I like this plugin (DockingPie) very much. However, recently, I run vina program via this plugin, PyMOL always reported the following issue. Could you help me to deal with it? Thank you!

File "d:\anaconda\lib\site-packages\pmg_tk\startup\DockingPie1\lib\docking_program_main\Functions\dockings_thread.py", line 396, in on_update_results_tab
self.tab.results_frame = ResultsFrame(parent=self.tab,
File "d:\anaconda\lib\site-packages\pmg_tk\startup\DockingPie1\lib\docking_program_main\docking_program_gui\frames.py", line 1019, in init
if Path(self.log_file).is_file():
File "d:\anaconda\lib\pathlib.py", line 1038, in new
self = cls._from_parts(args, init=False)
File "d:\anaconda\lib\pathlib.py", line 679, in _from_parts
drv, root, parts = self._parse_args(args)
File "d:\anaconda\lib\pathlib.py", line 663, in _parse_args
a = os.fspath(a)
TypeError: expected str, bytes or os.PathLike object, not NoneType

PyMOL>fetch 7roq
TITLE Alternative Structure of Human ABCA1
ExecutiveLoad-Detail: Detected mmCIF
CmdLoad: "./7roq.cif" loaded as "7roq".
CmdLoad: "/home/scientist/Downloads/Conformer3D_COMPOUND_CID_4912-2.sdf" loaded as "Conformer3D_COMPOUND_CID_4912-2".
Executive: object "temp_obj" created.
Executive: object temp_obj created.
Traceback (most recent call last):
File "/home/scientist/.pymol/startup/DockingPie1/lib/docking_program_main/docking_program_gui/tabs.py", line 2188, in generate_ligand_func
is_receptor = False)
File "/home/scientist/.pymol/startup/DockingPie1/lib/docking_program_main/Functions/general_docking_func.py", line 284, in init
self.generate_receptor()
File "/home/scientist/.pymol/startup/DockingPie1/lib/docking_program_main/Functions/general_docking_func.py", line 306, in generate_receptor
self.generate_checked_object()
File "/home/scientist/.pymol/startup/DockingPie1/lib/docking_program_main/Functions/general_docking_func.py", line 412, in generate_checked_object
os.rename(old_name, new_name)
FileNotFoundError: [Errno 2] No such file or directory: 'Conformer3D_COMPOUND_CID_4912-2.pdbqt' -> '01_Conformer3D-COMPOUND-CID-4912-2_Vina.pdbqt'
INFO and CONTACTS
Copyright (C): 2022 Serena Rosignoli, Alessandro Paiardini
Contacts: [email protected], [email protected]
For information on DockingPie 1.0 visit:
https://github.com/paiardin/DockingPie

DockingPie

• Version: 1.2.1
• Plugin path: /home/scientist/.pymol/startup/DockingPie1/lib/docking_program_main
• Config directory: /home/scientist/.pymol/startup/DockingPie1/lib/docking_program_main/config

PyMOL

• Version: 2.5.2
• Path: /home/scientist/pymol/bin/python
• Qt: PyQt5
• Has Conda: True

Python

• Version: 3.7.10 | packaged by conda-forge | (default, Feb 19 2021, 16:07:37)
  [GCC 9.3.0]
• Arch: 64
• Path: /home/scientist/pymol/bin/python

Operating system

• Platform: linux
• Arch: 64

Python libs

• PyQt5: 5.12.3
• Conda version: 4.10.3
• Numpy version: 1.21.2
• Biopython version: 1.79

I've used source codes from released page to install DockingPie plugin. And when I try to install packages with "configure" button. A 404 error was reported since that the given link is not correct.
This issue is just to remind somebody like me who tried that copy of source codes and got this error.
If the developers can notice this issue and updated a newer version of released source codes, it will be much better.

The error comes from a small mistake in the codes below.
The codes of the latest commit in branch "main", which is the same in the source codes from user guide

    def configure_external_tools_directory(self):

        if sys.platform == "linux":
            dir_link = "https://github.com/paiardin/DockingPie/releases/download/Files_v1.0.0/external_tools_linux.zip"
            dir_name = "external_tools_linux"
        if sys.platform == "darwin":
            dir_link = "https://github.com/paiardin/DockingPie/releases/download/Files_v1.0.0/external_tools_macOS.zip"
            dir_name = "external_tools_macOS"
        if sys.platform == "win32":
            dir_link = "https://github.com/paiardin/DockingPie/releases/download/Files_v1.0.0/external_tools_windows.zip"
            dir_name = "external_tools_windows"

The solution of this 404 error is simple, i.e., just to modify the codes and restart PyMol.

Hi, I am running through the tutorial example using PDB: 1OL5 but keep getting an error when clicking "Generate Ligand". All steps up to that point are fine. I have configured and installed everything as in the User Guide.

Traceback (most recent call last):
File "C:\Users\pgoldsmith\AppData\Local\anaconda3\envs\pymol_311\Lib\site-packages\pmg_tk\startup\DockingPie1\lib\docking_program_main\docking_program_gui\tabs.py", line 2183, in generate_ligand_func
generated_ligand = Generate_Object(self, dict = self.docking_programs_child_tabs.docking_programs.vina_ligands_dict,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\pgoldsmith\AppData\Local\anaconda3\envs\pymol_311\Lib\site-packages\pmg_tk\startup\DockingPie1\lib\docking_program_main\Functions\general_docking_func.py", line 284, in init
self.generate_receptor()
File "C:\Users\pgoldsmith\AppData\Local\anaconda3\envs\pymol_311\Lib\site-packages\pmg_tk\startup\DockingPie1\lib\docking_program_main\Functions\general_docking_func.py", line 306, in generate_receptor
self.generate_checked_object()
File "C:\Users\pgoldsmith\AppData\Local\anaconda3\envs\pymol_311\Lib\site-packages\pmg_tk\startup\DockingPie1\lib\docking_program_main\Functions\general_docking_func.py", line 412, in generate_checked_object
os.rename(old_name, new_name)
FileNotFoundError: [WinError 2] The system cannot find the file specified: 'obj01.pdbqt' -> '01_obj01_Vina.pdbqt'

DockingPie

• Version: 1.2.1
• Plugin path: C:\Users\pgoldsmith\AppData\Local\anaconda3\envs\pymol_311\Lib\site-packages\pmg_tk\startup\DockingPie1\lib\docking_program_main
• Config directory: C:\Users\pgoldsmith\AppData\Local\anaconda3\envs\pymol_311\Lib\site-packages\pmg_tk\startup\DockingPie1\lib\docking_program_main\config

PyMOL

• Version: 2.6.0a0
• Path: C:\Users\pgoldsmith\AppData\Local\anaconda3\envs\pymol_311\pythonw.exe
• Qt: PyQt5
• Has Conda: False

Python

• Version: 3.11.7 | packaged by Anaconda, Inc. | (main, Dec 15 2023, 18:05:47) [MSC v.1916 64 bit (AMD64)]
• Arch: 64
• Path: C:\Users\pgoldsmith\AppData\Local\anaconda3\envs\pymol_311\pythonw.exe

Operating system

• Platform: win32
• Arch: 64

Python libs

• PyQt5: 5.15.10
• Conda version: -
• Numpy version: 1.26.4
• Biopython version: 1.83

Plug-in automatically detects ligands and receptors. The ligand (peptide) I'm attempting to use is recognized as a receptor and I'm therefore unable to dock with it. Is there any way around this?