loos.Voronoi.Voronoi.VoronoiWrapper Class Reference

Public Member Functions
	__init__ (self, atomicGroup, pad=15.0)
	isPeriodic (self)
	num_atoms (self)
	update_atoms (self, atomicGroup)
	generate_padding_atoms (self)
	num_padding_atoms (self)
	get_region_from_atomid (self, atomid)
	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)

Member Function Documentation

generate_padding_atoms()

loos.Voronoi.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

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

• loos/src/loos/Voronoi/Voronoi.py