ramaPushPot
index
/home/schwitrs/xplor/python/ramaPushPot.py


 
Energy term used to add a repulsive energy term to regions of Ramachadran space
where a violation is detected (as informed by TorsionDB).

 
Classes
       
builtins.object
Restraint
pyPot.PyPot(builtins.object)
RamaPushPot

 
class RamaPushPot(pyPot.PyPot)
    RamaPushPot(name, selection='not pseudo', width=60, simulation=None)
 

 
 
Method resolution order:
RamaPushPot
pyPot.PyPot
builtins.object

Methods defined here:
__init__(s, name, selection='not pseudo', width=60, simulation=None)
Create a new RamaPushPot potential with the given instance name and
an optional simulation argument.
addRestraint(s, **kwargs)
ageRestraints(s)
calcEnergy(s)
calcEnergyAndDerivList(s, derivs)
clearRestraints(s)
configure(s, verbose=False, lifetime=0)
Configure the specified RamaPushPot based on the currently violated
residues.
numRestraints(s)
readRestraint(s, line)
readRestraints(s, restraintString)
Read in restraint table
restraints(s)
rms(s)
showRestraints(s)
violations(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 *'
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'
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'

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

 
class Restraint(builtins.object)
    Restraint(pot, phi, psi, width, size, comment='', lifetime=0)
 

 
  Methods defined here:
__init__(s, pot, phi, psi, width, size, comment='', lifetime=0)
Initialize self.  See help(type(self)) for accurate signature.
age(s)
deriv(s, dlist)
Called after energy.
diff(s)
energy(s)
For now, circular: width phi = width psi
 
(phi-s.phi0)**2 + (psi-s.psi0)**2
lifetime(s)
name(s)
violated(s)

Data descriptors defined here:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

 
list of weak references to the object (if defined)

 
Functions
       
analyze(potList)
perform analysis of RamaPushPot terms and return nicely formatted summary