[MMTK] additional_objects.py example in MMTK

Andrew D. Fant fant at pobox.com
Thu Mar 23 21:39:50 CET 2006

OK.  I'm trying to work with the additional_objects.py example in MMTK and two
questions come to mind.  I'm using MMTK-2.5.13 with ScientificPython 2.5.8 and
Numeric 23.7 on a 2,2 gHz Pentium 4 running Linux

1) Is it me, or is the eigenvectors routine either painfully slow or broken?  I
ran the code and nothing happened, so I waited, then I killed the process and
tried again.  After 5 minutes, I killed that process and instrumented the code a
little more closely.  The centering and orientation process took a few seconds
for insulin, which I could deal with, but when it came to the:

	diagonal, directions = LinearAlgebra.eigenvectors(inertia.array)

line, the system, goes into a period intense activity with the CPU meter pegged,
but nothing happens for at least 10 minutes (I entered the commands one-by-one
from the command line to verify this is where it hangs, and it is).  Is my
install well and truly borked, or am I impatient?

2)  Could someone show or help me see how to convert this example to work with a
 non-protein molecule (such as the heme example in the database)?  Most of what
I want to do with MMTK is small-molecule oriented, and the protein class isn't
quite what I want, but I need more than just a collection of atoms and bonds.


Andrew Fant    | And when the night is cloudy    | This space to let
Molecular Geek | There is still a light          |----------------------
fant at pobox.com | That shines on me               | Disclaimer:  I don't
Boston, MA     | Shine until tomorrow, Let it be | even speak for myself

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