Re: [Cdk-devel] Checking if an atom is in a ring

[Christoph S. <c.s...@un...>]

Uli Fechner wrote:

> I totally like the idea of carrying around an already calculated ringse=
t=20
> as a property of the respective AtomContainer. Of course, it is=20
> important to discriminate between AllRings and SSSR. I have two=20
> suggestions:
>=20
> - single property ringset; then the client who is dealing with the=20
> ringset has to figure out which one is actually stored in the property=20
> (e.g. with instanceof)
> - two different ringset properties (e.g. "ALLRINGS", "SSSRINGS")
>=20
> I personally favour the second one.

Me too.
So let's wait until monday evening for others to respond. Then we can go=20
for the implementation.

Cheers,

Chris

--=20
Priv. Doz. Dr. Christoph Steinbeck (c.s...@un...)
Head of the Research Group for Molecular Informatics
Cologne University BioInformatics Center (http://www.cubic.uni-koeln.de)
Z=FClpicher Str. 47, 50674 Cologne
Tel: +49(0)221-470-7426   Fax: +49 (0) 221-470-7786

What is man but that lofty spirit - that sense of enterprise.
... Kirk, "I, Mudd," stardate 4513.3..


Uli Fechner wrote:
 >>> I have an additional suggestion. In CDKConstants is the following
 >>> constant:
 >>>
 >>> /** Flag that is set when the chemobject is part of a ring.
 >>> */
 >>> public final static int ISINRING =3D 1;
 >>>
 >>> If the ring finder algorithms (cdk.ringsearch.{AllRingsFinder,
 >>> FiguerasSSSRFinder, SSSRFinder) actually set this flag for an Atom o=
r
 >>> Bond that is in a Ring the problem of identifying if an atom is part
 >>> of a ring w/o doing a ring search more than once would be solved.
 >>
 >>
 >>
 >> Most of the algorithms actually need to know which atom belongs to
 >> which ring, not just if it is in a ring.
 >> So we need the ringset with all the rings in it.
 >> We could introduce a property "Ringnumber", from which the ringset ca=
n
 >> be quickly reconstructed. Another, even more efficient solution shoul=
d
 >> be a property "ringset", to be set for an atomcontainer, which points
 >> to an already computed ringset. There, we also need to memorize,
 >> whether we are talking about a SetOfAllRings or an SSSR.
 >> This we are dealing with reference here, this should not be a memory
 >> problem.
 >
 >