FYI, Implicit hydrogens and kekulization branch

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FYI, Implicit hydrogens and kekulization branch

Noel O'Boyle
Administrator
If you're interested in what I hope will be the future of OB, you can
try out my work on changing the handling of implicit hydrogens and
implementing a new kekulization algorithm:
https://github.com/baoilleach/openbabel/tree/workingimph

This is partly to let people know that there's work in progress and
partly to get some early feedback or field questions. Essentially, the
main difference is that atoms record how many implicit hydrogens are
attached. Previously, OB performed heroic efforts to work this out
based on other information but at the expense of speed and the
occassional mistake.

It's by no means finished (several test failures), but it's all there
in broad strokes. It should be quite a bit faster than the current
release. I've added an option when reading SMILES to keep the
aromaticity present in the SMILES (a performance improvement when
reading aromatic SMILES written by OB, e.g. in a database context),
and the option to write kekule SMILES.

Regards,
- Noel

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Re: FYI, Implicit hydrogens and kekulization branch

Noel O'Boyle
Administrator
I'm feeling good. All tests now pass. A few bugs fixed here and there
in passing, and a lot of insight into parts of the code I've never
previously touched.

Now I need to tidy things up a bit, rebase and send a pull request.
Oh, and someone's going to have to review it. Good luck with that,
Geoff :-)

- Noel

On 14 April 2017 at 11:22, Noel O'Boyle <[hidden email]> wrote:

> If you're interested in what I hope will be the future of OB, you can
> try out my work on changing the handling of implicit hydrogens and
> implementing a new kekulization algorithm:
> https://github.com/baoilleach/openbabel/tree/workingimph
>
> This is partly to let people know that there's work in progress and
> partly to get some early feedback or field questions. Essentially, the
> main difference is that atoms record how many implicit hydrogens are
> attached. Previously, OB performed heroic efforts to work this out
> based on other information but at the expense of speed and the
> occassional mistake.
>
> It's by no means finished (several test failures), but it's all there
> in broad strokes. It should be quite a bit faster than the current
> release. I've added an option when reading SMILES to keep the
> aromaticity present in the SMILES (a performance improvement when
> reading aromatic SMILES written by OB, e.g. in a database context),
> and the option to write kekule SMILES.
>
> Regards,
> - Noel

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Re: FYI, Implicit hydrogens and kekulization branch

Geoff Hutchison
> Now I need to tidy things up a bit, rebase and send a pull request.
> Oh, and someone's going to have to review it. Good luck with that,
> Geoff :-)


Sounds great. I look forward to seeing it. :-)

Cheers,
-Geoff

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