execution issues

[Aleksandr-biochem]

In installed PoreAnalyser to a clean environment and attempted trial trajectory analysis as described in documentation. So the code is:

pdb_models = [
    f'../../aa_simulations/{model}/{model}_00{rep}/md_files/step7_1_nonW.tpr',
    f'../../aa_simulations/{model}/{model}_00{rep}/md_files/step7_1_nonW.xtc'
]

pore_analysis = pa.PoreAnalysis(
    pdb_array=pdb_models,
    trajectory=True,
    traj_frames=10
)

pore_analysis.hole_analysis()
pore_analysis.plt_trajectory_average(HOLE_profile=True)

for i in tqdm(range(10)):
    pore_analysis.ellipsoid_analysis(index_model=i)
    pore_analysis.plt_trajectory_average(HOLE_profile=False)

However, there seems to be a problem with HOLE2:

hole_analysis step7_1_nonW0_aligned_z.pdb
vmd surface created for step7_1_nonW0_aligned_z.pdb
Traceback (most recent call last):
  File "run_PoreAnalyser.py", line 32, in <module>
    pore_analysis.hole_analysis()
  File "envs/poreanalyser_env/lib/python3.11/site-packages/PoreAnalyser/poreanalyser.py", line 186, in hole_analysis
    fig, df = hole_analysis.analysis(self.pdb_array, labels=self.labels, 
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "envs/poreanalyser_env/lib/python3.11/site-packages/PoreAnalyser/hole_analysis.py", line 148, in analysis
    midpoints, means = hole_analysis(name=names[i], path=aligned_path, #typ='pdb',
                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "envs/poreanalyser_env/lib/python3.11/site-packages/PoreAnalyser/hole_analysis.py", line 87, in hole_analysis
    radii2, edges2 = ha2.bin_radii(bins=100, range=None)
                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "envs/poreanalyser_env/lib/python3.11/site-packages/mdahole2/analysis/hole.py", line 1185, in bin_radii
    range = (coords.min(), coords.max())
             ^^^^^^^^^^^^
  File "envs/poreanalyser_env/lib/python3.11/site-packages/numpy/_core/_methods.py", line 48, in _amin
    return umr_minimum(a, axis, None, out, keepdims, initial, where)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ValueError: zero-size array to reduction operation minimum which has no identity

Without hole_analysis I also cannot run ellipsoid_analysis, because it's looking for HOLE2 output:

ERROR could not find SPH file step7_1_nonW0_aligned_z.sph
...
FileNotFoundError: [Errno 2] No such file or directory: 'hole000.sph'