Hi,
I am working on a Pathvisio plugin that implements CDK for calculation
of metabolite properties, however I cannot get the InChIGenerator to
work.
I am using the following code which i adopted from the Groovy
Cheminformatics book by Egon Willighagen:
InChIGeneratorFactory factory = null;
InChIGenerator generator = null;
try {
generator = factory.getInChIGenerator(molecule);
System.out.println(generator.getLog());
String InChI = generator.getInchi();
String InChIKey = generator.getInchiKey();
in which the molecule is made using the SmilesParser (I also added
explicit hydrogens to the molecule).
When using this code, I'm getting the following exception:
Exception in thread "pool-2-thread-1" java.lang.NullPointerException
at metaboliteplugin.MetaboliteInfo.Inchi(MetaboliteInfo.java:311)
at metaboliteplugin.MetaboliteInfo.getContent(MetaboliteInfo.java:265)
at metaboliteplugin.MetaboliteInfo$2.run(MetaboliteInfo.java:146)
at
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110)
at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603)
at java.lang.Thread.run(Thread.java:679)
Which indicates that the problem lies at the line:
generator = factory.getInChIGenerator(molecule);
Thanks in advance for helping me out.
Best,
Rianne
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