Bioperl: 3D biomolecular structure handling for Bioperl
Fri, 18 Dec 1998 09:54:33 GMT
> > I am becoming convinced there should be a core molecular
> > representation which is very lightweight (stores atom&bonds), and
> > "views" of the molecule which provide specific interfaces. For
> > example from small molecules, some people like Kekule form and others
> > don't. The Kekule view of a molecule would have bonds that are
> > single/double while the non-Kekule view would have "aromatic" bonds.
> This is in-line with our thinking as well. But how best to represent
> the data in the core format? XML maybe?
I strongly support the idea of using XML for this and other elements
of Bioperl. I wonder how well the CML (Chemical Markup Language)
already fits these requirements?
Lincoln D. Stein Cold Spring Harbor Laboratory
email@example.com Cold Spring Harbor, NY
Positions available at my lab: see http://stein.cshl.org/#hire
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