[Openchemistry-developers] Google Summer of Code 2022

[Geoffrey Hutchison]

Dear Artiz,

Thanks very much for your proposal and interest in GSoC 2022! If you post your proposal on Google Docs or something that enables comments, I would be happy to make suggestions.

A few general suggestions.. At the moment, this reads like a collection of smaller tasks. Generally, Google prefers to see a larger arc to projects. So perhaps one way would be to say that you want to significantly improve Avo2 use for biomolecular simulation and editing? 

You mention the surface work. I would definitely love to see surfaces and properties integrated this summer. That may be a larger part than you're currently allocating in your timeline depending on your coding experience. I can share some PDFs - Marc (from Barcelona - https://serk12.github.io <https://serk12.github.io/>) had hoped to work on this last year, but ran out of time.

There are some formats (e.g., SDF) which support zero-order bonds to indicate coordination (https://pubs.acs.org/doi/abs/10.1021/ci200488k <https://pubs.acs.org/doi/abs/10.1021/ci200488k>) - on the other hand, it seems like the examples you give are problems with hydrogen addition to nitrogen .. which may be an easier fix.

The background on perceiveBondsSimple and element parsing is great. We prefer that candidates submit at least one patch to show they understand GitHub, etc. .. which you've already done. I'd definitely appreciate the patches for those and/or any other small pieces as you finish them.

Anyway, thank you for the early interest - I would be happy to help you improve your proposal!

Best regards,
-Geoff

---
Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geoffh at pitt.edu
twitter: @ghutchis
web: https://hutchisonlab.org/



> On Mar 7, 2022, at 6:17 PM, Aritz Erkiaga <aerkiaga3 at gmail.com> wrote:
> 
> Good evening,
> 
> I recently read that Google has opened its Summer of Code program to non-developers. Having used Avogadro for so long, and now even being an occasional contributor, I immediately rushed to write an application draft. Now I'm glad to see that Open Chemistry has been accepted.
> 
> Here's the draft: https://aerkiaga.github.io/docs/gsoc2022.pdf <https://aerkiaga.github.io/docs/gsoc2022.pdf>
> I've tried my best to be comprehensive and offer useful improvements, but this document is subject to further updates throughout the month. I'll happily accept any proposals to extend my scope, or take on an entirely different project, as long as it's within my general interest: the application of Avogadro components to biochemistry and drug design. Performance work is also a task I'd appreciate; I've in fact optimized Avogadro's PDB import and hydrogen adjustment in the last few days to be 50 and 15 times faster, respectively, so as to avoid long wait times during testing.
> 
> Regarding the changes I've already made, I'm unsure how or when I should publish them. I'm awaiting instructions on that front, and meanwhile I'll keep working on the code.
> 
> Cordially,
> 
> Aritz Erkiaga
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