I've a protocol that is part of a large workflow that substructure searches many molecules. The substructure component hangs on complex molecules that I'd like to filter out. I've been trying to somehow filter these out on the fly when the component hangs but I've had no success. "runprotocol" could be useful but I can't see a way of passing the last variable out of protocol before it timesout. I've tried writing a temporary file but this, unsurprisingly, takes too long.

Having trouble uploading example protocol and files.

Any help would be greatly appreciated.

Thanks

Murray