Hi all, This may interest anyone trying to get jCompoundMapper to work with a newer version of CDK.
Because of the recent J. Cheminf. paper "Effectiveness of molecular fingerprints for exploring the chemical space of natural products" at https://jcheminf.biomedcentral.com/articles/10.1186/s13321-024-00830-3 I decided to look more into the jCompoundMapper package, available at https://jcompoundmapper.sourceforge.net and released in 2012. There are two jar files: jCMapperCLI.jar - includes the jCompoundMapper package, an old version of CDK, and the other components needed to make a standalone executable jCMapperLibOnly.jar - only the jCompoundMapper package Neither are compatible with modern CDK. Doing so (through the JPype Python/Java adapter) gives me the exception: *** java.lang.java.lang.ClassCastException: java.lang.ClassCastException: class org.openscience.cdk.AtomContainer2$BaseAtomRef cannot be cast to class org.openscience.cdk.Atom (org.openscience.cdk.AtomContainer2$BaseAtomRef and org.openscience.cdk.Atom are in unnamed module of loader 'app') In a private exchange with John he pointed out that CDK has a backwards compatibility option, by including the following when starting the JVM: -DCdkUseLegacyAtomContainer=t With this I was able to get cdk-2.9 and jCMapper working together. Though do note, very few of the other CDK fingerprint types work with the legacy atom container - this is very much a one-or-the-other solution. Coming from the Python world, where most Python releases come with an ABI change, I am very impressed that a 12 year old package still works, and can be combined with a <1 year old cdk release. Best regards, Andrew da...@dalkescientific.com _______________________________________________ Cdk-user mailing list Cdk-user@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/cdk-user
