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JKlustor web example


  • Early access version is used for some of the ChemAxon proprietary dependencies. See build.gradle for details. Please note that the associated workarounds will be removed when the relevant features are available in a regular release.

  • ChemAxon public repository used by previous versions ( is changed. You can follow this getting started guide to ensure that you have access to resolve artifacts from the new repository ( Contact us at with further questions.

This code is under construction. Please note that the web example is not complete. Please note that these example codes might use beta or non-public APIs.

This is a usage example for ChemAxon JKlustor API for a web service environment. This project is intended for active API users of ChemAxon JKlustor API. Simple API usage example is also provided.

Further docs


This project will contain a working usage example for ChemAxon JKlustor API in a web environment. A simple chemical clustering workflow will be implemented providing the following functionalities:

  • User can upload molecule files
  • A selected clustering algorithm can be launched
  • The results are visualized in a hierarchic dendrogram
  • The dendrogram can be collapsed at an arbitrary similarity level into a non-hierarchical clustering
  • Results can be downloaded in various formats

Additionally some further basic examples of associated APIs can be found in src/main/java/com/chemaxon/clustering/examples.

Getting started

This project depends on ChemAxon proprietary APIs which are not available from open public repositories. To compile you need to request access to ChemAxon public repository and pass your credentials to the build script using Gradle properties. Descriptions below use the command line argument (-P<key>=<value>) approach. Further ways to set project properties are described in

See and Getting started with for details.

Installing license

  • Make sure that ChemAxon licenses for the used functionalities are available and installed. For details see ChemAxon Installing Licenses documentation.

Using ChemAxon Public repository

  • Note that old repository is deprecated, you need new credentials for accessing We expect further major changes in the repository configuration in the near future.
  • Note that the repository server at does not allow interactive logins.
  • Manual download and usage of JChem distribution is not supported now.
  • Make sure that you have the required credentials to access ChemAxon public repository described above
  • For low memory machines use export GRADLE_OPTS=-Xmx1768m
  • Launch ./gradlew -PcxnHubUser=<YOUR_PASS_EMAIL> -PcxnHubPass=<YOUR_HUB_API_KEY> bootRun to start embedded server.
  • Launch ./gradlew -PcxnHubUser=<YOUR_PASS_EMAIL> -PcxnHubPass=<YOUR_HUB_API_KEY> jar to compile API examples.
  • Launch ./gradlew -PcxnHubUser=<YOUR_PASS_EMAIL> -PcxnHubPass=<YOUR_HUB_API_KEY> createScripts to create linux/cygwin bash launcher scripts.
  • ChemAxon staff with access to internal build environment "Gluon" can use the project without providing these credentials.

Connecting to the embedded server

After a successful launch with the bootRun target use a browser and open http://localhost:8090.

Using launcher scripts

After a successful compilation with the createScript target invoke the following commands to launch simple API usage examples.

cat src/data/molecules/vitamins/vitamins.smi | ./build/scripts/cfpDissimilarityExample
cat src/data/molecules/vitamins/vitamins.smi | ./build/scripts/sphexExample
cat src/data/molecules/vitamins/vitamins.smi | ./build/scripts/hierarchicClusteringExample

Using API examples

After a successful compilation with the jar target invoke the following commands to launch simple API usage examples.

cat src/data/molecules/vitamins/vitamins.smi | java -classpath build/libs/jklustor-web-example-0.0.2-SNAPSHOT.jar com.chemaxon.clustering.examples.CfpDissimilarityExample
cat src/data/molecules/vitamins/vitamins.smi | java -classpath build/libs/jklustor-web-example-0.0.2-SNAPSHOT.jar com.chemaxon.clustering.examples.SphexExample
cat src/data/molecules/vitamins/vitamins.smi | java -classpath build/libs/jklustor-web-example-0.0.2-SNAPSHOT.jar com.chemaxon.clustering.examples.HierarchicClusteringExample

Further steps

  • Invoke ./gradlew eclipse to download public dependency sources.


This project is distributed under the Apache License 2.0. Some dependencies of this project are ChemAxon proprietary products which are not covered by this license. Please note that redistribution of ChemAxon proprietary products is not allowed.


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