[Cdk-devel] Question: Can CDK do ***? (Was: Update: IUPAC name generator)

[Egon W. <eg...@sc...>]

On Wednesday 11 September 2002 22:00, Egon Willighagen wrote:
> I've had a few hours to do further work on the IUPAC name generator...
> The design seems to be working:
>
> I've (partly) implemented two rules in Section A (1.1 and 2.1), and the
> current version can name these compounds in two languages (English
> and Dutch):
>
> methane, ethane, up to, decane (rule 1.1)
>
> and
>
> isobutane (rule 2.1)

Added isopentane and isohexane.

> Before I will do a first release I want to implement naming of Fragment
> class types, aka radicals... like ethyl, etc...

Done. It will now properly name methyl - decyl... It acutually already is a 
recursive algorithm... that is, it can now handle structures that need to be
split in smaller parts to be named. To be specific, it can name branched
alkanes now, but only the fragments, the output is not correctly ordered 
yet ;) Neither does it add localization numbers defining how the fragments
are connected yet...

> The output of the program is the IUPAC name (yes, of course ;), but also
> the applied rules... the latter is of much interest of you need to know
> which were applied (and in which order)... future version will even be able
> to map fragments of the named molecule with parts of the name, and the
> applicable rule...

I've been rewriting the data structures for the IUPAC name result. This is 
almost done. The software *will* include a mechanism that shows you which
part of the molecule resulted in which IUPAC name part (which I am very happy 
about)

But, I have two questions:

Can CDK:
1. ... saturate the molecule with hydrogen? How? (And remove them?)
2. ... draw 2D images with colored atoms?

The latter I want to use to color each IUPAC name part with a different color.
(Preferably, I want to highlight only one part, which you could select with 
the mouse... but I must start somewhere ;)

Egon