reduce lDDT memory peaks

lDDT computes all vs all pairwise distances within individual chains,
as well as between pairs of chains.
A chain of 5000 residues is already considered long and leads to
around 40000 atom positions. scipy cdist strictly operates on doubles
(64bit floats). In case of 40000 positions, it needs around 12GB
to hold all pairwise distances. The new implementation uses a fallback
for every cdist call above 20000 positions. cdist is called blockwise
and stores the 64 bit results for each block in a 32bit result matrix,
halving the memory requirements.