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


 

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

 
class HMXPot(pyPot.PyPot)
    HMXPot(name, selection, dummyAtoms, resids, data, repel=2.1)
 

 
 
Method resolution order:
HMXPot
pyPot.PyPot
builtins.object

Methods defined here:
__del__(self, destroy=0)
__init__(s, name, selection, dummyAtoms, resids, data, repel=2.1)
calcEnergy(s)
calcEnergyAndDerivList(s, derivs=None)
correlation(s)
numRestraints(s)
offset(s)
restraints(s)
scaleFactor(s)
selection(s)
showRestraints(s)
simulation(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'
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

 
class Restraint(builtins.object)
    Restraint(pot, segid, resname, resid, obs)
 

 
  Methods defined here:
__init__(s, pot, segid, resname, resid, obs)
Initialize self.  See help(type(self)) for accurate signature.
diff(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
       
addDummyAtom(resid, pos, segid=None)
analyze(potList)
perform analysis of HMXPot terms and return nicely formatted summary
correlation(potTerm)
create_HMXPot(name, fileName=None, data='', rnaSegid=None, selection='not PSEUDO', l=1.4, r=5, radiusScale=2.3)
data is input via lines of comma-separated values having the columns
resid, resname, contrib1, contrib2, hmx
Lines starting with a # are skipped.
getRegisteredTerms(sim)
return a list of all HMXPot objects registered to
the specified simulation.
registerTerm(term)
add the given HMXPot object to a list associated with its esim.
These objects will be automatically processed by topologySetup and
massSetup.
topologySetup(ivm, list=[])
Configure ivm.IVM object s.t. the dummy atom remains in its position
relative to the O2' and C2' atoms.
unRegisterTerm(term)
remove the given HMXPot object from a list associated with its esim

 
Data
        default_segid = 'ADUC'
registeredTerms = {}