posRMSDPotTools
index
/home/schwitrs/xplor/python/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(builtins.object)
RAPPot

 
realRAPPot = class RAPPot(posRMSDPot.PosRMSDPot)
    realRAPPot(name, selection, simulation=0, tol=0)
 
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
builtins.object

Methods defined here:
__init__(s, name, selection, simulation=0, tol=0)
specify 
name - instanceName
selection - atom to be restrained
simulation - optional simulation.Simulation object - 
             defaults to simulation.currentSimulation.
tol        - allowed inter-ensemble spread - defaults to 0.
constructPot(s, name, selection, simulation)
setTol(s, val)
tol(s)

Methods inherited from posRMSDPot.PosRMSDPot:
__deref__(self, *args, **kwargs) -> 'PosRMSDPot *'
__oldinit__ = __init__(self, *args, **kwargs)
__ref__(self, *args, **kwargs) -> 'PosRMSDPot &'
__repr__ = _swig_repr(self)
addEnsWeights(self, *args, **kwargs) -> 'void'
addRestraints(self, *args, **kwargs) -> 'void'
calcEnergy(self, *args, **kwargs) -> 'float_type'
calcEnergyAndDerivs(self, *args, **kwargs) -> 'float_type'
calcWDerivs(self, *args, **kwargs) -> 'bool const'
centerSel(self, *args, **kwargs) -> 'AtomSel const'
clearEnsWeights(self, *args, **kwargs) -> 'void'
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'
potName(self, *args, **kwargs) -> 'char const *'
potType(self, *args, **kwargs) -> 'PosRMSDPot::PosRMSD_PotType'
pyXplorHelp(self, *args, **kwargs) -> 'String'
refCnt(self, *args, **kwargs) -> 'int'
registerInstanceData(self, *args, **kwargs) -> 'void'
registerTo(self, *args, **kwargs) -> 'void'
resetInstanceName(self, *args, **kwargs) -> 'void'
resetPotName(self, *args, **kwargs) -> 'void'
restraints(self, *args, **kwargs) -> 'CDSList< CDS::rc_ptr< PosRMSDPot_Restraint > >'
rms(self, *args, **kwargs) -> 'double'
rmsdType(self, *args, **kwargs) -> 'PosRMSDPot::PosRMSD_RMSDType'
scale(self, *args, **kwargs) -> 'float_type const'
setCalcWDerivs(self, *args, **kwargs) -> 'void'
setCenterSel(self, *args, **kwargs) -> 'void'
setEnsWeights(self, *args, **kwargs) -> 'void'
setPotType(self, *args, **kwargs) -> 'void'
setRMSDType(self, *args, **kwargs) -> 'void'
setScale(self, *args, **kwargs) -> 'void'
setShowAllRestraints(self, *args, **kwargs) -> 'void'
setThreshold(self, *args, **kwargs) -> 'void'
setUseSimEnsWeights(self, *args, **kwargs) -> 'void'
setVerbose(self, *args, **kwargs) -> 'void'
showAllRestraints(self, *args, **kwargs) -> 'bool const'
showPositions(self, *args, **kwargs) -> 'String'
showRestraints(self, *args, **kwargs) -> 'String'
showViolations(self, *args, **kwargs) -> 'String'
simulation(self, *args) -> 'EnsembleSimulation 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'

Static methods inherited from posRMSDPot.PosRMSDPot:
__swig_destroy__ = delete_PosRMSDPot(...)

Data descriptors inherited from posRMSDPot.PosRMSDPot:
__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
       
RAPPot(*args)
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.