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Excuse me if this has been covered before, but it having started getting into
jmol I had a question. What does everyone think about creating an API for the
molecules in the system that is disconnected from any particular
“viewer”. Org.jmol.molsystem classes like Chain, Group,
Monomer, Protein Structure, but no renderers, etc and a new molsystem class Org.jmol.molsystem.io IO for reading/writing
molecule files into a mol system Molsystem I think would function like modelmanager in the
org.jmol.viewer, molsystem would contain all the atoms/bonds/etc. in addition
to various annotations on them. A viewer then would require a molsystem during its
construction. This viewer would contain additional info (such as boxes, etc,
basically additional View related information that falls outside the
representation of the molecules) This, I think, would make it easier to create tools
that could be used in headless operation to create/analyze/etc molecule files
and make it easier to integrate with other tools (ie spice, bioclipse,
yourCustomApp). This might even facilitate the creation of other viewer
engines. Although, it seems, modelManager might already do this, why not just
move it to a package to facilitate quicker understanding of the jmol code. -Robin Robin Emig Pioneer HiBred/Dupont 650-298-3564 This communication is for use by the intended recipient and contains information that may be Privileged, confidential or copyrighted under applicable law. If you are not the intended recipient, you are hereby formally notified that any use, copying or distribution of this e-mail, in whole or in part, is strictly prohibited. Please notify the sender by return e-mail and delete this e-mail from your system. Unless explicitly and conspicuously designated as "E-Contract Intended", this e-mail does not constitute a contract offer, a contract amendment, or an acceptance of a contract offer. This e-mail does not constitute a consent to the use of sender's contact information for direct marketing purposes or for transfers of data to third parties.
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