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Setting up the new RSpace Chemistry service on Docker

Updated by Ramon D'Agosta

Starting with RSpace 1.108, the new RSpace chemistry service replaces the existing Chemaxon chemistry service. This means you will need to install the new chemistry service to continue being able to access chemistry features inside of RSpace.

This guide only applies to on-prem RSpace installations. Cloud RSpace customers do not have to worry about this guide.

Installation steps (to be done on the RSpace server)

  1. Install docker (sometimes under the package name "docker.io") and docker-compose-v2 from the Ubuntu repos
  2. Create a folder in your home directory (or elsewhere that is suitable and has the correct permissions) to keep the docker config files
  3. Place the following files in the folder you just created:
    1. docker-compose.yaml file - https://github.com/rspace-os/chemistry/blob/main/docker-compose.yaml
    2. chemistry.jar file - https://github.com/rspace-os/chemistry/releases
  4. Optional: Add the docker user to your usergroup so you don't have to enter sudo before running any docker commands
  5. Stay in the same folder and run "docker compose up -d" to start the docker container
  6. You can check the docker container has started correctly by running "docker ps"
  7. In the RSpace deployment.properties file you will need to add some new entries and then restart tomcat9:
    1. REMOVE the line: chemistry.web.url=
    2. ADD the following lines:
      1. chemistry.provider=indigo
        chemistry.service.url=http://localhost:8090
        chemistry.service.indexOnStartup=true (optional, for reindexing previous chemicals, this can make RSpace startup take longer)
The GitHub repo contains more technical information on how docker runs: https://github.com/rspace-os/chemistry/
You will be able to test if the service is working correctly by launching chemical viewer / editor inside of RSpace and by also checking if the container is running with the command "docker ps"

Updating the service

We will push updates in the form of a new .jar file on the GitHub releases page. In order to update your container, do the following:

  1. Stop the container
  2. Remove the old chemistry.jar file
  3. Download and place the new chemistry.jar file from GitHub releases in the same location
  4. Start up the container

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