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Pydoc: module maxHeightPot
 
maxHeightPot		 index


 
Energy term on the maximum height of a molecular structure, using maximum 
and minimum values computed using softMax.SoftMax.

 
Classes
       
pyPot.PyPot(builtins.object)
MaxHeightPot

 
class MaxHeightPot(pyPot.PyPot)
    MaxHeightPot(name, selection, gamma=0.5, direction=(0, 0, 1), isProgress=False, target=None)
 

 
 
Method resolution order:
MaxHeightPot
pyPot.PyPot
builtins.object
Methods defined here:
__del__(self, destroy=0)
__init__(s, name, selection, gamma=0.5, direction=(0, 0, 1), isProgress=False, target=None)
Gamma is a distance in Angstrom - for smoothing the soft-max 
functions. The direction argument specifies which direction
the maximum is computed for (z-direction by default). This
function sets the targetHeight member to the initial value of 
height() unless the target value is given.
 
If isProgress is set to True, targetHeight is updated in every
call to calcEnergy() to the current value if it is less than
the current value.
calcEnergy(s)
calcEnergyAndDerivList(s, derivs=None)
direction(s)
Return the direction along which the maximum is computed.
gamma(s)
hardHeight(s)
Return the hard max value.
height(s)
Return the soft max value.
radii(s)
Return sequence of atomic radii.
selection(s)
setDirection(s, vec3)
Set the direction along which the maximum is computed.
setGamma(s, val)
setRadii(s, vec)
Specify atomic radii. The vec argument must have len(selection())
elements.
setSoftMaxType(s, val)
simulation(s)
softMaxType(s)
Methods inherited from pyPot.PyPot:
__deref__(self, *args, **kwargs) -> 'PyPot *'
__oldinit__ = __init__(self, *args, **kwargs)
__ref__(self, *args, **kwargs) -> 'PyPot &'
__repr__ = _swig_repr(self)
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 inherited from pyPot.PyPot:
__swig_destroy__ = delete_PyPot(...)
Data descriptors inherited from pyPot.PyPot:
__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
       
analyze(potList)
Perform analysis of MaxHeightPot terms and return nicely formatted
summary.
softHeight(term)