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.

previously this was done with residue ChemClasses. This is set by the
compound library anyways during processing when loading a structure.
The problem: when we suddenly need info on chemical components for stuff
that is in the SEQRES but nowhere resolved in the structure. I really
tried hard to avoid the requirement for the compound library in mmcif
writing but there seems no way around.

When defining custom mmCIF entities, we should check for valid input using
the latest mmCIF dictionary

Information from https://www.iucr.org/resources/cif/spec/version1.1/cifsyntax

Available as MMCifEntityDesc objects in MMCifInfo

If all residues in a chain are saccharides in some form, the
respective _entity.type should be "branched"

Minimum length for a chain in the target structure
to be considered in chain mapping. The chain mapping algorithm first
performs an all vs. all pairwise sequence alignment to identify
"equal" chains within the target structure. We go for simple sequence
identity there. Short sequences can be problematic as they may
produce high sequence identity alignments by pure chance.

BUT: if you're scoring peptides or short nucleotides, you
really want to be able to reduce the default thresholds
(pep: 10, nuc: 4)