gmx_MMPBSA aborts with line plot

[Dewald Schoeman]

Hi all,

I'm quite new to using gmx_MMPBSA. Everything during my installation seems to have gone fine and the tests didn't give any errors, so I believe everything installed the way it should.

However, when I generated data for my protein-protein interaction, I can only visualise bar plots in gmx_MMPBSA_ana. The option for line plots are there but every time I click on the line plot to generate it, gmx_MMPBSA_ana closes and I get the following in my terminal:

Warning: Ignoring XDG_SESSION_TYPE=wayland on Gnome. Use QT_QPA_PLATFORM=wayland to run on Wayland anyway.

Traceback (most recent call last):

  File "/home/dewald/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/analyzer/customitem.py", line 371, in fn_btn_group
    self.plotting_line(checked)
  File "/home/dewald/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/analyzer/customitem.py", line 398, in plotting_line
    self.lp_subw = LineChart(line_plot_data, self.line_chart_action, options=options, item_parent=self)
  File "/home/dewald/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/analyzer/plots.py", line 215, in __init__
    self.line_plot_ax = sns.lineplot(data=self.data, color=rgb2rgbf(options[('Line Plot', 'line-color')]),
  File "/home/dewald/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/seaborn/_decorators.py", line 46, in inner_f
    return f(**kwargs)
  File "/home/dewald/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/seaborn/relational.py", line 710, in lineplot
    p.plot(ax, kwargs)
  File "/home/dewald/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/seaborn/relational.py", line 471, in plot
    for sub_vars, sub_data in self.iter_data(grouping_vars, from_comp_data=True):
  File "/home/dewald/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/seaborn/_core.py", line 983, in iter_data
    data = self.comp_data
  File "/home/dewald/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/seaborn/_core.py", line 1054, in comp_data
    with pd.option_context('mode.use_inf_as_null', True):
  File "/home/dewald/.local/lib/python3.9/site-packages/pandas/_config/config.py", line 441, in __enter__
    self.undo = [(pat, _get_option(pat, silent=True)) for pat, val in self.ops]
  File "/home/dewald/.local/lib/python3.9/site-packages/pandas/_config/config.py", line 441, in <listcomp>
    self.undo = [(pat, _get_option(pat, silent=True)) for pat, val in self.ops]
  File "/home/dewald/.local/lib/python3.9/site-packages/pandas/_config/config.py", line 135, in _get_option
    key = _get_single_key(pat, silent)
  File "/home/dewald/.local/lib/python3.9/site-packages/pandas/_config/config.py", line 121, in _get_single_key
    raise OptionError(f"No such keys(s): {repr(pat)}")
pandas._config.config.OptionError: "No such keys(s): 'mode.use_inf_as_null'"
Aborted (core dumped)

I can't seem to identify the issue. I tried making sure that all my conda environment packages are installed and updated (they are), but I still get the same error with each of my different protein-protein complexes. It's not just with one of the complexes.

Please help. What am I doing wrong, or missing?

Thank you in advance!

[Mario Sergio Valdes]

This is probably related to the pandas' version. Please check that pandas<2.0.0 using conda list. If not, then downgrade it

[Dewald Schoeman]

Thank you very much for getting back to me!

It worked! Thank you!