[Joelib-devel] Re: [Cdk-devel] Octet-CDK interoperability

[Egon W. <eg...@sc...>]

On Wednesday 05 May 2004 04:35, rich apodaca wrote:
> One of the problems I came up against in using option (2) was that the CDK
> IO classes create their own instance of org.openscience.cdk.Molecule,
> rather than allow for one to be passed in and operated on. If this could be
> enabled, then clients could go:
>
> BasicCDKMolecule cyclohexane = new BasicCDKMolecule();
> SMILESReader reader = new SMILESReader(new StringReader("C1CCCCC1"));
>
> reader.read(cyclohexane); // or possibly reader.read(chemobject,
> cyclohexane);
>
> // now do something with cyclohexane

Yes, that should be changed. One complicating problem is that we also need the 
BasicCDKMolecule *and* the CDK Molecule to create Atom's !

Or does the BasicCDKMolecule except CDK Atom, and convert that internally?

> // we now have cyclohexane that can be used in either Octet or CDK - and
> the beauty is that CDK knew nothing about what just happened!
>
> Of course, there are other strategies for CDK-Octet interoperability that
> could be followed, and variants on the above two, but I think this give a
> feel for what might be possible.

No, this looks fine.

Egon