This allows IsValid() to work as intended without throwing an exception.
Because the validity of the underlying entity is now checked in CheckValidity,
it should no longer be a problem.

In both cases we check if we have a valid implementation AND if the
underlying entity is still there.

This checks whether the underlying handles are still valid before
returning pointers to them. Runs the check each time CheckValidity
is called on atom, residue and chain handles.

Previous behavior was to raise an error if any ligand was disconnected.
However, now with the reporting it is more consistent to complete and
report why no score was computed.

Both options perform lossy compression but have different hard
upper bounds of reconstruction error. LOSSY has 0.087A, INFER_POS
has 0.5A.

Xavier Robin authored 1 year ago and Xavier Robin committed 1 year ago

Removes code duplication

Add `unassigned=True` argument to the scorer object, and
additional properties with the unassigned ligands.

This introduces basic functionality to find out the reason why
a ligand (target or model) is not assigned.