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Pydoc: module xplorPot

xplorPot

index

access to native XPLOR potential terms The XplorPot class allows access to potential terms written using the XPLOR interface. The setup of these terms is performed within the XPLOR interface, or using the helper functions in the protocol module. Analysis of most XPLOR terms is handled by the analyze function in the simulationTools module. Constructor: XplorPot(NAME) NAME is a string (maximum 4 characters) which represents an XPLOR potential term. NAME can also be a list of XPLOR term names, separated by the "+" character. This is useful for certain terms, like PVDW, and VDW which do not evaluate correctly if evaluated separately. Methods: only the standard potential terms exist: potName() - returns 'XplorPot' instanceName() - returns NAME given in the constructor scale() - get/set a scale factor for this term setScale(scaleFac) - NOTE: this is independent of scalings set within the XPLOR interface. calcEnergy() - calc energy without and with gradient calcEnergyAndDerivs(DerivList) - evaluation. Return the energy value. rms() - return XPLOR-calculated RMSD for this term, if it is defined in python/xplorPotTools.py violations() - return XPLOR-calculated number of violations for this term, if it is defined in python/xplorPotTools.py numRestraints() - return XPLOR-calculated number of restraints for this term, if it is defined in python/xplorPotTools.py # 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

Modified

ModifiedBase

XplorPot

XplorPot_Delegate

PyXplorPot_Delegate

XplorPot_LetterClass

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 PyXplorPot_Delegate(XplorPot_Delegate)

PyXplorPot_Delegate(*args, **kwargs)

Method resolution order:: PyXplorPot_Delegate; XplorPot_Delegate; builtins.object

Methods defined here:

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

__repr__ = _swig_repr(self)

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

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

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

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

Static methods defined here:

__swig_destroy__ = delete_PyXplorPot_Delegate(...)

Data descriptors defined here:

thisown: The membership flag

Data descriptors inherited from XplorPot_Delegate:

__dict__: dictionary for instance variables (if defined)

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

class XplorPot_Delegate(builtins.object)

XplorPot_Delegate(*args, **kwargs)

Methods defined here:

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

__repr__ = _swig_repr(self)

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

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

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

Static methods defined here:

__swig_destroy__ = delete_XplorPot_Delegate(...)

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 XplorPot_LetterClass(builtins.object)

XplorPot_LetterClass(*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'

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

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

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

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

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

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

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

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

Static methods defined here:

__swig_destroy__ = delete_XplorPot_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

realXplorPot = class XplorPot(builtins.object)

realXplorPot(*args)

Methods defined here:

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

__init__ = construct(self, *args)

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

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

__repr__ = _swig_repr(self)

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

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

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

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

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

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

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

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

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

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'

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

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

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

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

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

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

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

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_XplorPot(...)

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

XplorPot(*args, **kwargs)

construct(self, *args)

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

pyXplorHelp(*args) -> 'String'