Ranking passed templates by H_excess if tied with H_missing

[rwxayheee]

This is a quick fix for #300. Passed current tests (in develop) and works for the triply protonated N-terminal residues. It implements the additional refinement of passed templates (previously forgiven with excess H) for minimal excess H.

My previous PR #211 caused the unexpected behavior. This is an amend to handle explicitly protonated linking atoms in the corect way.

@diogomart Would this be ok as a temporary fix? Sorry for implementing the bug ><

[rwxayheee]

Please hold off for a short while. I would like to include two additional bug fixes before finalizing this PR. They were included in #277 but I gave up on that PR. Only need very minimal changes.

[rwxayheee]

Added two commits that were part of #277. More detail is explained in #277.

• Bug fix for Excess (padding) hydrogens in the exported PDB from mk_export.py  #280. This is a quick fix without changing other parts of the code. Refactor CovalentBuilder, Enable Custom Tether Atoms within Receptor, and Export Modified Polymer to PDB  #277 has more efficient handling of covalent docking results, but requires too many changes.

• Improvement for Report (raise warning or error for) lone hydrogens from bad input PDB  #231. This does not change the behavior of template matching.

Added example file from #300 as a test.