Is there any way to make xbindkeys intercept hotkeys for certain programs only?

Let's say I have two programs: Program A and Program B. I want to use some hotkey to trigger certain action in Program A. So, I add corresponding lines in xbindkeysrc (telling the daemon what to do and what the hotkey is). It works just fine with Program A. The problem is that the same hotkey is used in Program B to do something as well (which I am totally happy with). But Program B does not trigger that action anymore because xbindkeys intercepts the hotkey now. Is it possible make xbindkeys to intercept hotkeys for certain programs only or should I take a look at another tool (if so, which one)?