Executing drupal file using shell_exec
Drupal imposes no limits on how you can use php. If it's possible to do what you need to do in php, it's possible in Drupal. 

There are no Drupal-specific API methods to help execute code through the shell, so just approach this as you would if Drupal wasn't involved.

A simple method, depending on what you need to do, might be to install Drush and invoke commands using that. Then the bootstrap/file includes will be handled for you automatically and you'll need to write less boilerplate code.