Re: [Cdk-user] RFC: SMILES parser responsibilities?

[Egon W. <ego...@gm...>]

On 9/30/07, Rajarshi Guha <rg...@in...> wrote:
> On Sep 30, 2007, at 2:26 AM, Egon Willighagen wrote:
> > On 9/29/07, Rajarshi Guha <rg...@in...> wrote:
> > Why not simple WYSIWYG? -> You see no double bonds (SMILES, MDL), but
> > marks of sp2 (SMILES) or aromaticity (MDL bond type 4), so you get no
> > double bonds but markers of sp2 or aromaticity.
>
> That's fine - but you're going to have to put up a very big notice,
> preferably in flashing neon, reminding people that after SMILES
> parsing one must do bond deduction etc etc.

OK, we can surely put in some <font style="color: neon"/> in the
JavaDoc and there used to be some <blink> in HTML too.

> It still seems, that the process is as follows
>
> set atom typng
> read in molecular file format
> return processed molecule
>
> The reason I put atom typing up front, is so that the file reading
> code will use that to process the data. I understand that this goes
> against the Lego philosophy - but if nothing else, there should be a
> utility class that does this

Go on. What atom type list would you suggest? I only know of Mol2 that
actually uses this approach. SMILES does not generally have this
approach, though valencies are defined for the organic subset. How do
you envision the 'setting'? Why is that prior to the reading, instead
of during the reading? And why does this contradict the Lego
philosophy?

Egon

-- 
----
http://chem-bla-ics.blogspot.com/