An individual pdf file can be password encrypted to avoid trivial access. Two passwords are available, a user and owner password. Here we set them both to be the same. The key length for encryption is also specified, with possible lengths being 40, 128, and 256. We choose 256 which is the PDF 2.0 encryption method and is supported by Acrobat X. The -- stops processing command line options. Two filenames are expected, the input pdf and the output pdf**.
\$ qpdf --encrypt <password> <password> 256 -- mydoc.pdf mydoc_enc.pdf