Thank you for the message. I'm glad you liked PyRx and I'm excited to hear about PyRx success stories. Saving the receptor structure along with the docked ligand is not implemented yet. This is because it's a low priority since one can copy/paste the receptor structure text into the output file to get the desired result.
Regarding making this software commercial: I'm currently not getting any financial support for developing PyRx. I've opted-in to receive donations at http://pyrx.sourceforge.net
, but I haven't got any and don't expect donations any time soon. I'm thinking to charge for new Windows and Mac installers in a couple of years if need be. I'm also open to new projects and collaborations.
Thank you for using PyRx!