Maastricht University

Egon Willighagen

In [the
CDK2024](https://chem-bla-ics.linkedchemistry.info/2024/04/07/cdk2024.html)
[grant](https://chem-bla-ics.linkedchemistry.info/2024/05/18/cdk2024-2.html)
we wrote about updating various software projects using the [Chemistry
Development Kit](https://cdk.github.io/). 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.

``` git
commit c5cbf9b5dd49baf582afc595c9cbafc714c5199f
Author: Egon Willighagen 
Date:   Fri Apr 10 12:34:42 2009 +0200

    Initial copy of the current draft; converted into separate project for easier branching
    for tunes of the book for workshops and sorts
```

The original version was in LaTeX and [sold online via
Lulu.com](https://chem-bla-ics.blogspot.com/2011/02/groovy-cheminformatics.html).
Because all code examples were run (the first public edition had 72
pages with 75 code examples), like RMarkdown of Jupyter Notebooks by
design, I was able to make [many
releases](https://chem-bla-ics.blogspot.com/search?q=lulu). The big
advantage of this was that when [API](https://en.wikipedia.org/wiki/API)
changes happened, this would be visible by code not compiling or by
output changing.

At some point I open sourced the book
(doi:[10.6084/M9.FIGSHARE.2057790.V1](https://doi.org/10.6084/M9.FIGSHARE.2057790.V1))
and then realized that I can [convert the book to
Markdown](https://github.com/egonw/cdkbook/commit/2630699aa280200188f2ae9ef3f0698964926752):

``` git
commit 2630699aa280200188f2ae9ef3f0698964926752
Author: Egon Willighagen 
Date:   Mon Dec 24 16:59:14 2018 +0100

    Create chapter3.md
```

This is the version available at
[egonw.github.io/cdkbook/](https://egonw.github.io/cdkbook/) for some
time now. So, now that for SMARTCyp I need to update the visualization,
I went book to my book of code examples (I have a collection of more
than 200 examples), but then found that the chapter on
[Depiction](https://egonw.github.io/cdkbook/depiction) was missing. I
was not looking forward to this, because I know that the code examples
predate a massive improvement by [John
Mayfield](https://scholia.toolforge.org/author/Q28796322) of the
rendering stack and I never got around to see if the examples from the
book work well enough with that new API (one is actually updated).

That is when I realized that the *Groovy Cheminformatics* book actually
also is a downstream project that needs updating. I have been doing this
already and it's fairly smooth so that I did not think of including it
in the grant, other than updating the
[Migration](https://egonw.github.io/cdkbook/migration) chapter. I now
had enough time to dive into [this
project](https://github.com/cdk/nwo-openscience-2024/issues/30). I need
that, because the goal of the project is also to learn about all the
meta science aspects of project maintenance, roles, communication, etc.
Therefore also this blog post: we need a track record, to collect data.

Anyway, porting [the first
script](https://egonw.github.io/cdkbook/code/RenderMolecule.code.html)
went fairly easy, but I am now running into a stacktrace:

:::: {.language-plaintext .highlighter-rouge}
::: {.highlight}
``` highlight
Processing  RenderSelection.groovyin
doing RenderSelection.out ...
org.codehaus.groovy.control.MultipleCompilationErrorsException: startup failed:
/home/egonw/var/Projects/hub/cdkbook-source/code/RenderSelection.groovy: 39: unable to resolve class ExternalHighlightGenerator
 @ line 39, column 16.
   generators.add(new ExternalHighlightGenerator());
                  ^
org.codehaus.groovy.syntax.SyntaxException: unable to resolve class ExternalHighlightGenerator
 @ line 39, column 16.
```
:::
::::

That brings us to the task of how to find where that class is coming
from, which happens to be something I already [had to write
up](https://github.com/cdk/nwo-openscience-2024/issues/29) for up for
`RingSearch`{.language-plaintext .highlighter-rouge}. Dependency galore.

#### References

- [10.6084/M9.FIGSHARE.2057790.V1](https://doi.org/10.6084/M9.FIGSHARE.2057790.V1)


Edition 1.4.1-0 of Groovy Cheminformatics with the Chemistry Development Kit

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
<em>
 Groovy Cheminformatics with the Chemistry Development Kit
</em>
book is a project that has run since 2009.

cdk2024 #3: an unexpected downstream project

Publishing grant proposal is still not very common. The proposal
published in Research Ideas and Outcomes)
(doi:[10.3897/rio.10.e124884](https://doi.org/10.3897/rio.10.e124884))
for the [NWO Open Science grant for the CDK](/2024/04/07/cdk2024.html)
is, however, not the first and hopefully not the last. Interestingly, it
is already cited in (the German) Wikipedia. It is used
[there](https://de.wikipedia.org/wiki/Chemistry_Development_Kit) to
support a statement which tools use the Chemistry Development Kit.


Publishing grant proposal is still not very common. The proposal published in Research Ideas and Outcomes) (doi:10.3897/rio.10.e124884) for the NWO Open Science grant for the CDK is, however, not the first and hopefully not the last. Interestingly, it is already cited in (the German) Wikipedia. It is used there to support a statement which tools use the Chemistry Development Kit.

cdk2024 #2: publishing grant proposals

We recently got awarded our
[second](https://chem-bla-ics.blogspot.com/2022/03/bridgedb-nwo-grant-update-1-first-steps.html?q=bridgedb)
NWO Open Science grant
([OSF23.2.097](https://www.nwo.nl/en/projects/osf232097)), this time for
the [Chemistry Development Kit](https://cdk.github.io/) (CDK). "We" here
is me and [Alyanne de Haan](https://orcid.org/0000-0003-0896-0906), René
van der Ploeg, and [Marc Teunis](https://orcid.org/0000-0002-3496-6669)
from Hogeschool Utrecht. The proposal has been submitted for public
dissemination in [RIO Journal](https://riojournal.com/), like [we
did](https://chem-bla-ics.blogspot.com/2022/04/bridgedb-nwo-grant-update-2-building-up.html?q=bridgedb)
with the first NWO Open Science grant.

The project formally started on April 1 but we had our kick-off meeting
in Maastricht on April 4-5. We were joined by Javier and on the second
day by Marvin, and Ozan from our [BiGCaT research
group](https://www.maastrichtuniversity.nl/research/bioinformatics) in
Maastricht. During this hackathon, I gave a (repeat)
[presentation](https://zenodo.org/records/6414204) about the history of
the CDK which also included the problem that software using the CDK does
not always use the most recent version.

And that, upgrading tools using the CDK with the latest CDK version, is
the main topic of this grant (work package 2, WP2). The full proposal
has the focus list of tools, but most of it is also listed in [the issue
tracker](https://github.com/cdk/nwo-openscience-2024/issues) we have set
up as project management tool on GitHub.

Second, we actually hacked together on two first tools, one on our focus
list, but the other that was [requested we have a look at
too](https://github.com/cdk/nwo-openscience-2024/issues/22): SMARTCyp.
The latest version uses [RDKit](https://www.rdkit.org/)
(doi:[10.1093/bioinformatics/btz037](https://doi.org/10.1093/bioinformatics/btz037)),
but the original version uses the CDK
(doi:[10.1021/ml100016x](https://doi.org/10.1021/ml100016x)).

We downloaded the source code of SMARTCyp 2.4.2, started taking
[notes](https://github.com/cdk/nwo-openscience-2024/blob/main/monitoring/smartcyp.md),
Javier [started](https://github.com/cdk/smartcyp) a Maven build
environment, updated a lot of code, but we seem quite close to a version
that can be tested by people that have integrated SMARTCyp in other
tools. This is based on [CDK
2.9](https://github.com/cdk/cdk/releases/tag/cdk-2.9) and if you ignore
the 2D depiction glitch, it looks it was a nice first choice:

![](/assets/images/smartcyp.png)

On a final note, we plan to record carefully our steps, in an open
notebook science approach, with the intention to extract general upgrade
steps. For example, we will update the
[Migration](https://egonw.github.io/cdkbook/migration.html) section of
the [Groovy Cheminformatics with the Chemistry Development
Kit](https://egonw.github.io/cdkbook/).


We recently got awarded our second NWO Open Science grant (OSF23.2.097), this time for the Chemistry Development Kit (CDK). “We” here is me and Alyanne de Haan, René van der Ploeg, and Marc Teunis from Hogeschool Utrecht. The proposal has been submitted for public dissemination in RIO Journal, like we did with the first NWO Open Science grant.

Rogue Scholar Posts

cdk2024 #3: an unexpected downstream project

cdk2024 #2: publishing grant proposals

cdk2024 #1: NWO Open Science grant for the Chemistry Development Kit