Reduce precision on geometry group values

There were random fluctuations showing up in git diffs, that were
not physically significant  (one billionth of an angstrom and below)
Don't set lower limits below zero
Cope with missing uncertainties.

For now we assume 0.1 Angstrom
Print the bounds matrices at various stages
Print number of embedding attempts
Change the VdW tweak to avoid unsmoothable matrices.

We now essentially do part of the triangle smoothing algorithm, to figure 
out the minimum approach distance of two atoms (which had previously been
the sum of the VdW radii). This should stop "cannot smooth" errors.
Check if bounds matrix is flawed after smoothing.

This should be entirely redundant, if RDkit is coded right.
(Because the triangleSmoothing should return False if this test would fail)
Try more embedding attempts