LOOS  v2.3.2
Voronoi.VoronoiWrapper Class Reference

Public Member Functions

def __init__ (self, atomicGroup, pad=15.0)
 
def isPeriodic (self)
 
def num_atoms (self)
 
def update_atoms (self, atomicGroup)
 
def generate_padding_atoms (self)
 
def num_padding_atoms (self)
 
def get_region_from_atomid (self, atomid)
 
def generate_voronoi (self)
 

Public Attributes

 atoms
 
 edges
 
 pad
 
 padding_atoms
 
 voronoi
 
 regions
 
 superRegions
 
 atoms_to_regions
 

Detailed Description

Wrap the scipy Voronoi class, which in turn is a wrapper around QHull.
So, it's a wrapper wrapper, and if this program is called from a script,
then we'd have a wrapper wrapper wrapper.  Now I just need m4 and Tod will 
approve.

atomicgroup is a LOOS AtomicGroup
pad is a float specifying how far out we will generate padding atoms 
    (fake "image" atoms used to emulate periodicity).  15 ang is a good 
    default if you're using all atoms or all heavy atoms, but you may 
    need to go farther if you're using a sparser selection (e.g. just 
    lipid phosphates)

Definition at line 47 of file Voronoi.py.

Member Function Documentation

def Voronoi.VoronoiWrapper.generate_padding_atoms (   self)
Build the list of atoms in the periodic images surrounding the central
image.

This is necessary because QHull doesn't know anything about periodicity,
so we need to do fake it; otherwise, you'd have bizarre or infinite
areas for atoms near the edge of the box

Definition at line 81 of file Voronoi.py.


The documentation for this class was generated from the following file: