JKlustor web example
Early access version is used for some of the ChemAxon proprietary dependencies. See
build.gradlefor details. Please note that the associated workarounds will be removed when the relevant features are available in a regular release.
ChemAxon public repository (repository.chemaxon.com) used by previous versions is changed. Please ensure that you have access to the new repository (hub.chemaxon.com). Contact us at firstname.lastname@example.org 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.
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
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 https://hub.chemaxon.com and pass your credentials to the
build script using Gradle properties. Descriptions below use the command line argument (
Further ways to set project properties are described in http://mrhaki.blogspot.hu/2010/09/gradle-goodness-different-ways-to-set.html.
- 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 repository https://repository.chemaxon.com is deprecated, you need new credentials for accessing https://hub.chemaxon.com. We expect further major changes in the repository configuration in the near future.
- Manual download and usage of JChem distribution is not supported now.
- Make sure that you have the required credentials to access ChemAxon public repository https://hub.chemaxon.com described above
- For low memory machines use
./gradlew -PcxnHubUser=<YOUR_PASS_EMAIL> -PcxnHubPass=<YOUR_HUB_API_KEY> bootRunto start embedded server.
./gradlew -PcxnHubUser=<YOUR_PASS_EMAIL> -PcxnHubPass=<YOUR_HUB_API_KEY> jarto compile API examples.
./gradlew -PcxnHubUser=<YOUR_PASS_EMAIL> -PcxnHubPass=<YOUR_HUB_API_KEY> createScriptsto create linux/cygwin
- 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
./gradlew eclipseto 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.