When you need to protect PDF files using password, you can use following iText codes to encrypt PDF using passwords.
String ownerPasswd="owner";
String userPasswd="user";
PdfReader reader = new PdfReader("/apps/abc.pdf");
PdfStamper stamper = new PdfStamper(reader, new FileOutputStream("/apps/abc_pw.pdf"));
stamper.setEncryption(userPasswd.getBytes(), ownerPasswd.getBytes(),
PdfWriter.ALLOW_PRINTING, PdfWriter.ENCRYPTION_AES_128 | PdfWriter.DO_NOT_ENCRYPT_METADATA);
stamper.close();
reader.close();
Library versions used,
itextpdf-5.5.10.jar
bcprov-ext-jdk14-1.47.jar
You can use preferred encryption algorithms. Refer documentations.