A QMForge user (Andy S.) brought a problematic file to my attention that aborts when parsing because the assert HOMO == self.homos[0] check fails. I believe the issue is that it uses the Guess(Fragment) command. Unfortunately, he wasn't willing to place the file in the Public Domain.

We potentially need two things to address this issue:

1. An example file (BH3CO, see below), but it crashes for a reason I can't figure out. @langner, can you see if you have better luck?
2. If we can reproduce the problem, then the problem with the parser needs to be fixed.

%chk=BH3CO_fragment_guess.chk
%nproc=2
%mem=1000MB
#p B3LYP/STO-3G Guess=(Only,Fragment=2) pop=none

BH3CO with Fragment guess

0 1 0 1 0 1
B(Fragment=1)       0.06457       -0.02790        0.01364
H(Fragment=1)       0.03117       -0.02317        1.21604
H(Fragment=1)       1.16348        0.05251       -0.46818
H(Fragment=1)      -0.66778       -0.82424       -0.51225
C(Fragment=2)      -0.61187        1.40183       -0.37553
O(Fragment=2)      -1.07258        2.37408       -0.64075