I'd have to hunt through the code more carefully, but in formats like Gaussian,
we know that all atoms (including hydrogens) are explicit.
Unfortunately, that's not true from PDB — in the vast majority of cases,
hydrogens are omitted and implicit.
So, for example in src/formats/pdbformat.cpp
Den 2019-10-18 kl. 23:04, skrev Geoffrey Hutchison:
How about Gaussian log files? It works with those as well.
Somehow there bond orders are derived correctly as well although no such
information is extracted from the log files.
Are you saying that PDB is giving you different information than
