squonk2-cdk

CDK jobs repository contains Java code running molecular property predictions using the Chemistry Development Kit. These are made available as a "tool", typically represented as a Java class. Those tools become available as:

a command line application
a command line application running in a Docker container
a Squonk2 job that runs using the Docker container

For more details on Squonk2 jobs look at our main virtual-screening repo that contains more documentation and examples.

We anticipate a wider range of functions being incoporated as additional tools in the futures. Suggestions and contributions are welcome.

One purpose of this repo is as a prototype for creating Squonk2 jobs using Java (most current ones are Python based).

This repo illustrates:

Creating a Java class that can be executed as CLI application. See DescriptorsExec.java. We use the Apache Commons CLI library for handling the command line options.
Use the Gradle build tool for building everything. See app/build.gradle for details.
Create a Docker container image (details in the build.gradle) that is pushed to DockerHub.
Write the Squonk2 job definition, including a jote test. See data-manager/cdk.yaml

Running

To run a tool through gradle:

$ ./gradlew run --args="--all -i ../data/dhfr_3d.sdf -o foo.sdf"

> Task :app:run
2022-04-06T09:05:19+00:00 # INFO -EVENT- squonk.jobs.cdk.DescriptorsExec --all -i ../data/dhfr_3d.sdf -o foo.sdf
2022-04-06T09:05:19+00:00 # INFO -EVENT- Calculating 10 descriptors
2022-04-06T09:05:22+00:00 # INFO -EVENT- Processed 756 molecules, 0 errors.
2022-04-06T09:05:22+00:00 # INFO -COST- 7560.0 1

BUILD SUCCESSFUL in 3s

This runs the default class which reads a SDF, calculates all properties and writes out a new SDF with those calculations as additional properties. See the build.gradle application task for more details. Note that this is effectively executed from the app directory, hence the path to the test SDF.

Build the docker container image:

$ ./gradlew dockerBuildImage

Builds an image named informaticsmatters/squonk2-cdk:latest.

Running the docker container:

$ docker run -it -v $PWD:$PWD -w $PWD -u 1000:1000 informaticsmatters/squonk2-cdk:latest java squonk.jobs.cdk.DescriptorsExec --all -i data/dhfr_3d.sdf -o foo.sdf
2022-04-06T09:14:40+00:00 # INFO -EVENT- squonk.jobs.cdk.DescriptorsExec --all -i data/dhfr_3d.sdf -o foo.sdf
2022-04-06T09:14:40+00:00 # INFO -EVENT- Calculating 10 descriptors
2022-04-06T09:14:44+00:00 # INFO -EVENT- Processed 756 molecules, 0 errors.
2022-04-06T09:14:44+00:00 # INFO -COST- 7560.0 1

InformaticsMatters/squonk2-cdk

squonk2-cdk

Running