<html><head><meta http-equiv="Content-Type" content="text/html; charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div class="">Dear Artiz,</div><div class=""><br class=""></div><div class="">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.</div><div class=""><br class=""></div><div class="">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? </div><div class=""><br class=""></div><div class="">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 - <a href="https://serk12.github.io" class="">https://serk12.github.io</a>) had hoped to work on this last year, but ran out of time.</div><div class=""><br class=""></div><div class="">There are some formats (e.g., SDF) which support zero-order bonds to indicate coordination (<a href="https://pubs.acs.org/doi/abs/10.1021/ci200488k" class="">https://pubs.acs.org/doi/abs/10.1021/ci200488k</a>) - on the other hand, it seems like the examples you give are problems with hydrogen addition to nitrogen .. which may be an easier fix.</div><div class=""><br class=""></div><div class=""><div class="">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.</div></div><div class=""><br class=""></div><div class="">Anyway, thank you for the early interest - I would be happy to help you improve your proposal!</div><div class=""><br class=""></div><div class=""><div class="">Best regards,</div><div class="">-Geoff</div></div><div class=""><br class=""></div><div class=""><div class="">---</div><div class="">Prof. Geoffrey Hutchison</div><div class="">Department of Chemistry</div><div class="">University of Pittsburgh</div><div class="">tel: (412) 648-0492</div><div class=""><a href="mailto:geoffh@pitt.edu" class="">email: geoffh@pitt.edu</a></div><div class="">twitter: @ghutchis</div><div class="">web: <a href="https://hutchisonlab.org/" class="">https://hutchisonlab.org/</a></div></div><div class=""><br class=""></div><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Mar 7, 2022, at 6:17 PM, Aritz Erkiaga <<a href="mailto:aerkiaga3@gmail.com" class="">aerkiaga3@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class="">
<meta http-equiv="content-type" content="text/html; charset=UTF-8" class="">
<div class=""><p class="">Good evening,</p><p class="">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.</p><p class="">Here's the draft: <a href="https://aerkiaga.github.io/docs/gsoc2022.pdf" class="moz-txt-link-freetext">https://aerkiaga.github.io/docs/gsoc2022.pdf</a></p><p class="">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.<br class="">
</p><p class="">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.</p><p class="">Cordially,</p>
<blockquote class="">Aritz Erkiaga</blockquote>
</div>
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