The icon is thoroughly designed to feel native on Yosemite:
And is beautifully detailed:
Download the Atom.icns file. Go to the Applications folder, right click the Atom, and select "Get info". Just drag the downloaded icon onto an old small icon in the top-left corner. Then update icon in the Dock:
killall Dock
That's it! Enjoy your new icon.
Made in Sketch with the help of awesome Generate ICNS plugin by Nathan Rutzky.