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Pydoc: module posRMSDPotTools

posRMSDPotTools

index

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) -> 'EnsembleSimulationBase 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, **kwargs)

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.