Java can be hacked to be executed line by line: http://www.javarepl.com/console.html
However, it’s not pleasant, and I wouldn’t recommend it. If you really like java and also really want an interpreted language, Scala is pretty close, and comes with a repl by default.
All that said, atom is an editor. Java, by design, nearly requires the use of an IDE to code effectively. It has very strict formatting requirements, a lot of ways to do the same thing, and a tendency toward longer variable/class names, lines of code, and files (verbosity).
I use atom at work to write ruby and python, and intellij for java. If you really want to run java programs in atom, why not try one of the terminal programs? https://atom.io/packages/terminal-plus works pretty well, and you can javac and java there just like you could regularly on the command line.