Re: [Cdk-devel] proposal to modify class from cdk

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

=2D----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

On Friday 19 November 2004 10:23, Miguel Rojas Cherto wrote:
> I've been using 3 class ( AtomContainer, UniversallsomorphismTester and
> Molecules) which I've modified.  And I think that they are interesting.

Could you send 'cvs diff -u src/org/openscience/cdk/AtomContainer.java' etc?

> A) knowledge if a atom has single electron: AtomContainer Class:

Ok, this is to store radical information, correct? Does the SingleElectron=
=20
class extend the ElectronContainer?

> 1: New function - getSingleElectron

<code skipped/>

> 2: New Function -  getSingleElectronSum

<code skipped/>

> B)  Problems with compare to molecules: UniversallsomorphismTester:
> extension Inserted into nodeConstructor. Now not only create an
> association node between symbolAtom and symbolAtom but Hydrogen for this
> atom, its charge and its singleElectrons.
> Example:
> (bondsA1[i].getAtomAt(0).getSymbol().equals(bondsA2[j].getAtomAt(0).getSy=
mb
>ol()) ...
> (bondsA1[i].getAtomAt(0).getHydrogenCount() =3D=3D
> bondsA2[j].getAtomAt(0).getHydrogenCount())
> ...
> (bondsA1[i].getAtomAt(0).getFormalCharge() =3D=3D
> bondsA2[j].getAtomAt(0).getFormalCharge())
> ...
> (ac1.getSingleElectronSum(bondsA1[i].getAtomAt(0))  =3D=3D
> ac2.getSingleElectronSum(bondsA2[j].getAtomAt(0))
> ...

Such code should no longer be in UniversalIsomorphismTest at all... That so=
rt=20
of things should be covered by AtomMatcher's... Please send a 'cvs diff -u'=
=20
so that we can further discuss this...

> C) Problems with a molecule to clone: Molecules: Into clone function
> I've inserted a funtion to compare for each atom  these funcionalities
> und adds in this new cloned molecule those funcionalities that the
> OBJECT.clone function cann't clone (Ohh!!). Naturally the return of the
> function is a Object.

Ok, I need a cvs diff for this too...

> I hope you can have a look at these new proposal to modify

Send the additional info, and I'll look at it. (BTW, all sounds good=20
though...)

Egon

=2D --=20
eg...@us...
=2D ---------------------------------------
CDK: http://cdk.sf.net/
JChemPaint: http://jchempaint.sf.net/
Jmol: http://www.jmol.org/
=2D----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.0.7 (SunOS)

iD8DBQFBnbE9d9R8I9Yza6YRAq4zAJ9A50kKKM7vXQiilnLjpMpKhy6WIwCeKDIW
2XIIUh+p5LknMNJ8NyzbGAY=3D
=3DZwU1
=2D----END PGP SIGNATURE-----