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#cdk25ugm

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The Chemistry Development Kit<p>Jonas Schaub: "Last week, I presented my work on algorithmic substructure extraction (scaffolds, functional groups, and aglycones) at the Chemistry Development Kit User Group Meeting (<a href="https://fosstodon.org/tags/CDK25UGM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>CDK25UGM</span></a>) in Maastricht.</p><p>You can now find my slides on Zenodo: <a href="https://doi.org/10.5281/zenodo.15058008" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">doi.org/10.5281/zenodo.1505800</span><span class="invisible">8</span></a>"</p><p><a href="https://fosstodon.org/tags/cheminformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>cheminformatics</span></a> <a href="https://fosstodon.org/tags/openscience" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>openscience</span></a></p>
Egon Willighagen<p><span class="h-card" translate="no"><a href="https://mastodon.social/@egonw" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<span>egonw@mastodon.social</span></a></span> one things I learned about was the notion of "attachment points" in CXSMILES... works nicely in @wikidata :) (ht to John Mayfield)</p><p><a href="https://social.edu.nl/tags/CDK25UGM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>CDK25UGM</span></a></p>
Egon Willigh☮gen 🟥<p>the <a href="https://mastodon.social/tags/CDK25UGM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>CDK25UGM</span></a> was great and exhausting. the rest of the week I did get around to writing up some notes from the second day, but I did now: <a href="https://doi.org/10.59350/n7e6r-p1e93" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://</span><span class="">doi.org/10.59350/n7e6r-p1e93</span><span class="invisible"></span></a></p>
Matthias Mailänder<p><a href="https://mastodon.social/tags/JChemPaint" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>JChemPaint</span></a> based on <span class="h-card" translate="no"><a href="https://fosstodon.org/@cdk" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<span>cdk</span></a></span> really is a gem from the 90s. The 2D chemical structure editor got a beta release yesterday after nearly a decade and during the <a href="https://mastodon.social/tags/CDK25UGM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>CDK25UGM</span></a> hackathon I created a <a href="https://mastodon.social/tags/flatpak" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>flatpak</span></a> at <a href="https://flathub.org/apps/io.github.jchempaint.JChemPaint" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">flathub.org/apps/io.github.jch</span><span class="invisible">empaint.JChemPaint</span></a> for it.</p>
The Chemistry Development Kit<p>a beta release of JChemPaint 3.4 is now out: <a href="https://github.com/JChemPaint/jchempaint/releases/tag/3.4b" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">github.com/JChemPaint/jchempai</span><span class="invisible">nt/releases/tag/3.4b</span></a></p><p><a href="https://fosstodon.org/tags/CDK25UGM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>CDK25UGM</span></a></p>
The Chemistry Development Kit<p>you can now also find a mirror of on <span class="h-card" translate="no"><a href="https://social.anoxinon.de/@Codeberg" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<span>Codeberg</span></a></span>: chemistry-development-kit <a href="https://fosstodon.org/tags/CDK25UGM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>CDK25UGM</span></a></p>
Egon Willighagen<p><span class="h-card" translate="no"><a href="https://toots.nu/@dalke" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<span>dalke</span></a></span> <span class="h-card" translate="no"><a href="https://fosstodon.org/@cdk" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<span>cdk</span></a></span> okay, here you go: <a href="https://codeberg.org/chemistry-development-kit/cdk" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">codeberg.org/chemistry-develop</span><span class="invisible">ment-kit/cdk</span></a></p><p><a href="https://social.edu.nl/tags/CDK25UGM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>CDK25UGM</span></a></p>
Egon Willigh☮gen 🟥<p>I like it how I can now have FAIR metadata about funder grants related to my blog posts :) And <span class="h-card" translate="no"><a href="https://wisskomm.social/@rogue_scholar" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<span>rogue_scholar</span></a></span> picks it up nicely! Works already for <span class="h-card" translate="no"><a href="https://ec.social-network.europa.eu/@EUCommission" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<span>EUCommission</span></a></span> funding already (see screenshot), and I will use it for NWO grants too, thx to <span class="h-card" translate="no"><a href="https://fosstodon.org/@bioregistry" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<span>bioregistry</span></a></span> :)</p><p><a href="https://mastodon.social/tags/CDK25UGM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>CDK25UGM</span></a> <br><a href="https://mastodon.social/tags/openscience" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>openscience</span></a></p>
Egon Willighagen<p><span class="h-card" translate="no"><a href="https://fosstodon.org/@cdk" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<span>cdk</span></a></span> the hackathon has started. you can "see" us in action at <a href="https://github.com/cdk" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://</span><span class="">github.com/cdk</span><span class="invisible"></span></a></p><p><a href="https://social.edu.nl/tags/CDK25UGM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>CDK25UGM</span></a></p>
Egon Willighagen<p>after a great first <span class="h-card" translate="no"><a href="https://fosstodon.org/@cdk" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<span>cdk</span></a></span> user group meeting (see "cdk2024 #4: Chemistry Development Kit User Group Meeting - Day 1", <a href="https://doi.org/10.59350/e08pe-thb38" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://</span><span class="">doi.org/10.59350/e08pe-thb38</span><span class="invisible"></span></a>), today we will have a hackathon (starting in about an hour)</p><p><a href="https://social.edu.nl/tags/CDK25UGM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>CDK25UGM</span></a></p>
Egon Willighagen<p>the last speaker was Matthias Mailänder (<span class="h-card" translate="no"><a href="https://mastodon.social/@MatthiasMailaender" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<span>MatthiasMailaender</span></a></span>, Lablicate GmbH): “Live demo of where OpenChrom uses the CDK”</p><p>OpenChrom is an (open source) chromatography / mass spec (and some NMR) tool where the CDK is used to depict chemical structures with which peaks in the chromatograms / spectra are annotated by the user</p><p><a href="https://social.edu.nl/tags/CDK25UGM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>CDK25UGM</span></a></p>
Egon Willighagen<p>now speaking is Zhixu Ni (TU Dresden about: “A Fuzzy Solution for Lipid Structures Using CXSMILES”</p><p>TIL that aspirin actually inhibits a lipid synthesis pathway</p><p><a href="https://social.edu.nl/tags/CDK25UGM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>CDK25UGM</span></a></p>
Egon Willighagen<p>Sonja Herres-Pawlis of RWTH Aachen (not on Mastodon??) about organometalics in the InChI</p><p>She also shows this nice InChI demo website: <a href="https://iupac-inchi.github.io/InChI-Web-Demo/" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">iupac-inchi.github.io/InChI-We</span><span class="invisible">b-Demo/</span></a></p><p><a href="https://social.edu.nl/tags/CDK25UGM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>CDK25UGM</span></a></p>
Egon Willighagen<p>next up was Yajie Ding, a ERC from <span class="h-card" translate="no"><a href="https://social.edu.nl/@universityofgroningen" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<span>universityofgroningen</span></a></span>, talking about her <a href="https://social.edu.nl/tags/cheminformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>cheminformatics</span></a> needs for glycan modifications of proteins. We discussed formats LINUCS, WURCS, and SNGF</p><p><a href="https://social.edu.nl/tags/CDK25UGM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>CDK25UGM</span></a></p>
Egon Willighagen<p>now speaking is Lyudvika Radeva (Ideaconsult Ltd, University of Plovdiv), about “Ambit-SLN. Processing of chemical objects via SYBYL Line Notation (SLN)”, see this paper: <a href="https://onlinelibrary.wiley.com/doi/full/10.1002/minf.202100027" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">onlinelibrary.wiley.com/doi/fu</span><span class="invisible">ll/10.1002/minf.202100027</span></a></p><p>I did not know SLN can be used for nanomaterials too</p><p><a href="https://social.edu.nl/tags/CDK25UGM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>CDK25UGM</span></a></p>
Egon Willighagen<p>new things I learned is that the CDK core is downloaded about 10 times per day from Maven Central, and given those are cached locally, that's not a bad number at all :)</p><p>Some of the speedups are very significant. For examples, to determine if atoms are in a ring (not a trivial question) is much faster now, being able to handle 700k structures per second</p><p><a href="https://social.edu.nl/tags/CDK25UGM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>CDK25UGM</span></a></p>
Egon Willighagen<p>we're already after lunch, and after I introduced the project (see <a href="https://riojournal.com/article/124884/" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://</span><span class="">riojournal.com/article/124884/</span><span class="invisible"></span></a>), John Mayfield gave his "What's New" talk, and we just had a presentation by Jonas Schaub about various tools from the <span class="h-card" translate="no"><a href="https://nfdi.social/@steinbeck" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<span>steinbeck</span></a></span> lab <a href="https://social.edu.nl/tags/CDK25UGM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>CDK25UGM</span></a></p>
Egon Willighagen<p>yesterday already met with John Mayfield, a key <span class="h-card" translate="no"><a href="https://fosstodon.org/@cdk" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<span>cdk</span></a></span> developer. Awesome as always! <a href="https://social.edu.nl/tags/CDK25UGM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>CDK25UGM</span></a> </p><p>He demonstrated a keyboard shortcuts of JChemPaint, which I really, really have to learn. So far, I quickly drew chemical structures with CDK Depict, but I think with JChemPaint I can be even faster with drawing 2D chemical structures :)</p><p><a href="https://social.edu.nl/tags/chemistry" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>chemistry</span></a> <a href="https://social.edu.nl/tags/openscience" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>openscience</span></a></p>
Egon Willighagen<p>heading to Maastricht for a two day <span class="h-card" translate="no"><a href="https://fosstodon.org/@cdk" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<span>cdk</span></a></span> User Group Meeting <a href="https://social.edu.nl/tags/CDK25UGM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>CDK25UGM</span></a></p><p>Rough schedule and list of speakers: <a href="https://cdk.github.io/nwo-openscience-2024/" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">cdk.github.io/nwo-openscience-</span><span class="invisible">2024/</span></a></p><p>If you like to listen in via Zoom, email me</p><p><a href="https://social.edu.nl/tags/openscience" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>openscience</span></a> <a href="https://social.edu.nl/tags/chemistry" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>chemistry</span></a></p>
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