ECFP feature lookup demo
This project depends on ChemAxon proprietary
jchem.jar available in JChem Suite platform independent (.zip) distribution. This distribution can be downloaded manually or retrieved from https://repository.chemaxon.com with proper credentials. Both approach are detailed.
- Make sure that ChemAxon licenses for the used functionalities are available and installed. For details see ChemAxon Installing Licenses documentation.
Manual download of JChem distribution
- Make sure that you have the required registration to access ChemAxon product downloads and download JChem Suite - platform independent (.zip) distribution from https://www.chemaxon.com/download/jchem-suite/.
- Unpack the downloaded file.
- Locate file
jchem/lib/jchem.jarin the unpacked directory.
./gradlew -Pcxn_jchem_jar=<PATH TO JCHEM JAR> installDist
Note that you can point to the location of
jchem.jar in an existing JChem Suite installation.
- Make sure that you have the username and password required to access ChemAxon Public Repository. For access send a request to email@example.com. For details see https://docs.chemaxon.com/display/jchembase/Introduction+for+Java+applications#IntroductionforJavaapplications-swreq
./gradlew -Pcxn_repo_user=<USERNAME> -Pcxn_repo_pass=<PASSWORD> installDist
After executing the
installDist task a self contained distribution (including the compiled sources, dependencies, launch scripts) is built in directory
To get command line help launch
To generate SMARTS illustration of ECFP features launch
cat build/install/ecfpf/data/caffeine.smiles | build/install/ecfpf/bin/ecfpf -idname > features-caffeine-ecfp4.smarts
To use a custom ECFP config XML use command line option
cat build/install/ecfpf/data/caffeine.smiles | build/install/ecfpf/bin/ecfpf -c build/install/ecfpf/data/ecfp-6.xml -idname > features-caffeine-ecfp6.smarts
Other property setting mechanisms
The above examples used command line property settings (
-P<NAME>=<VALUE>). There are other ways to pass properties to a gradle build script, for details see http://mrhaki.blogspot.hu/2010/09/gradle-goodness-different-ways-to-set.html.
The two configurations (manual download of JChem distribution/using ChemAxon Public Repository) are not equivalent. In the first case only the specified
jchem.jar file and the built
jar file are used in the classpath of the launcher scripts. In the second case all of the dependencies of
jchem.jar are included in the classpath of the launcher scripts. On windows the resulting long command line causes problems.
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.