On 10/06/2014 08:38 PM, Robert Hanson wrote:
Probably not. I didn't realize we were talking about quite so many nodes.
Still, the UFF field is interesting because it might work with any geometry
-- leaving angles out all together. We might have to add something to get
it to ignore certain energy components. Angles and dihedrals, for instance.
The more I think about it the more I doubt it really makes sense for me
to dig deep into UFF and spend a lot of time just to find out that it
doesn't really fit to the task. I took a quick look at a paper on UFF
from Rappe et al (J. Am. Chem. Soc. 114:10024-10035, 1992) and can't
really imagine how I would be able to fit this into my task.
Bob, maybe if I would describe some possibly suitable (initial) layout
strategies that came into my mind you could give me a hint if it would
really be worth the effort to try to make UFF work for networks.
For a specific ageing factor there will be for example two types of
networks:
1) All observations in which the ageing factor participates and all
other ageing factors that are also involved in these observations.
This means there will be one central ageing factor node connected to all
observations. And each observation will be connected to currently up to
six other ageing factors.
2) An iterative combination of type 1 networks for each ageing factor
from type 1 into a huge combined network. This will be much more complex
with a lot of smaller and larger centers, connected by one or more
observations.
Finding a suitable layout for type 1 might not be too complicated. I
thought about two strategies:
1a) The observation nodes are evenly distributed within a sphere around
the central ageing factor node. The other ageing factor nodes are then
again distributed evenly within a sphere around their observation node.
Nodes with more connections are preferably positioned in the outer parts.
1b) The other ageing factor nodes are evenly distributed within a sphere
around the central ageing factor node. The observation nodes are then
evenly distributed in the non-overlapping part of a second larger sphere
around the central ageing factor.
This will be more complicated to achieve than 1a but it has the
advantage that it will be possible to group the ageing factors and
separately also the observations by user-defined criteria. For example
on one side of the sphere could be placed all observations that decrease
the lifespan. On the other side could be the observations that increase
the lifespan. And in the middle could be the neutral ones.
Building type 2 will presumably be more complicated. Only strategy 1a
would fit in here I would guess. I don't think that strategy 1b is
compatible with type 2, at least not without containing nodes
redundantly. (But maybe without a real center...?)
My final goal would be to develop a general purpose JSmol-based network
viewer (not just AgeFactDB-related). I guess it will be somehow similar
to the Jena3D viewer for PDB structures but ideally without a server
backend (except maybe as additional information source).
Finally I have a related question:
Q: Does JSmol allow that an atom is part of more than one residue or
would this interfere with something?
I ask this because it would enable to use residue-based functions for
handling observations. (A residue would consist of the observation node
and all connected ageing factor nodes. Ageing factor nodes might then be
part of a larger number of residues.) I really hope that this is
possible because it would speed up things a lot and also spare me a lot
of development time.
Regards,
Rolf
--
Rolf Huehne
Postdoc
Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI)
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E-Mail: rhue...@fli-leibniz.de
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