This article shows how to Encrypt a pdf.

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// Get Documents directory path
NSArray *paths = NSSearchPathForDirectoriesInDomains(NSDocumentDirectory, NSUserDomainMask, YES);

NSString *documentsDirectory = [paths objectAtIndex:0];
// Set the encrypted file path

NSString *docPath = [documentsDirectory stringByAppendingPathComponent:@"enc_file.pdf"];
// Set the pdf file id

NSString *pdfId = @"123456789abcdefghijklmnopqrstuv";
unsigned char c = [pdfId cStringUsingEncoding:NSUTF8StringEncoding];

// Encrypt the current pdf file
[m_doc encryptAs:docPath :@"user" :@"admin" :0x4 :4 :&c];