Bioperl: 3D biomolecular structure handling for Bioperl

Lincoln Stein
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			                  Cold Spring Harbor, NY
Positions available at my lab: see
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