That was stupid before

Only initial work done for a base scoring class that takes care
of ligand prep, computing ligand symmetries and calling score computation
functionality from child classes. Child class for SCRMSD is already there
with basic testing.

Can occur in chain_mapping._ChainMappings that provides an iterator
of all possible ways to map mdl chains onto fixed ref chains.

The situation where a chem group (group of chains in the reference) is
empty but the respective group of chains in the model is not can be
correctly resolved.

Can be considered backup commit and still contains debug output

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

There are structures with only atoms that lie on top of each other.
This is typically a fuckup but hey, better a nice error than the segfault
that would be caused by this...

This indicates a bug that must be fixed but at least we don't run
forever.

Use a very large inclusion radius. This should not impact the exhaustivity
of the chain mapping search by much, but makes it less likely to impact
low/medium RMSD scores.

These are two independent ways to speed up the processing but they
make no sense in combination and could lead to unexpected effects.

This prepares for testing with full_bs_search where a model ligand can
no longer be too far from the actual binding site.

- separate scrmsd and lddtpli computations in separate functions
- optionally reduce the binding site search space in the model

This should not change behavior but will make it easier to speedup
binding site extraction

LigandScorer uses ChainMapper.GetRepr to match binding sites between target
and model. This commit limits the search space for model binding sites to
locations where there actually is a ligand.