Shape-it - large datasets

[AJK-dev]

The shape-it workflow has difficulties handling larger datasets.
For datasets of at least up to 250 000 conformers it works just fine, but at 500 000 the java snippet hangs after a few hours.
While the shape-it calculations are completed successfully the Java snippet is hanging in "execution mode". On the other hand, the align-it workflow works just fine for the same datasets (align-it is also a bit faster than shape-it, maybe something with a time-out?).