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1. What do you mean by "programmatically create a pdf with an empty signature field"? The word that puzzles me is "programmatically"? Are you writing a PDF generator? If so you need Acrobat SDK which comes with fairly extensive documentation, or some other PSD-creation SDK. It'd be too extensive work to write from scratch a program that generates PDF.
2. Which signatures are you talking about: e-signatures (which are just stamps with text or image) or digital signatures signed with a certificate? The rest of my response is for the digital signatures.
3. You can use Acrobat to add form fields to your PDF. You add a signature field at any place you want in your PDF, i.e. at the bottom of some page. You select the field's name. It can be anything you want (there is a default name, like "Signature 1"). Different signature fields in the same PDF (yes, there may be more than one), must have different names. When the user clicks on the unsigned signature field field a "Sign" dialog pops up which guides the user through the signing process. Remember that the digital signature applies to the complete document. The page/place where it appearance appears (location of the signature field for this signature) is insignificant. It is only for convenience of the user to see it in a certain place in the document.
4. Adobe Reader has less capabilities than Acrobat. To activate in the Reader some functionality that Reader normally does not have but Acrobat has, one can use Acrobat to Reader-extend a PDF with additional rights to perform some actions that the Reader normally does not provide. This is what is called "rights enabled". Before Reader 11.0.07, signing with certificate was not one of the actions that Reader provided. However, when a PDF was Reader-extended to allow the user to sign, Reader could sign such PDF. Starting with Reader 11.0.07 signing with certificates is a standard Reader function which does not require Reader-extension.
Thanks for the answer. I needed to programmatically generate pdfs with a sign field in them so that a 3rd party program would know where to place the signature. I was using pdfbox library to generate pdfs. I was quite frustrated since I did not know much about pdf internals. Anyways I solved the problem by going trough the iso-32000 pdf specification(which is quite long but very well done). I needed this object with a sign/annotation dictionary
3 0 obj
/Rect [132.4523 614.862 418.171 201.093]
/P 4 0 R
I needed to set up the /SigFlags 3 key value pair in the acroform dictionary and attach the annotation to the page(without doing the later some pdf readers recognize the signature box and others do not.)
Hope this helps someone in the future.