Bond guessing is turned on in two ways in Universe creation: to_guess("bonds") or guess_bonds=True. The latter should probably be deprecated , as well as the other kwargs related to bond guessing (fudge_factor and friends).
Current version of MDAnalysis
Which version are you using? (run python -c "import MDAnalysis as mda; print(mda.__version__)")
Expected behavior
Bond guessing is turned on in two ways in Universe creation:
to_guess("bonds")orguess_bonds=True. The latter should probably be deprecated , as well as the other kwargs related to bond guessing (fudge_factor and friends).Current version of MDAnalysis
python -c "import MDAnalysis as mda; print(mda.__version__)")python -V)?