data structure design question
Thomas Hamelryck
thamelry at vub.ac.be
Thu Feb 17 09:45:10 CET 2000
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
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