Plexus Analysis Installation and System Requirements

Plexus Analysis, like the other members of the Plexus Suite, is a web-based application, which runs on a central server and users can interact with it through a web browser on their own client computer.

Running Plexus Analysis standalone or integrated to another Plexus tool has the following requirements:

Hardware and software requirements

On the server side:

  • Java 8 distributed by Oracle.

On the client side:

  • JavaScript enabled web browser. Currently supported browsers are Google Chrome, Mozilla Firefox, Internet Explorer 11, Microsoft Edge and Safari 7 or higher.

License requirement

Running Plexus Analysis requires the Plexus Analysis license. A valid license file has to be placed in the ${HOME}/.chemaxon/licenses/ (in Unix systems) or in the %USERPROFILE%\chemaxon\licenses\ (in Windows systems) folder, where ${HOME} (or %USERPROFILE%) means the home directory of the user running the web server.

The Plexus Analysis license covers the followings:

  • the functionality of the Plexus Analysis tool;

  • calculating physico-chemical properties and adding calculated columns to the compound database through Plexus Connect;

  • sending chemical and alphanumeric data from Connect to Analysis.

Please not that for the last two, you will need a Plexus Connect license as well for connecting to your database, opening your custom forms and searching in your data.
Please consult our sales team ([email protected]) if you would like to require a license for Plexus Analysis or if you need help in handling your license file.

Running Plexus Analysis

Plexus Analysis is available as a .zip file. In order to download the installation package, please navigate to the download page of Plexus Analysis on the ChemAxon website. Before you can download the file, you will be asked to log in with your ChemAxon username and password.

After you downloaded the .zip file and unzipped it, you can start the Plexus Analysis application.

The /bin directory contains scripts for both Linux and Windows which start the application on the default port (9999).

Integration with Plexus Connect

While deploying Plexus Connect, you have to specify the URL where Plexus Analysis is deployed.

Start Plexus Connect with the following parameter: -Dplexus.analysis.url=http://urltoplexusanalysis/.


  • PID file: use the -Dpidfile.path parameter in the conf/application.ini file to configure pidfile location.

  • Application configuration: when starting the application, use the -Dconfig.file=/some/custom/path/application.conf parameter to specify application.conf location; By default, the config file specified in the classpath is used.

Setting Up a Memory Limit

The administrator of Plexus Analysis can set up a server side limit for the allowed memory usage in a single session (a single imported table) as well as for the entire server by using the following by modifying the limit of the following properties in the application.conf file:

  • maximum memory heap size in megabytes for a single table:

  • maximum memory heap size in megabytes for the entire system:

The default memory limit for a single table is 220MB, while for the entire system it is 2000MB.
Please note that setting these properties to 0 means that they will be ignored and there will be no limitation on the allowed memory usage.