Problems about trying examples in documentation about docking_py HOT 1 CLOSED

Hi,

The message "File name doesn't finish with .pdb read it as .pdb anyway"
is just a warning, as you are using a pdbqt file. It is fine and expected

Concerning the RMSD calculation :

rmsd_list = test_dock.compute_dock_rmsd(test_dock.lig_pdb)

You should use the test_dock.lig_pdbqt as reference structure instead. Otherwise the atom number is different, this is an issue for RMSD calculation.
The difference in rmsd, is also expected, as you cannot run exactly the same run on different machines.

Anyway, I have updated the Usage page, and add exemples to look with nglview at the dock structures:
https://docking-py.readthedocs.io/en/latest/notebook/Usage.html

To enbale the 3D viz, you'll need to install nglview and mdanalysis:

conda install -c conda-forge nglview
conda install -c conda-forge MDAnalysis

Cheers,
Samuel

from docking_py.