Data preprocessing code breaks for some of the truncated PDBs

[kmnis]

The pipeline failed for some of the files like 6z2m_trunc.pdb or 7joo_trunc.pdb. It broke on the step where it was creating the antibody.h5 file, more specifically, in this line. After some exploration, I found that these files were missing the light chain completely from them after truncation. I'm not sure if it's the issue with the truncation code or the files itself are corrupted.

I tested it on a MacOS Mojave 10.14.6 with python 3.6