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)
energyMaybeDerivs0(*args)
energyMaybeDerivs1(*args)
energyMaybeDerivs2(*args)
energyMaybeDerivs3(*args)
energyMaybeDerivs4(*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)
setPotType(*args)
setRMSDType(*args)
setScale(*args)
setShowAllRestraints(*args)
setThreshold(*args)
setVerbose(*args)
showAllRestraints(*args)
showPositions(*args)
showRestraints(*args)
showViolations(*args)
simulation(*args)
threshold(*args)
unRegister(*args)
updateValues(*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 0xe855c8>
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.