Yes and no

The current java converter tool was written with Jemplode in mind, so it is easily integrated into Jemplode. However, mschrag and company have been tweaking some of the internals of Jemplode for the next release, and the .pdb exporter depends on some of those internals. They aren't complete yet, so I can't write the exporter into Jemplode until the next release.

If I get some time I might write a java program to convert directly from the .csv file to .pdb without manual tweaking.