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How to use a dynamic library?

See original GitHub issue

Hi,
thanks a lot for this cool project!!

I would like to explore it for cheminformatics analysis and would therefore like to use the Java bindings of the RDKit toolkit. The bindings consist of a jar artifact and a dynamic library (.so for Linux). In the Idea IDE, I configure the program for the location of the dynamic library with this line in the build.gradle.kts:

jvmArgs = listOf("-Djava.library.path=$rdkitKnime")

with rdkitKnime being the path to the dynamic library.

Then, in the program, I call System.loadLibrary("GraphMolWrap") once, to actually load the library.

Is there a corresponding possibility to modify the java.library.path in kotlin-jupyter?

@file:Repository("file:///home/pahl/dev/github/knime-rdkit/org.rdkit.knime.bin.linux.x86_64/os/linux/x86_64")

followed by

System.loadLibrary("GraphMolWrap")

in a new cell does not work, it gives a no GraphMolWrap in java.library.path error.

Many thanks for your help.

Kind regards,
Axel

Issue Analytics

State:
Created 2 years ago
Comments:10

Top GitHub Comments

2reactions

ileasilecommented, May 1, 2021

Thanks, reproduced. It is a weird issue related to classloaders, but I’ve built up a JAR for you (unpack it from ZIP first). It works without any additional settings, just specify path to it in the @file:DependsOn() and you’re all set. rdkit-jupyter-1.0.0.jar.zip

I have also published this JAR in Maven Central, so you may avoid downloading it manually: @file:DependsOn("org.jetbrains.kotlinx:rdkit-jupyter:1.0.0")

You may also build this JAR from this repo using ./gradlew shadowJar

1reaction

apahlcommented, May 1, 2021

Wow, very cool.
I did not understand half of your explanation (only getting started with Kotlin and have no real prior experience with the JVM, but have used a number of other programming languages).

Thanks a TON for your help!!!

Kind regards,
Axel

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