(*args)
resetPotName(*args)
rms(*args)
scale(*args)
setScale(*args)
setThreshold(*args)
simulation(*args)
subPot(self)
threshold(*args)
unRegister(*args)
updateValues(*args)
violations(*args)

Properties inherited from avePot1.AvePot:
instanceData_
get = AvePot_instanceData__get(...)
set = AvePot_instanceData__set(...)
modified
get = AvePot_modified_get(...)
set = AvePot_modified_set(...)
registeredSimulations
get = AvePot_registeredSimulations_get(...)
set = AvePot_registeredSimulations_set(...)

Data and other attributes inherited from avePot1.AvePot:
__dict__ = <dictproxy object at 0xde94b0>
dictionary for instance variables (if defined)
__swig_getmethods__ = {'instanceData_': <built-in function AvePot_instanceData__get>, 'modified': <built-in function AvePot_modified_get>, 'registeredSimulations': <built-in function AvePot_registeredSimulations_get>}
__swig_setmethods__ = {'instanceData_': <built-in function AvePot_instanceData__set>, 'modified': <built-in function AvePot_modified_set>, 'registeredSimulations': <built-in function AvePot_registeredSimulations_set>}
__weakref__ = <attribute '__weakref__' of 'AvePot' objects>
list of weak references to the object (if defined)

 
class AvePotPtr(avePot1.AvePotPtr)
   
    this so that potDerive.createDerivedPot works correctly.
    wrapper around avePot1.AvePotPtr:
      construct from a pointer to avePot1.AvePot
 
      __getattr__ is defined such that first the avePot1.AvePot attributes are
      used, and then those of the subPot are attempted.
    
 
 
Method resolution order:
AvePotPtr
avePot1.AvePotPtr
avePot1.AvePot
__builtin__.object

Methods defined here:
__getattr__(self, name)
__init__(self, pointer)

Methods inherited from avePot1.AvePot:
__del__(self, destroy=<built-in function delete_AvePot>)
__deref__(*args)
__mul__(*args)
__oldinit__ = __init__(self, *args)
__repr__(self)
__setattr__ lambda self, name, value
calcEnergy(*args)
calcEnergyAndDerivs(*args)
energyMaybeDerivs0(*args)
energyMaybeDerivs1(*args)
energyMaybeDerivs2(*args)
energyMaybeDerivs3(*args)
energyMaybeDerivs4(*args)
help(*args)
incrRefCount(*args)
instanceData(*args)
instanceName(*args)
numRestraints(*args)
pointer(*args)
potName(*args)
rcPot(*args)
registerInstanceData(*args)
registerTo(*args)
resetPotName(*args)
rms(*args)
scale(*args)
setScale(*args)
setThreshold(*args)
simulation(*args)
subPot(self)
threshold(*args)
unRegister(*args)
updateValues(*args)
violations(*args)

Properties inherited from avePot1.AvePot:
instanceData_
get = AvePot_instanceData__get(...)
set = AvePot_instanceData__set(...)
modified
get = AvePot_modified_get(...)
set = AvePot_modified_set(...)
registeredSimulations
get = AvePot_registeredSimulations_get(...)
set = AvePot_registeredSimulations_set(...)

Data and other attributes inherited from avePot1.AvePot:
__dict__ = <dictproxy object at 0xde71d8>
dictionary for instance variables (if defined)
__swig_getmethods__ = {'instanceData_': <built-in function AvePot_instanceData__get>, 'modified': <built-in function AvePot_modified_get>, 'registeredSimulations': <built-in function AvePot_registeredSimulations_get>}
__swig_setmethods__ = {'instanceData_': <built-in function AvePot_instanceData__set>, 'modified': <built-in function AvePot_modified_set>, 'registeredSimulations': <built-in function AvePot_registeredSimulations_set>}
__weakref__ = <attribute '__weakref__' of 'AvePot' objects>
list of weak references to the object (if defined)

 
Functions
       
help()

 
Data
        env = {'LESS': '-X', 'TOPPAR_C22': '/home/schwitrs/xpl...ttp://www.hec.utah.edu/~schwitrs/bookmarks.html'}