QPDF is a command-line program that does structural, content-preserving transformations on PDF files.
QPDF is capable of creating linearized (also known as web-optimized) files and encrypted files. It is also capable of converting PDF files with object streams (also known as compressed objects) to files with no compressed objects or to generate object streams from files that don't have them (or even those that already do). QPDF also supports a special mode designed to allow you to edit the content of PDF files in a text editor.