Geoff,
I think this is a great initiative!
I like pretty much every single one of the ideas you proposed.
One thing I would like to add is the support for processing SMIRKS reactions, which would
improve a lot the spectrum of applications of OpenBabel. In terms of popularity, it seems
the topic appeared in the mailing list at least 31 times (not bad for a feature not
implemented nor documented).
Currently, beside the supported for file format conversions, there is a very minimal
functionality that is used for generating the protonation states (applying the
transformations in phmodel.txt).
When I tried to extend the pH model, I found several limitations which prevents the
definition of more complex protonation states.
This would benefit also the tautomer generation, which might be another useful feature to
have (we talked about this a while back). There are other open source projects such as
MolVS that could provide inspiration and data for it.
I imagine the first one to be relatively complex, but the second one looks fairly simple
(when looking at the MolVS template).
My 2 cents.
S
On 2020-03-26 11:16, Geoffrey Hutchison wrote:
As many of you may know, Open Babel is participating in Google Summer of Code
2020. The last two years, we've been lucky to have Naruki working on the
fragment-based builder in 3.0 as well as improvements in the not-quite-finished
distance geometry builder.
If you know of students who might be interested in participating in GSoC 2020,
it's not too late to apply. The deadline is March 31st and more details are
here:
https://wiki.openchemistry.org/Applying_to_GSoC
https://wiki.openchemistry.org/GSoC_Ideas_2020
Beyond that, it's probably a good time to ask for ideas, suggestions, pain
points, etc. Let's say there are developers with time on their hands during
this global pause.. What would you like to see added or changed with Open Babel?
I'd like to open the discussion, but also point people to the issue tracker on
GitHub; https://github.com/openbabel/openbabel/issues
I have a few ideas:
- Improved bond order perception - we're finishing up something for this in my
group
- A bullet-proof 3D coordinate generator
- Improved 2D depiction using the CoordGen library contributed to RDKit last
year by Schrodinger
Thanks,
-Geoff
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Center for Computational Structural Biology
Dept. of Integrative Structural
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