On Sep 30, 2007, at 2:26 AM, Egon Willighagen wrote:
> On 9/29/07, Rajarshi Guha <[EMAIL PROTECTED]> wrote:
>
> Mmm... What about type 4 bonds in MDL files then? Should we do the
> bond order deduction there too then?
>
> 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.
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
-------------------------------------------------------------------
Rajarshi Guha <[EMAIL PROTECTED]>
GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE
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667:
The neighbor of the beast.
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