xplorPot
index
/home/schwitrs/bzr-repo/xplor-python3/bin.Linux_x86_64/xplorPot.py

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)
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)
construct(self, *args)
oldConstructor = __init__(self, *args)
pyXplorHelp(*args) -> 'String'