On 31.05.2011 21:00, Egon Willighagen wrote:
> Yes, the SDG does not handle disconnected structures.
Clear.
> The proper way of doing is, is to check first of the IAtomContainer
> you got from the getInChIToStructure() method is connected (using the
> ConnectivityCehcker) and to partition is if not.
Thanks. That is new to me... Have anybody come across the problem of
rendering a IMoleculeSet? What about rendering reactions in CML format?
> I do not understand this question. And IAtomContainer and IMolecule to
> be the same by implementation is just because we do not want the
> IMolecule to check if an edit results in a disconnected structure
> (computationally expensive). But the semantics are there.
OK, I got the point: IAtomContainer may contain disconnected structures
and IMolecule may not (but only semantically; programmer may still mess
things).
On the other hand InChI at the moment do not support mixtures, at least
I am not aware of any InChI, that encodes 2 molecules in one string. But
in general you are right: potentially (in the nearest future) InChI may
be able to encode several molecules.
Thanks also for code snippet below. Hopefully I'll do some effort to
improve this peace of API.
>> And second is that getInChIToStructure() needs to be passed a
>> IChemObjectBuilder instance, which most cases is a CDK default one.
>
> Yeah, I'm wondering why, because the nonotify classes are in fact faster.
> I guess performance is not so important after all :)
>
>> Perhaps the API should include the set of methods without
>> IChemObjectBuilder argument.
>
> Yes, I have been thinking about that. We could instantiate a
> ChemObjectBuilderFactory, which will try to load one of the two main
> implementations. This will most certainly not work for all situations
> (e.g. not in Bioclipse or any other place with custom class loaders,
> unless we start making the Factory instantiated with that custom
> ClassLoader...)...
>
> Something like:
>
> /**
> * @cdk.module core
> */
> public class ChemObjectFactory {
>
> public abstract IChemObjectBuilder getBuilder(ClassLoader loader)
> throws ClassNotFoundException, InstantiationException {
> String[] knownBuilders = new String[
> "org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder",
> "org.openscience.cdk.nonotify.DefaultChemObjectBuilder"
> ];
> for (int i=0; i<knownBuilders.length; i++) {
> IChemObjectBuilder builder =
> loader.loadClass(knownBuilders[i]).getInstance();
> return builder;
> }
> }
> return new SomeAppropriateException();
> }
>
> Finish the patch (full JavaDoc, unit testsing, etc, etc), two people
> to approve of the patch, and I'll apply it to cdk-1.4.x.
>
> Egon
--
With best regards,
Dmitry
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