{ "version": "https://jsonfeed.org/version/1.1", "title": "chem-bla-ics", "description": "Chemblaics (pronounced chem-bla-ics) is the science that uses open science and computers to solve problems in chemistry, biochemistry and related fields.", "home_page_url": "https://chem-bla-ics.linkedchemistry.info/", "feed_url": "https://chem-bla-ics.linkedchemistry.info/2024/06/16/cdk2024-3.json", "icon": "https://chem-bla-ics.linkedchemistry.info/assets/images/chem-bla-ics_logo.png", "language": "en", "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286", "_orcid": "0000-0001-7542-0286" } ], "items": [ { "id": "https://doi.org/10.59350/dtfq8-5x011", "url": "https://chem-bla-ics.linkedchemistry.info/2024/06/16/cdk2024-3.html", "title": "cdk2024 #3: an unexpected downstream project", "content_html": "

In the CDK2024\ngrant we wrote about\nupdating various software projects using the Chemistry Development Kit.\nWe even wrote that “[r]equired API changes will be publicly shared and disseminated with the\nGroovy Cheminformatics with the Chemistry Development Kit book (egonw.github.io/cdkbook/)”.\nThe Groovy Cheminformatics with the Chemistry Development Kit book is a project that has\nrun since 2009.

\n\n
commit c5cbf9b5dd49baf582afc595c9cbafc714c5199f\nAuthor: Egon Willighagen <egon.willighagen@gmail.com>\nDate:   Fri Apr 10 12:34:42 2009 +0200\n\n    Initial copy of the current draft; converted into separate project for easier branching\n    for tunes of the book for workshops and sorts\n
\n\n

The original version was in LaTeX and\nsold online via Lulu.com .\nBecause all code examples were run (the first public edition had 72 pages with 75 code examples),\nlike RMarkdown of Jupyter Notebooks by design, I was able to\nmake many releases.\nThe big advantage of this was that when API changes happened,\nthis would be visible by code not compiling or by output changing.

\n\n

At some point I open sourced the book (doi:10.6084/M9.FIGSHARE.2057790.V1)\nand then realized that I can convert the book to Markdown:

\n\n
commit 2630699aa280200188f2ae9ef3f0698964926752\nAuthor: Egon Willighagen <egon.willighagen@gmail.com>\nDate:   Mon Dec 24 16:59:14 2018 +0100\n\n    Create chapter3.md\n
\n\n

This is the version available at egonw.github.io/cdkbook/\nfor some time now. So, now that for SMARTCyp I need to update the visualization, I went book to my book of\ncode examples (I have a collection of more than 200 examples), but then found that\nthe chapter on Depiction was missing. I was not\nlooking forward to this, because I know that\nthe code examples predate a massive improvement by John Mayfield\nof the rendering stack and I never got around to see if the examples from the book work well enough\nwith that new API (one is actually updated).

\n\n

That is when I realized that the Groovy Cheminformatics book actually also is a downstream\nproject that needs updating. I have been doing this already and it’s fairly smooth so that I did\nnot think of including it in the grant, other than updating the\nMigration chapter. I now had enough time\nto dive into this project. I need that,\nbecause the goal of the project is also to learn about all the meta science aspects of\nproject maintenance, roles, communication, etc. Therefore also this blog post: we need a track\nrecord, to collect data.

\n\n

Anyway, porting the first script went fairly easy,\nbut I am now running into a stacktrace:

\n\n
Processing  RenderSelection.groovyin\ndoing RenderSelection.out ...\norg.codehaus.groovy.control.MultipleCompilationErrorsException: startup failed:\n/home/egonw/var/Projects/hub/cdkbook-source/code/RenderSelection.groovy: 39: unable to resolve class ExternalHighlightGenerator\n @ line 39, column 16.\n   generators.add(new ExternalHighlightGenerator());\n                  ^\norg.codehaus.groovy.syntax.SyntaxException: unable to resolve class ExternalHighlightGenerator\n @ line 39, column 16.\n\n
\n\n

That brings us to the task of how to find where that class is coming from, which happens\nto be something I already had to write up\nfor up for RingSearch. Dependency galore.

\n\n

References

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\n
Willighagen, E. (2015). Edition 1.4.1-0 of Groovy Cheminformatics with the Chemistry Development Kit. Figshare. https://doi.org/10.6084/M9.FIGSHARE.2057790.V1 CrossRef Scholia
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", "summary": "In the CDK2024 grant we wrote about updating various software projects using the Chemistry Development Kit. We even wrote that “[r]equired API changes will be publicly shared and disseminated with the Groovy Cheminformatics with the Chemistry Development Kit book (egonw.github.io/cdkbook/)”. The Groovy Cheminformatics with the Chemistry Development Kit book is a project that has run since 2009.", "image": "https://chem-bla-ics.linkedchemistry.info/assets/images/cdkDepictChapter.png", "date_published": "2024-06-16T00:00:00+00:00", "date_modified": "2025-03-11T00:00:00+00:00", "tags": ["cdk","grant","cdk2024"], "_references": [ { "url": "https://doi.org/10.6084/M9.FIGSHARE.2057790.V1", "doi": "10.6084/M9.FIGSHARE.2057790.V1" } ], "_funding": [{"award": { "title" : "The Chemistry Development Kit in 2024: improving cheminformatics research", "acronym" : "CDK2024", "uri" : "drc.filenumber:osf232097" }, "funder": { "name": "Dutch Research Council", "ror": "04jsz6e67" } }], "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ] } ] }