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Pydoc: module ramaPushPot

ramaPushPot

index

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