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Pydoc: module jCoupPot

jCoupPot

index

J-Coupling Potential term Constructor: JCoupPot(instanceName , restraints , simulation ) - creates a potential term with the given name. restraints is a string which contains a restraint table (defaults to an empty string). simulation defaults to simulation.currentSimulation. Methods: calcEnergy() - calcs energy calcEnergyAndDerivs(DerivList) - calcs energy and derivative info note that these routines also update all other potential-specific data. addRestraints(restraints)- add entries to the restraint table. 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. Read-Write Accessors: A - coefficient of cos^2 term (see formula below). B - coefficient of cos term (see formula below). C - constant term (see formula below). phase - phase in j-coupling formula (see formula below). potType - potential type: 'harmonic' or 'square' [harmonic]. verbose - if true, sporadically spit out info [False] threshold - threshold in violation calculation ( defaults to 0). 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. [1] useSimEnsWeight - whether to use the ensemble wieghts set with setEnsWeights or to use those of the underlying EnsembleSimulation. Read-only accessors: violations() - return number of violations. Defined in terms of jDiff_i. rms() - return rms of jDiff_i numRestraints() - the number of restraints defined for this term. deviation() - ensemble deviation of jCalc-jObs averaged over all restraints simulation() - simulation used by this shape term. Is an EnsembleSimulation. info() - return string synopsis of potential info. showRestraints(violated) - return pretty-printed restraint info. showViolations() - return pretty-printed violation info. The potential term is defined as E = scale() * sum_i jDiff_i^2 where jDiff = jCalc - jDiff if potType=='harmonic' if potType=='square, jDiff is jCalc-jObs-jPlus if jCalc-jObs>jPlus jCalc-jObs+jMinus if jCalc-jObs<-jMinus 0 otherwise jObs is the observed j-coupling value. jCalc is the ensemble-average calulated j-coupling value: jCalc = A*cos(phi+phase)^2 + B*cos(phi+phase) + C where the constants A,B,C, and phase are inputs, and phi is the dihedral angle as specified in the assignment table. The j-coupling assignment table consists of entries of the following form ASSIgn (sel1) (sel2) (sel3) (sel4) jObs jMinus [jPlus] where the four single atom selections specify the dihedral angle. jMinus and jPlus specify the range of the square potential, with jPlus defaulting to jMinus if it is omitted. Note that the degenerate assignments of the XPLOR COUP term are not implemented here yet. # 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_JCoup_Restraint

EnsemblePot

JCoupPot_LetterClass

JCoupPot

Modified

ModifiedBase

Restraint_JCoupPot

JCoup_Restraint

VarEnsWeights

rc_EnsemblePot

rc_ptr_JCoup_Restraint

class CDSList_JCoup_Restraint(builtins.object)

CDSList_JCoup_Restraint(*args)

Methods defined here:

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

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

__getslice__(self, *args, **kwargs) -> 'CDSList< CDS::rc_ptr< JCoup_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_JCoup_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 JCoupPot_LetterClass(EnsemblePot)

JCoupPot_LetterClass(*args, **kwargs)

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

Methods defined here:

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

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

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

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

__repr__ = _swig_repr(self)

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

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

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'

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

potType(self, *args, **kwargs) -> 'JCoupPot::JCoupPotType'

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Static methods defined here:

__swig_destroy__ = delete_JCoupPot_LetterClass(...)

Data descriptors defined here:

phaseInRadians

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'

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

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 JCoup_Restraint(Restraint_JCoupPot)

JCoup_Restraint(*args, **kwargs)

Method resolution order:: JCoup_Restraint; Restraint_JCoupPot; builtins.object

Methods defined here:

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

__repr__ = _swig_repr(self)

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

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

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

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

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

Static methods defined here:

__swig_destroy__ = delete_JCoup_Restraint(...)

Data descriptors defined here:

contrib

thisown: The membership flag

verbose

Methods inherited from Restraint_JCoupPot:

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

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

violated(self, *args, **kwargs) -> 'bool'

Data descriptors inherited from Restraint_JCoupPot:

__dict__: dictionary for instance variables (if defined)

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

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 Restraint_JCoupPot(builtins.object)

Restraint_JCoupPot(*args, **kwargs)

Methods defined here:

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

__repr__ = _swig_repr(self)

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

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

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

violated(self, *args, **kwargs) -> 'bool'

Static methods defined here:

__swig_destroy__ = delete_Restraint_JCoupPot(...)

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 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_JCoup_Restraint(builtins.object)

rc_ptr_JCoup_Restraint(*args)

Methods defined here:

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

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

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

__repr__ = _swig_repr(self)

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

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

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

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

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

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

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

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

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

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

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

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

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

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

violated(self, *args, **kwargs) -> 'bool'

Static methods defined here:

__swig_destroy__ = delete_rc_ptr_JCoup_Restraint(...)

Data descriptors defined here:

__dict__: dictionary for instance variables (if defined)

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

contrib

thisown: The membership flag

verbose

realJCoupPot = class JCoupPot(builtins.object)

realJCoupPot(*args, **kwargs)

Methods defined here:

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

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

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

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

__init__(self, *args, **kwargs)

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

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

__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'

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

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'

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

potName(self, *args, **kwargs) -> 'char const *'

potType(self, *args, **kwargs) -> 'JCoupPot::JCoupPotType'

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< JCoup_Restraint > >'

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

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

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

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

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

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

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

setPhase(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'

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 defined here:

__swig_destroy__ = delete_JCoupPot(...)

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

phaseInRadians

registeredSimulations

thisown: The membership flag

Functions

JCoupPot(*args, **kwargs)

pyXplorHelp(*args) -> 'String'