posRMSDPotTools
index
posRMSDPotTools.py


 
tools to aid in setup/analysis of potential terms restricting atomic
positions in ensemble calculations.
 
this module provides functions to simplify the creation and
analysis of posRMSDPot.POSRMSDPot potential terms. 

 
Classes
       
posRMSDPot.PosRMSDPot(__builtin__.object)
RAPPot

 
class RAPPot(posRMSDPot.PosRMSDPot)
   
 
relative atomic position (RAP) potential term based on a
posRMSDPot.PosRMSDPot. This potential term is
only meaningful in the context of ensembleSimulation calculations.
 
 
Method resolution order:
RAPPot
posRMSDPot.PosRMSDPot
__builtin__.object

Methods defined here:
__init__(s, name, selection, simulation=0)

 
constructPot(s, name, selection, simulation)

 
setTol(s, val)

 
tol(s)

 

Methods inherited from posRMSDPot.PosRMSDPot:
__del__(self, destroy=<built-in function delete_PosRMSDPot>)

 
__deref__(*args)

 
__getattr__ lambda self, name

 
__mul__(*args)

 
__oldinit__ = __init__(self, *args)

 
__repr__(self)

 
__setattr__ lambda self, name, value

 
addRestraints(*args)

 
calcEnergy(*args)

 
calcEnergyAndDerivs(*args)

 
centerSel(*args)

 
decrRefCount(*args)

 
energyMaybeDerivs0(*args)

 
energyMaybeDerivs1(*args)

 
energyMaybeDerivs2(*args)

 
energyMaybeDerivs3(*args)

 
energyMaybeDerivs4(*args)

 
ensWeight(*args)

 
help(*args)

 
incrRefCount(*args)

 
info(*args)

 
instanceData(*args)

 
instanceName(*args)

 
numRestraints(*args)

 
pointer(*args)

 
potName(*args)

 
potType(*args)

 
registerInstanceData(*args)

 
registerTo(*args)

 
resetPotName(*args)

 
restraints(*args)

 
rms(*args)

 
rmsdType(*args)

 
scale(*args)

 
setCenterSel(*args)

 
setEnsWeights(*args)

 
setPotType(*args)

 
setRMSDType(*args)

 
setScale(*args)

 
setShowAllRestraints(*args)

 
setThreshold(*args)

 
setUseSimEnsWeights(*args)

 
setVerbose(*args)

 
showAllRestraints(*args)

 
showPositions(*args)

 
showRestraints(*args)

 
showViolations(*args)

 
simulation(*args)

 
threshold(*args)

 
unRegister(*args)

 
updateDelta(*args)

 
updateValues(*args)

 
useSimEnsWeights(*args)

 
verbose(*args)

 
violations(*args)

 

Properties inherited from posRMSDPot.PosRMSDPot:
instanceData_

 
get = PosRMSDPot_instanceData__get(...)

 
set = PosRMSDPot_instanceData__set(...)

 
modified

 
get = PosRMSDPot_modified_get(...)

 
set = PosRMSDPot_modified_set(...)

 
registeredSimulations

 
get = PosRMSDPot_registeredSimulations_get(...)

 
set = PosRMSDPot_registeredSimulations_set(...)

 

Data and other attributes inherited from posRMSDPot.PosRMSDPot:
__dict__ = <dictproxy object at 0x1fd1c58>

 
dictionary for instance variables (if defined)
__swig_getmethods__ = {'instanceData_': <built-in function PosRMSDPot_instanceData__get>, 'modified': <built-in function PosRMSDPot_modified_get>, 'registeredSimulations': <built-in function PosRMSDPot_registeredSimulations_get>}
__swig_setmethods__ = {'instanceData_': <built-in function PosRMSDPot_instanceData__set>, 'modified': <built-in function PosRMSDPot_modified_set>, 'registeredSimulations': <built-in function PosRMSDPot_registeredSimulations_set>}
__weakref__ = <attribute '__weakref__' of 'PosRMSDPot' objects>

 
list of weak references to the object (if defined)

 
Functions
       
analyze(potList)

 
perform analysis of PosRMSDPot terms and return nicely formatted summary
create_BFactorPot(name, file=0, restraints='', centerSel='', simulation=0)

 
create a posRMSDPot.PosRMSDPot term appropriate for refining
against crystallographic temperature factors. This potential term is
only meaningful in the context of ensembleSimulation calculations.
to_RAPPot(ptr)

 
cast an rc_Pot to a RAPPot
Note: the tol member is lost.

 
Data
        __package__ = None