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=[], options=[]) 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 = {}