How do I integrate custom PHP application with Drupal?
If your application can be displayed inside a Drupal page, writing a small custom module is the easiest clean solution. You don't need to rewrite your application, but only to provide some integration code. Your application should avoid output the complete HTML for the page, only its own content. It should also not initialize the PHP session as Drupal will take care of that. Otherwise it is as simple as:

/**
 * Implements hook_menu().
 */
function your_application_menu() {
  return array(
    'title' =&gt; 'Your Application',
    'page callback' =&gt; 'your_application_page',
    'access callback' =&gt; TRUE,
    'type' =&gt; MENU_CALLBACK,
  );
}

/**
 * Page callback: Displays Your Application on the page.
 *
 * @see your_application_menu()
 */
function your_application_page() {
   module_load_include('php', 'your application', 'your_application');
   $path = drupal_get_path('module', 'your application');
   drupal_add_js($path . '/js/angular.js');
   drupal_add_js($path . '/js/your_application.js');
   drupal_add_css($path . '/css/your_application.css');
   return your_application_output();
}


You may also be interested by the Angular JS module, which likely provide a much nicer way to embed Angular JS applications in Drupal.