On Thu, Mar 28, 2013 at 6:47 AM, Chris Morley <c.mor...@gaseq.co.uk> wrote:
> On 27/03/2013 17:35, Geoffrey Hutchison wrote:
> >> Maybe a proposed simplification of the valence system
> >> http://forums.openbabel.org/ImplicitH-failures-td2990439.html
> >> should be looked at again.
> >
> >
> > Copy/paste from Chris's earlier message:
> >> A simpler and more obvious model for this purpose has essentially a
> >> single IMPVAL for each charge state of the molecule. ...
> >
> >
> > I would be strongly in favor of implementing such a change now.
> Performance testing has suggested that we perform way too many SMARTS
> matching when doing typical things like parsing SDF or aromaticity
> detection.
> >
> > Chris, do you think your revised model can be integrated now? Based on
> my schedule, I think a v2.4 release would be mid-summer. I would like to
> finish my distance geometry implementation for coordinate generation and
> conformer sampling and I think there would be plenty for a new release.
> >
> > It seems like Craig and Noel are strongly in support of this too.
>
> I'll have a go at resurrecting this.
>
> I agree with Craig that the inner workings of OB are a bit of a hotch-
> potch, probably reflecting what several different people thought was
> "obvious". Bit I suspect making all the changes suggested would be a lot
> of (boring) work - this was why MolCore was proposed.
>
I suspect one of the hardest problems will be maintaining backwards
compatibility while adding new functions/behavior to correct the problems.
It may not even be possible.
Craig
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