There seems to be two different requests there: 1) Automation of docking submission, 2) Automation of experimental data conversion into interaction restraints. Which one did you have in mind?
We do not provide automated ways to submit docking runs, we do not have unlimited resources so such scripts would potentially quickly overload our clusters.
However, if your docking runs have a certain degree of similarity you can certainly use the File Upload interface. This interface allows you to submit a unique parameter file (
haddockparam.web) that will hold all the information the web server needs to run a docking.