[octet-devel] Re: [QSAR-devel] Proposal for Molecule, Atom, BondingSystem API changes

[E.L. W. <e.w...@sc...>]

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On Saturday 27 November 2004 19:56, rich apodaca wrote:
> I would like to propose some additional changes to the
> Octet API (http://octet.sf.net).
>
> These methods would be removed from the Atom
> interface:
>
> iterateNeighbors()
> countNeighbors()
> isConnectedTo(Atom atom)
> countElectrons()
> iterateBondingSystems()
> countBondingSystems()
> countReservedElectrons()
> toNeighborArray()
> toBondingSystemArray()
> getConfiguration()
>
> ... and their equivalents would be placed into either
> the Molecule or AtomGraph interface. For example,
> Atom.getConfiguration() would become
> Molecule.getConfiguration(Atom atom).  AtomGraph
> already has iterateNeighbors(Atom atom) and
> countNeighbors(Atom atom).
>
> I believe these changes will result in a more
> consistent, robust system.

CDK uses the same approach... those kind of methods are in AtomContainer,
and not in Atom itself. So no objection I guess.

Egon

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e.w...@sc...
PhD-student on Molecular Representation in Chemometrics
Radboud University Nijmegen
http://www.cac.science.ru.nl/people/egonw/
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