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Pydoc: module potList

potList

An ordered collection of Pot objects - which is itself a Pot object. An instantiated object will act like a Python Sequence- it is iterable, indexable (by position number, and by instance name), and the len() builtin works as expected. Constructor: PotList(NAME) NAME is a name given to this instance of the PotList class. Methods: only the standard potential terms exist: potName() - returns 'PotList' instanceName() - returns NAME given in the constructor scale()/ setScale(scaleFac) - get/set a scale factor for this term NOTE: this is independent of scalings set within the XPLOR interface. calcEnergy() - calc energy without and with gradient calcEnergyAndDerivs(DerivList) - evaluation. Return the value of energy - these calculate and sum energy of each term - in the list. energyReports() - return a list of energyReport.EnergyReports for each term. This list is sorted by the instanceNames of each term. clearEnergyReports() - clear the EnergyReport list. violations() - report the sum of all violations rms() - report the average rmsd. If the PotList consists of term which are all the same type, and which contain restraints, the returned value R is computed as R^2 = sum_i N_i * w_i * R_i^2 / (sum_i N_i * w_i) where for term i, R_i is rms(), w_i is scale(), N_i is numRestraints(). If the terms are of the same type, but don't have a meaningful concept of restraint (numRestraints()==-1), then N_i is set to 1 in the above equation. If all terms return rms=-1, then return rms, else skip those terms which have negative rms numRestraints() - return the sum of the values of numRestraints() for all included potential terms, for positive values of numRestraints. append(pot) - add a new term to the end of the list. remove(name) - remove the term with the given name. removeAll() - remove all terms. makeCopy(name="") - return a copy of this PotList, with the argument giving the instanceName of the new term. If name is omitted, the name will be instanceName()+"_copy". byName(instanceName) - return the potential term specified. keys() - return a list of instanceNames of all potential terms in the list. ensWeights() - ensemble weights. Not directly used in any computations. setEnsWeights() - set ensemble weights for all contain potential terms. isParallel() - if True, run all the energy terms in parallel, setIsParallel(val=False) using OpenMP. This requires thread-safe behavior of all the contained energy terms, and currently no term is tested to work correctly. # 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

PotList_LetterClass

rc_Pot

PotList

rc_ptr_Pot

class CDSList_rc_Pot(builtins.object)

CDSList_rc_Pot(*args)

Methods defined here:

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

__getitem__(self, *args) -> 'CDSList< rc_Pot >'

__getslice__(self, *args, **kwargs) -> 'CDSList< rc_Pot >'

__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_rc_Pot(...)

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 PotList_LetterClass(builtins.object)

PotList_LetterClass(*args, **kwargs)

Methods defined here:

__getitem__(self, cnt)

__getslice__(self, *args, **kwargs) -> 'PotList'

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

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

__repr__ = _swig_repr(self)

add(self, pot)

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

append(self, pot)

byName(self, *args, **kwargs) -> 'rc_Pot'

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

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

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

copy(self, potList)

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'

energyReports(self, *args, **kwargs) -> 'CDSList< EnergyReport >'

getitem_int(self, *args, **kwargs) -> 'rc_Pot'

getitem_string(self, *args, **kwargs) -> 'rc_Pot'

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

keys(self)

list(self, *args, **kwargs) -> 'CDSList< rc_Pot >'

makeCopy(self, *args)

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

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

remove(self, name)

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

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

renamed_makeCopy(self, *args, **kwargs) -> 'rc_DerivedPot< PotList >'

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

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

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

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

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

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

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

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

Static methods defined here:

__swig_destroy__ = delete_PotList_LetterClass(...)

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:

noViolationStats = True

class rc_Pot(builtins.object)

rc_Pot(*args, **kwargs)

Methods defined here:

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

__repr__ = _swig_repr(self)

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

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

instanceData(self, *args, **kwargs) -> 'PyObject *'

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

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

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

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

Static methods defined here:

__swig_destroy__ = delete_rc_Pot(...)

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_Pot(builtins.object)

rc_ptr_Pot(*args)

Methods defined here:

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

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

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

__repr__ = _swig_repr(self)

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Static methods defined here:

__swig_destroy__ = delete_rc_ptr_Pot(...)

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

realPotList = class PotList(rc_Pot)

realPotList(*args)

Method resolution order:: PotList; rc_Pot; builtins.object

Methods defined here:

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

__getitem__(self, cnt)

__getslice__(self, *args, **kwargs) -> 'PotList'

__init__(self, *args)

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

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

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

__repr__ = _swig_repr(self)

add(self, pot)

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

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

append(self, pot)

byName(self, *args, **kwargs) -> 'rc_Pot'

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

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

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

copy(self, potList)

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'

energyReports(self, *args, **kwargs) -> 'CDSList< EnergyReport >'

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

ensWeights(self, *args, **kwargs) -> 'CDSList< float_type >'

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

getEnsWeights(self, *args, **kwargs) -> 'CDSList< VarEnsWeights > &'

getitem_int(self, *args, **kwargs) -> 'rc_Pot'

getitem_string(self, *args, **kwargs) -> 'rc_Pot'

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

instanceData(self, *args, **kwargs) -> 'PyObject *'

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

keys(self)

list(self, *args, **kwargs) -> 'CDSList< rc_Pot >'

makeCopy(self, *args)

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

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

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

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

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

remove(self, name)

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

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

renamed_makeCopy(self, *args, **kwargs) -> 'rc_DerivedPot< PotList >'

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

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

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

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

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

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

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

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

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

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

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

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

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'

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

Static methods defined here:

__swig_destroy__ = delete_PotList(...)

Data descriptors defined here:

instanceDataCleanup

instanceDataCreate

instanceData_

modified

registeredSimulations

thisown: The membership flag

Data and other attributes defined here:

noViolationStats = True

Methods inherited from rc_Pot:

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

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

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

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

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

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

Data descriptors inherited from rc_Pot:

__dict__: dictionary for instance variables (if defined)

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

Functions

PotList(*args)

pyXplorHelp(*args) -> 'String'