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