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#cdk2024

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Egon Willigh☮gen 🟥<p>is there a name for this? just trying to wrap up <a href="https://doi.org/10.3897/rio.10.e124884" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="">doi.org/10.3897/rio.10.e124884</span><span class="invisible"></span></a></p><p><a href="https://mastodon.social/tags/cdk2024" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>cdk2024</span></a></p>
Egon Willighagen<p>oh boy... finally getting there... so close to finalizing and release a new SMARTCyp?</p><p>See for context <a href="https://chem-bla-ics.linkedchemistry.info/2024/04/07/cdk2024.html" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">chem-bla-ics.linkedchemistry.i</span><span class="invisible">nfo/2024/04/07/cdk2024.html</span></a> and <a href="https://chem-bla-ics.linkedchemistry.info/2024/06/16/cdk2024-3.html" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">chem-bla-ics.linkedchemistry.i</span><span class="invisible">nfo/2024/06/16/cdk2024-3.html</span></a> <a href="https://social.edu.nl/tags/cdk2024" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>cdk2024</span></a> </p><p><a href="https://social.edu.nl/tags/opensource" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>opensource</span></a> <a href="https://social.edu.nl/tags/cheminformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>cheminformatics</span></a></p>
Egon Willighagen<p>okay, what a year :(</p><p>Managed to get the background color changed, finally: <a href="https://egonw.github.io/cdkbook/depiction.html" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">egonw.github.io/cdkbook/depict</span><span class="invisible">ion.html</span></a></p><p><a href="https://social.edu.nl/tags/cdk2024" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>cdk2024</span></a></p>
Egon Willighagen<p>new blog: "cdk2024 #6: wrapping up already" <a href="https://chem-bla-ics.linkedchemistry.info/2025/03/30/cdk2024-4.html" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">chem-bla-ics.linkedchemistry.i</span><span class="invisible">nfo/2025/03/30/cdk2024-4.html</span></a></p><p>"Tomorrow is already the last day of the NWO Open Science grant for the Chemistry Development Kit. We are wrapping up, but I am happy we have a few weeks more to finish up the reporting. We held a user group meeting earlier this month (btw, check out the slides by Jonas), and I did a few more JUnit testing updates last week"</p><p><a href="https://social.edu.nl/tags/cdk2024" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>cdk2024</span></a> <a href="https://social.edu.nl/tags/openscience" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>openscience</span></a></p>
Egon Willighagen<p>okay, that was annoying. to quote Snow Patrol: "It shouldn't need to be so fucking hard"</p><p>Well, I think I'm onto a reasonable solution: <a href="https://github.com/cdk/cdk/pull/1086" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="">github.com/cdk/cdk/pull/1086</span><span class="invisible"></span></a> <a href="https://social.edu.nl/tags/cdk2024" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>cdk2024</span></a></p>
Egon Willighagen<p>okay, was doing some <a href="https://social.edu.nl/tags/cdk2024" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>cdk2024</span></a> code clean up. Thought it was going to be easy. Just trying to disentangle some circular dependency. But after an hour of code duplication (hopefully temporarily) I am going up for today</p>
Egon Willigh☮gen 🟥<p>new blog post: "cdk2024 #3: an unexpected downstream project" <a href="https://chem-bla-ics.linkedchemistry.info/2024/06/16/cdk2024-3.html" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">chem-bla-ics.linkedchemistry.i</span><span class="invisible">nfo/2024/06/16/cdk2024-3.html</span></a> <a href="https://mastodon.social/tags/cdk2024" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>cdk2024</span></a></p>
Egon Willighagen<p>new blog post: "cdk2024 #3: an unexpected downstream project" <a href="https://chem-bla-ics.linkedchemistry.info/2024/06/16/cdk2024-3.html" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">chem-bla-ics.linkedchemistry.i</span><span class="invisible">nfo/2024/06/16/cdk2024-3.html</span></a> <a href="https://social.edu.nl/tags/cdk2024" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>cdk2024</span></a></p>
Egon Willighagen<p>for the <a href="https://social.edu.nl/tags/cdk2024" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>cdk2024</span></a> project, we are porting software that uses the Chemistry Development Kit to a newer version (see <a href="http://chem-bla-ics.linkedchemistry.info/2024/04/07/cdk2024.html" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">http://</span><span class="ellipsis">chem-bla-ics.linkedchemistry.i</span><span class="invisible">nfo/2024/04/07/cdk2024.html</span></a>), but as you can see, I need to update the depiction. I then realized that the Groovy Cheminformatics with the CDK book (<a href="https://egonw.github.io/cdkbook/" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="">egonw.github.io/cdkbook/</span><span class="invisible"></span></a>) did not actually have the "Depiction" chapter in the original LaTeX version.</p><p>Well, I started porting it: <a href="https://egonw.github.io/cdkbook/depiction.html" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">egonw.github.io/cdkbook/depict</span><span class="invisible">ion.html</span></a></p>
Egon Willighagen<p>Okay, I know there are 7 hours left, but the picture is clear. Here goes: <a href="https://egonw.github.io/chempyformatics/code/UniqueSMILES.code" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">egonw.github.io/chempyformatic</span><span class="invisible">s/code/UniqueSMILES.code</span></a> <a href="https://social.edu.nl/tags/python" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>python</span></a> <a href="https://social.edu.nl/tags/cdk2024" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>cdk2024</span></a> <a href="https://social.edu.nl/tags/cheminformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>cheminformatics</span></a></p>
Egon Willighagen<p>Blog post: "cdk2024 #1: NWO Open Science grant for the Chemistry Development Kit" <a href="https://chem-bla-ics.linkedchemistry.info/2024/04/07/cdk2024.html" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">chem-bla-ics.linkedchemistry.i</span><span class="invisible">nfo/2024/04/07/cdk2024.html</span></a> <a href="https://social.edu.nl/tags/openscience" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>openscience</span></a> <a href="https://social.edu.nl/tags/cheminformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>cheminformatics</span></a> <a href="https://social.edu.nl/tags/cdk2024" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>cdk2024</span></a></p>
Egon Willighagen<p>making good progress with updating SMARTCyp 2.4.2 to use CDK 2.9. Deps updated and the code upgraded. In going from CDK 2.2 to CDK 2.9 we see some distortion of the aromatic ring depiction. Should not be too hard to fix that. <a href="https://social.edu.nl/tags/chemistry" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>chemistry</span></a> <a href="https://social.edu.nl/tags/cdk2024" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>cdk2024</span></a></p>
Egon Willighagen<p>hi, do I have a follower who uses the command line version of SMARTCyp (<a href="http://smartcyp2.sund.ku.dk/download.php" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">http://</span><span class="ellipsis">smartcyp2.sund.ku.dk/download.</span><span class="invisible">php</span></a>)? We are looking for someone to test a new version of it. <a href="https://social.edu.nl/tags/cheminformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>cheminformatics</span></a> <a href="https://social.edu.nl/tags/metabolism" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>metabolism</span></a> <a href="https://social.edu.nl/tags/CDK2024" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>CDK2024</span></a></p>
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