Thread AWT-EventQueue-0 (Suspended (exception NullPointerException))
SMILESReader.readMoleculeSet(IMoleculeSet) line: 184

Okay so if this is on cdk-1.4.x

184: String line = input.readLine().trim();

readLine() will throw an EOFException if it's reached the end or generally an IO exception. 

Therefore I'd imagine the "input" is null. Looking at the code though I can't see how it would be possible to set it to null. I'm also not sure why the commit would cause this… 

As a quick test try adding this before the getChemModelFromReader()/read() just to check:

Field field = cor.getClass().getField("input");
field.setAccessible(true); // >_> encapsulation..
System.out.println("SMILES input value: " + field.get(cor));

if this is on 1.14.4

184: logger.debug("Line: ", line);

this is actually quite likely as logging involves some runtime loading… but i'm guessing you're getting logging messages so it's probably not this