distance constraints for connecting fragments

[leclercfl]

implement customized distance contraints, e.g. distance O3'(n)-O5T(n+1)
max_dist_O3O5T = 2.0;
The idea is to select close fragments with a partial overlap between O3' and O5T; from various tests, it improves the geometry of the connection between nucleotides.

[leclercfl]

I guess the *_noptach selection allows to exclude the O5T, C5T and connected hydrogens from the clashes but we still need to have the coordinates of O5T.
N.B.: it seems that the *_nopatch does not allow to use the patched atoms in any constraint because it removes the atoms and its coordinates