PyPot: base class used by potential terms written in Python.
 
to write a potential term in Python, define a class which derives from
pyPot.PyPot, and make sure to call the base class' constructor.
Then, the new class should define two methods: 
calcEnergy, and calcEnergyAndDerivList(derivList). The constructor is
PyPot(self,name,defaultSimulation=None). If simulation is omitted, it
defaults to simulation.currentSimulation().
 
Note that the derivList argument contains the sum of gradients up to
the position of the current term in a potList, so this should be
added to, and not cleared, or wholesale scaled in any user-defined
energy term. The derivList argument is indexed by atom, as seen below.
Alternatively, a method named calcEnergyAndDerivs(indexDerivList) can be
defined, where the indexing is instead done via atom index in the PyPot's
simulation. 
 
Here is a simple example of a potential term for a single bond:
 
from pyPot import PyPot ; from vec3 import norm, Vec3
class BondPot(PyPot):
    ''' example class to evaluate energy, derivs of a single bond
    '''
    def __init__(self,name,atom1,atom2,length,forcec=1):
        ''' constructor - force constant is optional.'''
        PyPot.__init__(self,name) #first call base class constructor
        self.a1 = atom1     ; self.a2     = atom2
        self.length = length; self.forcec = forcec
        return
    def calcEnergy(self):
        self.q1 = self.a1.pos() ; self.q2 = self.a2.pos()
        self.dist = norm(self.q1-self.q2)
        return 0.5 * self.scale() * self.forcec * (self.dist-self.length)**2
    def calcEnergyAndDerivList(self,derivs):
        energy = self.calcEnergy()
        deriv1 = Vec3(map(lambda x,y:x*y,
                       [self.forcec * (self.dist-self.length) / self.dist]*3 ,
                         ( self.q1[0]-self.q2[0], 
                           self.q1[1]-self.q2[1], 
                           self.q1[2]-self.q2[2] )))
        derivs[self.a1] += self.scale() * deriv1
        derivs[self.a2] -= self.scale() * deriv1
        return energy
    pass
 
# The term can be instantiated like:
p = BondPot('bond',AtomSel('resid 1 and name C')[0],
                   AtomSel('resid 1 and name O')[0], length=1.5)
 
 
 
# 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 PyPot PyPot_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 PyPot(builtins.object)     PyPot(*args, **kwargs)       Methods defined here: __deref__(self, *args, **kwargs) -> 'PyPot *' __init__ = construct(self, *args, **kwargs) __oldinit__ = __init__(self, *args, **kwargs) __ref__(self, *args, **kwargs) -> 'PyPot &' __repr__ = _swig_repr(self) calcEnergy(self, *args, **kwargs) -> 'float_type' calcEnergyAndDerivs(self, *args, **kwargs) -> 'float_type' decrRefCnt(self, *args, **kwargs) -> 'void' 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' pythonPot(self, *args, **kwargs) -> 'PyObject *' 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' 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_PyPot(...) 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   class PyPot_LetterClass(builtins.object)     PyPot_LetterClass(*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' pyXplorHelp(self, *args, **kwargs) -> 'String' pythonPot(self, *args, **kwargs) -> 'PyObject *' rms(self, *args, **kwargs) -> 'float_type' violations(self, *args, **kwargs) -> 'float_type' Static methods defined here: __swig_destroy__ = delete_PyPot_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   realPyPot = class PyPot(builtins.object)     realPyPot(*args, **kwargs)       Methods defined here: __deref__(self, *args, **kwargs) -> 'PyPot *' __init__ = construct(self, *args, **kwargs) __oldinit__ = __init__(self, *args, **kwargs) __ref__(self, *args, **kwargs) -> 'PyPot &' __repr__ = _swig_repr(self) calcEnergy(self, *args, **kwargs) -> 'float_type' calcEnergyAndDerivs(self, *args, **kwargs) -> 'float_type' decrRefCnt(self, *args, **kwargs) -> 'void' 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' pythonPot(self, *args, **kwargs) -> 'PyObject *' 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' 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_PyPot(...) 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
		construct(self, *args, **kwargs) fromPy(*args, **kwargs) -> 'void' oldConstructor = __init__(self, *args) pyXplorHelp(*args) -> 'String'