[Joelib-devel] Re: [QSAR-devel] Common molecule interface

[E.L. W. <eg...@sc...>]

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On Wednesday 28 April 2004 11:05, Joerg K. Wegner wrote:
> > Do you consider AtomPair a "descriptor"? I noticed it is present in
> > JOELib. Octet also has an AtomPair interface. However, in Octet, AtomPa=
ir
> > simply represents an association between two atoms (no electrons involv=
ed
> > - that happens through BondingSystem). To find all the atoms that are
> > associated in a Molecule, use Molecule.iterateAtomPairs(). Your point
> > about hashCode() is well-taken.
>
> Not i'm taking it as a descriptor. IT IS a descriptor in medicinal
> chemistry community. So i've no problem with this definition, but there
> are already some papers out there which uses the same name !
> You can generalize, if you add distance and occurence variables. But
> here also a atom can be a more abstract label than a simple atom, e.g. a
> mix of special atom properties.
> So i would prefer a redesign or at least another name.

I don't think anyone can restrict atom pair to match a specific descriptor.=
=2E.=20
it's something like making "windows" a registered trade mark. "Atom pair" i=
s=20
a general term and cannot be restricted to just denote on descriptor.

=46ortunately, we will have dictionaries... where the descriptor "AtomPair"=
 can=20
be explaned...=20

Egon

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eg...@sc...
PhD on Molecular Representation in Chemometrics
Nijmegen University
http://www.cac.sci.kun.nl/people/egonw/
GPG: 1024D/D6336BA6

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