data structure design question

[Thomas Hamelryck]

Felix Thibault <felixt at dicksonstreet.com> wrote:
: I'm looking at kjbuckets now, but I have a question about the graphs-
: the documentation says:

: 	[Graphs] relate Python hashable objects to other objects,
: 	 with no significance to order or redundancies on the 
: 	pairings. Technically, kjGraph defines a directed graph 
: 	abstract data type...

: Does this mean that I can use a graph to show which atoms are connected,
: but I need to find some other way to show whether a bond
: is a single or multiple bond...or else have nucleus-nodes inter-connected
: by electron=pair-nodes ?

Yes. You can store the connectivity in a graph, but you need to find another way to store 
the information about the bonds. Everything depends of course on what you are trying
to do. A data structure that will be used to draw simple chemical structures will of 
course be different from one that will be used to refine a protein structure. 

One possible solution is to attach an atom type to each atom. You can then do a look 
up in a dictionary to find the information associated with a bond between two atoms
of a certain type. This is e.g. done in the macromolecular modeling program X-PLOR.
You might want to take a look at MMTK, a molecular modeling package written in Python
by Konrad Hinsen (http://starship.python.net/crew/hinsen/MMTK/).

BTW, If you want to do heavy numerical stuff like matrix multiplication and vector
operations  you must check out the numerical extension NumPy 
(http://numpy.sourceforge.net/). 

Cheers, 

---
Thomas Hamelryck    Institute of Molecular and Structural Biology
Aarhus University   Gustav Wieds Vej 10C
DK-8000 Aarhus C    Denmark