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Pydoc: module orderPot

orderPot

index

S^2 Order parameter potential allows refinement against the S2 order parameter, usually obtained from relaxation experiments. This potential term should be used with ensembleSimulation.EnsembleSimulation calculations. constructor: OrderPot(instanceName, restraints, simulation) instanceName is a user-specified identifier. restraints is an optional XPLOR-style restraints table- see below for details. simulation is an optional simulation.Simulation specification. methods: addRestraints(restraintList) - add the specified restraints- see below for details on the format. Note that this is a string and not a filename. calcEnergy() - calc energy, returns the value of energy. calcEnergyAndDerivs(derivs) - calc energy, derivs, returns the energy value. rms() - return the rms of calcedS2 - effS2 numRestraints() - return the number of restraints defined for this term. violations() - return number of violations info() - current info about the state of this instance showViolations() - return a string listing violated restraints. restraints() - return a list of restraints. See the description of the Restraint class below. simulation() - return the associated simulation. ensWeigth(index) - return the ensemble weight associated with the specified member. setEnsWeights(vals) - use the specified ensemble weights instead of those in the underlying EnsembleSimulation. The following parameters can be set [defaults in square brackets] verbose - if true, sporadically spit out info [False] scale - scale factor (force constant) [1] threshold - threshold in violation calculation [0] potType - type of potential: "harmonic" or "square" ["harmonic"] showAllRestraints - boolean which changes the behavior of showViolations. If this parameter is set to True, the behavior of showViolations is modified such that all restraints are printed. Violated restraints are indicated by an asterisk in the first column. [0] useSimEnsWeight - whether to use the ensemble wieghts set with setEnsWeights or to use those of the underlying EnsembleSimulation. the above quantities may be retrieved using the member function form quantity(), while they are set using the form setQuantity(value). assignment table: entries in the restraint list have the following form assign ( sel m ) ( sel n ) obsS2 error1 [error2] [! optional comment] the m and n selections specify the bonded atoms involved in the interaction. the observed value of S2 is given by the obsS2 argument, and the error bounds are given by error1 and error2. If error2 is absent, it defaults to error1. The calculated order parameter is given by the equation calcedS2 = sum_ij w_i w_j ( 3/2 cos(dot(u_i,u_j)^2 - 1/2 ) where w_i is the weight of ensemble member i (usually 1/Ne), and u_i is the unitvector in the direction q_ni - q_mi. The energy function is defined as scale * rscale * (calcedS2 - effS2)^2 where for potType=harmonic, effS2 = obsS2, and rscale = 1/error1^2 (if error1!=0). For potType=square, rscale=1, and effS2 = calcedS2, if obsS2-error1 < calcedS2 < obsS2+error2 = calcedS2+error1, if calcedS2 < obsS2-error1 = calcedS2-error2, if calcedS2 > obsS2+error2 Restraint class methods: energy() - energy due to this restraint calcd() - calculated value of S2. obs() - observed value of S2. diff() - return S2-effS2 plusErr(), minusErr() - bounds for the square well potential aSel() - atomSel for atom A bSel() - atomSel for atom B comment() - return the optional comment string # This file was automatically generated by SWIG (http://www.swig.org). # Version 4.0.2 # # Do not make changes to this file unless you know what you are doing--modify # the SWIG interface file instead.

Classes

builtins.object

CDSList_OrderPot_Restraint

EnsemblePot

OrderPot_LetterClass

Modified

ModifiedBase

OrderPot

OrderPot_Restraint

VarEnsWeights

rc_EnsemblePot

rc_ptr_OrderPot_Restraint

class CDSList_OrderPot_Restraint(builtins.object)

CDSList_OrderPot_Restraint(*args)

Methods defined here:

__delitem__(self, *args, **kwargs) -> 'void'

__getitem__(self, *args) -> 'CDSList< CDS::rc_ptr< OrderPot_Restraint > >'

__getslice__(self, *args, **kwargs) -> 'CDSList< CDS::rc_ptr< OrderPot_Restraint > >'

__init__(self, *args): Initialize self. See help(type(self)) for accurate signature.

__len__(self, *args, **kwargs) -> 'int'

__repr__ = _swig_repr(self)

__setitem__(self, *args, **kwargs) -> 'void'

append(self, *args, **kwargs) -> 'void'

help(self, *args, **kwargs) -> 'String'

remove(self, *args, **kwargs) -> 'void'

removeAll(self, *args, **kwargs) -> 'void'

Static methods defined here:

__swig_destroy__ = delete_CDSList_OrderPot_Restraint(...)

Data descriptors defined here:

__dict__: dictionary for instance variables (if defined)

__weakref__: list of weak references to the object (if defined)

thisown: The membership flag

class EnsemblePot(builtins.object)

EnsemblePot(*args, **kwargs)

Methods defined here:

__init__(self, *args, **kwargs): Initialize self. See help(type(self)) for accurate signature.

__repr__ = _swig_repr(self)

addEnsWeights(self, *args, **kwargs) -> 'void'

calcEnergy(self, *args, **kwargs) -> 'float_type'

calcEnergyAndDerivs(self, *args, **kwargs) -> 'float_type'

calcWDerivs(self, *args, **kwargs) -> 'bool const'

clearEnsWeights(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 > &'

setCalcWDerivs(self, *args, **kwargs) -> 'void'

setEnsWeights(self, *args, **kwargs) -> 'void'

setUseSimEnsWeights(self, *args, **kwargs) -> 'void'

simulation(self, *args) -> 'EnsembleSimulationBase const *'

updateEnsWeights(self, *args, **kwargs) -> 'void'

useSimEnsWeights(self, *args, **kwargs) -> 'bool const'

Static methods defined here:

__swig_destroy__ = delete_EnsemblePot(...)

Data descriptors defined here:

__dict__: dictionary for instance variables (if defined)

__weakref__: list of weak references to the object (if defined)

thisown: The membership flag

class Modified(builtins.object)

Modified(*args, **kwargs)

Methods defined here:

__call__(self, *args, **kwargs) -> 'int': Call self as a function.

__init__(self, *args, **kwargs): Initialize self. See help(type(self)) for accurate signature.

__repr__ = _swig_repr(self)

asString(self, *args, **kwargs) -> 'String'

assertClear(self, *args, **kwargs) -> 'void'

clear(self, *args, **kwargs) -> 'void'

set(self, *args, **kwargs) -> 'void'

update(self, *args, **kwargs) -> 'void'

value(self, *args, **kwargs) -> 'int'

Static methods defined here:

__swig_destroy__ = delete_Modified(...)

Data descriptors defined here:

__dict__: dictionary for instance variables (if defined)

__weakref__: list of weak references to the object (if defined)

thisown: The membership flag

Data and other attributes defined here:

MOD_SELF = 1

MOD_SIMULATION = 2

class ModifiedBase(builtins.object)

ModifiedBase(*args, **kwargs)

Methods defined here:

__init__(self, *args, **kwargs): Initialize self. See help(type(self)) for accurate signature.

__repr__ = _swig_repr(self)

registerTo(self, *args, **kwargs) -> 'void'

unRegister(self, *args, **kwargs) -> 'void'

updateValues(self, *args, **kwargs) -> 'void'

Static methods defined here:

__swig_destroy__ = delete_ModifiedBase(...)

Data descriptors defined here:

__dict__: dictionary for instance variables (if defined)

__weakref__: list of weak references to the object (if defined)

modified

registeredSimulations

thisown: The membership flag

class OrderPot_LetterClass(EnsemblePot)

OrderPot_LetterClass(*args, **kwargs)

Method resolution order:: OrderPot_LetterClass; EnsemblePot; builtins.object

Methods defined here:

__init__(self, *args, **kwargs): Initialize self. See help(type(self)) for accurate signature.

__repr__ = _swig_repr(self)

addRestraints(self, *args, **kwargs) -> 'void'

energyMaybeDerivs0(self, *args, **kwargs) -> 'float_type'

energyMaybeDerivs1(self, *args, **kwargs) -> 'float_type'

energyMaybeDerivs2(self, *args, **kwargs) -> 'float_type'

info(self, *args, **kwargs) -> 'String'

numRestraints(self, *args, **kwargs) -> 'int'

potType(self, *args, **kwargs) -> 'OrderPot::OrderPotType'

pyXplorHelp(self, *args, **kwargs) -> 'String'

restraints(self, *args, **kwargs) -> 'CDSList< CDS::rc_ptr< OrderPot_Restraint > >'

rms(self, *args, **kwargs) -> 'float_type'

setPotType(self, *args, **kwargs) -> 'void'

setShowAllRestraints(self, *args, **kwargs) -> 'void'

setVerbose(self, *args, **kwargs) -> 'void'

showAllRestraints(self, *args, **kwargs) -> 'bool const'

showViolations(self, *args, **kwargs) -> 'String'

simulation(self, *args, **kwargs) -> 'EnsembleSimulationBase *'

verbose(self, *args, **kwargs) -> 'bool const'

violations(self, *args, **kwargs) -> 'float_type'

Static methods defined here:

__swig_destroy__ = delete_OrderPot_LetterClass(...)

Data descriptors defined here:

thisown: The membership flag

Data and other attributes defined here:

HARMONIC = 0

SQUARE = 1

Methods inherited from EnsemblePot:

addEnsWeights(self, *args, **kwargs) -> 'void'

calcEnergy(self, *args, **kwargs) -> 'float_type'

calcEnergyAndDerivs(self, *args, **kwargs) -> 'float_type'

calcWDerivs(self, *args, **kwargs) -> 'bool const'

clearEnsWeights(self, *args, **kwargs) -> 'void'

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 > &'

setCalcWDerivs(self, *args, **kwargs) -> 'void'

setEnsWeights(self, *args, **kwargs) -> 'void'

setUseSimEnsWeights(self, *args, **kwargs) -> 'void'

updateEnsWeights(self, *args, **kwargs) -> 'void'

useSimEnsWeights(self, *args, **kwargs) -> 'bool const'

Data descriptors inherited from EnsemblePot:

__dict__: dictionary for instance variables (if defined)

__weakref__: list of weak references to the object (if defined)

class OrderPot_Restraint(builtins.object)

OrderPot_Restraint(*args, **kwargs)

Methods defined here:

__init__(self, *args, **kwargs): Initialize self. See help(type(self)) for accurate signature.

__repr__ = _swig_repr(self)

aSelection(self, *args, **kwargs) -> 'AtomSel'

bSelection(self, *args, **kwargs) -> 'AtomSel'

calcVectors(self, *args, **kwargs) -> 'void'

calcd(self, *args, **kwargs) -> 'double'

comment(self, *args, **kwargs) -> 'String const'

deriv(self, *args, **kwargs) -> 'void'

energy(self, *args, **kwargs) -> 'double'

minusErr(self, *args, **kwargs) -> 'double'

name(self, *args, **kwargs) -> 'String'

obs(self, *args, **kwargs) -> 'double'

ok(self, *args, **kwargs) -> 'int'

plusErr(self, *args, **kwargs) -> 'double'

setComment(self, *args, **kwargs) -> 'void'

setObs(self, *args, **kwargs) -> 'void'

Static methods defined here:

__swig_destroy__ = delete_OrderPot_Restraint(...)

Data descriptors defined here:

__dict__: dictionary for instance variables (if defined)

__weakref__: list of weak references to the object (if defined)

thisown: The membership flag

u

vecNorm

class VarEnsWeights(builtins.object)

VarEnsWeights(*args, **kwargs)

Methods defined here:

__init__(self, *args, **kwargs): Initialize self. See help(type(self)) for accurate signature.

__repr__ = _swig_repr(self)

Static methods defined here:

__swig_destroy__ = delete_VarEnsWeights(...)

Data descriptors defined here:

__dict__: dictionary for instance variables (if defined)

__weakref__: list of weak references to the object (if defined)

ensWeights

mult

thisown: The membership flag

class rc_EnsemblePot(builtins.object)

rc_EnsemblePot(*args, **kwargs)

Methods defined here:

__init__(self, *args, **kwargs): Initialize self. See help(type(self)) for accurate signature.

__repr__ = _swig_repr(self)

Static methods defined here:

__swig_destroy__ = delete_rc_EnsemblePot(...)

Data descriptors defined here:

__dict__: dictionary for instance variables (if defined)

__weakref__: list of weak references to the object (if defined)

thisown: The membership flag

class rc_ptr_OrderPot_Restraint(builtins.object)

rc_ptr_OrderPot_Restraint(*args)

Methods defined here:

__deref__(self, *args, **kwargs) -> 'OrderPot_Restraint *'

__init__(self, *args): Initialize self. See help(type(self)) for accurate signature.

__ref__(self, *args, **kwargs) -> 'OrderPot_Restraint &'

__repr__ = _swig_repr(self)

aSelection(self, *args, **kwargs) -> 'AtomSel'

bSelection(self, *args, **kwargs) -> 'AtomSel'

calcVectors(self, *args, **kwargs) -> 'void'

calcd(self, *args, **kwargs) -> 'double'

comment(self, *args, **kwargs) -> 'String const'

count(self, *args, **kwargs) -> 'int'

decr(self, *args, **kwargs) -> 'void'

deriv(self, *args, **kwargs) -> 'void'

energy(self, *args, **kwargs) -> 'double'

forceDelete(self, *args, **kwargs) -> 'void'

incr(self, *args, **kwargs) -> 'void'

minusErr(self, *args, **kwargs) -> 'double'

name(self, *args, **kwargs) -> 'String'

obs(self, *args, **kwargs) -> 'double'

ok(self, *args, **kwargs) -> 'int'

plusErr(self, *args, **kwargs) -> 'double'

ptr(self, *args, **kwargs) -> 'OrderPot_Restraint *'

release(self, *args, **kwargs) -> 'OrderPot_Restraint *'

reset(self, *args, **kwargs) -> 'void'

setComment(self, *args, **kwargs) -> 'void'

setObs(self, *args, **kwargs) -> 'void'

Static methods defined here:

__swig_destroy__ = delete_rc_ptr_OrderPot_Restraint(...)

Data descriptors defined here:

__dict__: dictionary for instance variables (if defined)

__weakref__: list of weak references to the object (if defined)

thisown: The membership flag

u

vecNorm

realOrderPot = class OrderPot(builtins.object)

realOrderPot(*args, **kwargs)

Methods defined here:

__deref__(self, *args, **kwargs) -> 'OrderPot *'

__init__(self, *args, **kwargs)

__oldinit__ = __init__(self, *args, **kwargs)

__ref__(self, *args, **kwargs) -> 'OrderPot &'

__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'

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) -> 'OrderPot::OrderPotType'

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< OrderPot_Restraint > >'

rms(self, *args, **kwargs) -> 'float_type'

scale(self, *args, **kwargs) -> 'float_type const'

setCalcWDerivs(self, *args, **kwargs) -> 'void'

setEnsWeights(self, *args, **kwargs) -> 'void'

setPotType(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'

showViolations(self, *args, **kwargs) -> 'String'

simulation(self, *args, **kwargs) -> 'EnsembleSimulationBase *'

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 defined here:

__swig_destroy__ = delete_OrderPot(...)

Data descriptors defined here:

__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

OrderPot(*args, **kwargs)

pyXplorHelp(*args) -> 'String'