QS-score which is used as default target function for chain mappings.
However, thats protein specific. As soon as nucleotides are involved,
lDDT with an increased inclusion radius of 30A is now used
in ChainMapper.GetMapping.

It was a bit embarassing that lDDT mappings were about an order of
magnitude slower than QS-score mappings. A specialized backbone only
lDDT has therefore been introduced that uses matrix operations.
This is not a replacement of the lDDTScorer. But it doesnt need to
produce per-residue scores and doesn't need to deal with symmetries
etc.

and some cleanup...

This is no final product but just a first working version as a
starting point. Plenty of testing/cleanup/speedup required.

Until now, the actions were failing with somewhat cryptic messages
raised from arbitrary locations. This one should be more user-friendly.

CreateBU always returns a valid entity. We already check if it's empty
separately.

This is made possible now that we have a CreateBU function.

It turns out for some reason we were reading them from chains, based on
the ChainType of the chain. This prevented extracting anything from
legacy PDB files and didn't match the documented behavior in the action.

Now extraction is based on the IsLigand flag only, and documentation is
consistent throughout. Behavior on PDB files is tested.

Move long description to separate properties

Yolo, this code is totally untested. Xavier, please give it a try ;)

Following fixes in cd701347, setting seqres=True is no longer required
for these things to work.

A null character is added by OST in case of empty insertion code. This is not part of the actual insertion code, and could make it harder for third party software to handle our output.

A global chain mapping can now be enabled with --global-chain-mapping as
a complement to the existing local chain mapping. This can be evaluated
for the scoring paper.

This makes the ligand scoring script more independent of an up-to-date
compound library, which is a strong requirement of Molck.
This was a problem for the April 2023 Modeling Championship where the
script was run with an out of date library and the element of an atom of
the ligand was silently changed, preventing the symmetry correction to
find isomorphisms and resulting in the absence of scores.

This may be necessary in case SDF ligands have the same chain/residue
number, which can happen with some input.