analyze_bound_poses gives error + typo in script

[sheshe9]

Using analyze_bound_poses function in the demo script gives

File "python_interaction.py", line 68, in
pose_rmsd_data = li.analyze_bound_poses(binding_site_id=None, pose_format=save_pose_format)
File "/home/asma97/.local/lib/python3.8/site-packages/pylipid/api/api.py", line 869, in analyze_bound_poses
selected_pose_id = [np.random.choice(i_core_sample, 1)[0] for i_core_sample in core_sample_indices]
File "/home/asma97/.local/lib/python3.8/site-packages/pylipid/api/api.py", line 869, in
selected_pose_id = [np.random.choice(i_core_sample, 1)[0] for i_core_sample in core_sample_indices]
File "mtrand.pyx", line 903, in numpy.random.mtrand.RandomState.choice
ValueError: a must be greater than 0 unless no samples are taken

I wonder what could be a possible fix to this.
typo: li.compute_residue_lipidcount instead of li.compute_residue_lipidcout

Thank you.

[wlsong]

Hi,

Thanks for pointing out the typo.. I have corrected.
I have also corrected the issue with the reported error. Please update to the latest version by 'pip install pylipid --upgrade'. Let me know if you have issues with the updated version.

Wanling

[wlsong]

The latest version is 1.4.5.

[sheshe9]

Hello,

Thanks for your reply.

The error then appears to be fixed but is now in the next function:

File "python_interaction.py", line 69, in
surface_area_data = li.compute_surface_area(binding_site_id=None, radii=radii)
File "/home/asma97/.local/lib/python3.8/site-packages/pylipid/api/api.py", line 946, in compute_surface_area
plot_surface_area(surface_area_data,
File "/home/asma97/.local/lib/python3.8/site-packages/pylipid/plot/plot1d.py", line 349, in plot_surface_area
axes[row_idx, col_idx].plot(df["Time"], df[bs_name], color=colors[col_idx],

IndexError: too many indices for array: array is 1-dimensional, but 2 were indexed

[wlsong]

In order to fix the error, could you please let me know how many binding sites were calculated by pylipid and how many trajectories were used for calculation?

[wlsong]

My guess is probably just one binding site was detected. I tried to fix the bug based on that. Please update pylipid to 1.4.6 and see if this issue is fixed.

[sheshe9]

Hi,

One trajectory was used. There were seven BS_id7.pdf files produced. I will test the new update.

[wlsong]

Hi,

I have figured out what issue is and fixed the bug. Please use the 1.4.7 version.