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


 

 
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.