Several PDB files fail on OFFTK 0.17.1

[Yoshanuikabundi]

0.17.1 introduced a check that all molecules in the final topology have contiguous atom indices. This broke 13 PDB files in this repo:

FAILURE: DNA/133d.pdb       has discontinuity between atom indices   122 and   242 in molecule 0
FAILURE: RNA/2q1r.pdb       has discontinuity between atom indices   256 and   257 in molecule 0
FAILURE: DNA/122d.pdb       has discontinuity between atom indices   204 and   406 in molecule 0
FAILURE: DNA/130d.pdb       has discontinuity between atom indices   246 and   524 in molecule 0
FAILURE: DNA/144d.pdb       has discontinuity between atom indices   246 and   525 in molecule 0
FAILURE: proteins/8e8i.pdb  has discontinuity between atom indices  4327 and  5966 in molecule 0
FAILURE: proteins/7xjf.pdb  has discontinuity between atom indices  8545 and  9316 in molecule 2
FAILURE: proteins/6cww.pdb  has discontinuity between atom indices  3064 and  6711 in molecule 0
FAILURE: proteins/6mtg.pdb  has discontinuity between atom indices  4696 and 11072 in molecule 0
FAILURE: proteins/7pvu.pdb  has discontinuity between atom indices 10903 and 11460 in molecule 2
FAILURE: proteins/7qt2.pdb  has discontinuity between atom indices 12846 and 14103 in molecule 3
FAILURE: proteins/7fse.pdb  has discontinuity between atom indices 17202 and 17256 in molecule 1
FAILURE: proteins/8ovp.pdb  has discontinuity between atom indices  7889 and 17815 in molecule 0

It'll become clear whether earlier versions of the Toolkit produce nonsense for these PDBs or not as I progress openforcefield/openff-pablo#131

FAILURE: RNA/2q1r.pdb has discontinuity between atom indices 256 and 257 in molecule 0

We might have an off-by-one error somewhere