SetElement sets default properties for mass and radius. Previously
set charge and anisou got wiped in the process. Charge and anisou
are now transferred and only mass and radius are reset.

use greedy full strategy with contact map pruning enabled

If enabled, the greedy extension only checks chains which have at least 3
contacts in trg/mdl towards the already mapped chains where contact is defined
as CB distance < 8A.

This should prevent any further "substructure has residue [...] which is not
in self.target" errors. Add test and doc to clarify what we ignore.

This fixes a problem where ties aren't being resolved correctly

This improves error messages when the counts line is invalid and the
calls to substr() return raw C++ errors.

comes at limited additional runtime costs

trust me, its a bit better that way...

Apply crude collision detection to avoid pairwise distance computations
between chains that are far apart.