Keep in mind that anything rendered by AngularJS is done after the document.ready event fires. Thus, any scripts that rely on that event to scan the DOM and look for things to interact with will do so before Angular has had a chance to place those items.
The solution to this will vary depending on the library. If the library allows for delayed action, you may be able to create a directive that calls the appropriate script once it has rendered out the appropriate nodes.
In general, when trying to integrate non-angular JS with angular, you will need to create some type of adapter, whether it be a directive or a service.