>On Mon, Aug 3, 2009 at 5:36 PM, Geoffrey Hutchison <
geoff@...> wrote:
Hi Peter,
>When you visited Pittsburgh this spring, I mentioned Avogadro and that
we were interested in representing as much as possible in our CML files.
>First off... grids / cubes. We plot molecular surfaces, but these are
essentially just representations of a function f(x, y, z) or "cube."
That is, for each point xyz, we have a value. We'd like to represent
this in CML, but from our discussion in person, this wasn't yet
possible?
Thanks very much Geoff for this exciting use of CML.
One simple method would be to have something like:
<cml convention="blueobelisk:grid3d" dictRef="avogadro:cubes">
<scalar dictRef="geom:x0" units="units:A">10.0</scalar>
<scalar dictRef="geom:deltax" units="units:A">0.1</scalar>
<scalar dictRef="geom:x1" units="units:A">12.0</scalar>
<scalar dictRef="geom:y0" units="units:A">20.0</scalar>
<scalar dictRef="geom:deltay" units="units:A">0.1</scalar>
<scalar dictRef="geom:y1" units="units:A">23.0</scalar>
<scalar dictRef="geom:z0" units="units:A">30.0</scalar>
<scalar dictRef="geom:deltaz" units="units:A">0.1</scalar>
<scalar dictRef="geom:z1" units="units:A">34.0</scalar>
<matrix rows="21" columns="31" units="units:electronA3">..... values
...</matrix>
<matrix rows="21" columns="31" units="units:electronA3">..... values
...</matrix>
<matrix rows="21" columns="31" units="units:electronA3">..... values
...</matrix>
...
<matrix rows="21" columns="31" units="units:electronA3">..... values
...</matrix>
</cml>
Here there are enough explicit semantics that anyone can understand the
file.
There is no need to edit the schema. Let's see what the BO think about it so
I have copied them in.
P.
>
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Peter MurrayRust
Reader in Molecular Informatics
Unilever Centre, Dep. Of Chemistry
University of Cambridge
CB2 1EW, UK
+441223763069
