you have to encrypt the pdf file using code
i hope this code will help you .

import sys

from pyPdf import PdfFileWriter, PdfFileReader

 def secure_pdf(InPdf, OutPassPdf, Passwd):

     output = PdfFileWriter()

     input1 = PdfFileReader(file(InPdf, "rb"))

     for i in range(0, input1.getNumPages()):

         output.addPage(input1.getPage(i))

     outputStream = file(OutPassPdf, "wb")

     output.encrypt(Passwd, use_128bit=True)

     output._header

     output.write(outputStream)

     outputStream.close()

     return True

secure_pdf("/Input.pdf",

           "/OutPut.pdf",

           str(email_id))