Not entirely sure that I want to get into the business of executing external programs; it's a bit of a can of worms that one. There are some options, though, for people who are willing to do a bit of work: SketchEl can be invoked and manipulated by other Java programs that link it in, and it can also be embedded as an applet in a web page. So for example if you were to throw together some PHP script with a little bit of JavaScript to grab the molecule from the SketchEl applet and send it through to PHP to convert it into InChI, or SMILES, or whatever you want, then that could work quite nicely.