Fix loading of ligands when three letter code matches NCAA (#480)
When a ligand params file provided with
`-extra_res_fa` has a three letter code which matches an NCAA three
letter code from the database, that ligand ResidueType is never selected
on PDB read-in, even if it's a much better match for the names in the
PDB.
The reason for this is that the PDB reader residue typer prioritizes
patched polymeric terminus types (those with TERMINUS properties) for
residues at the ends of chains, discarding the ligand types as a
possibility before even encountering the name-based selection.
This PR adjusts how the typer selects residues. Instead of having
chain-terminal residues preferring terminus properties, actually look at
the connection points, and look for residues which have/don't have the
UPPER & LOWER connection points. (This is really what
"is_lower_terminus" and "is_upper_terminus" in PoseFromSFRBuilder
signifies: is this residue polymerically connected to the adjacent
residue.)