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Pydoc: module densPotTools

densPotTools

index

Classes

pyPot.PyPot(builtins.object)

DensPot

class DensPot(pyPot.PyPot)

DensPot(name, selection, target=1.1, radiusType='heavyatom', radii=None, mass=None)

Method resolution order:: DensPot; pyPot.PyPot; builtins.object

Methods defined here:

__del__(self, destroy=0)

__init__(s, name, selection, target=1.1, radiusType='heavyatom', radii=None, mass=None): target is the target density in units of amu/A^3

calcEnergy(s)

calcEnergyAndDerivList(s, derivs=None)

density(s, derivs=None): calculate molecular density based on the surface defined by the
sa member. If derivs is specified, the gradient of the density
with respect to each atom will be calculated.

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
		create_DensPot(name, selection='not PSEUDO', targetDens=1.1, rSolvent=0) create a DensPot including all atoms in selection. targetDens specifies the target density value used in energy calculation. The target density is given in units of amu/A^3. For rSolvent=0 we have found that the density is 1.101 +/- 0.010 for 30 high-resolution crystal structures.