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Valdes-Tresanco-MS / AMDock

(Linux and macOS) AMDock: Assisted molecular docking with AutoDock4 and AutoDockVina
GNU General Public License v3.0
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Using PyMOL installed with macport on macOS 10.13.6? #19

Closed houdini69 closed 2 years ago

houdini69 commented 2 years ago

Hi, Is it possible to use AMDock with PyMOL installed with macport on macOS 10.13.6? In this case pathway of PyMOL starting script is /opt/local/bin/pymol. I've tried to compile pymol directly from source but it failed... Laurent

Valdes-Tresanco-MS commented 2 years ago

I need to do the tests since I am not an expert in macOS. I remember that I spent a lot of work to get the pymol installation to work. I will test and let you know

houdini69 commented 2 years ago

Thank you. On my side I think I am not far from being able to compile PyMOL from sources.

houdini69 commented 2 years ago

Hi, I finally succeeded to compile PyMOL with Conda package manager from PyMOL sources. However, I couldn't select Plugin-> Plugin Manager to install grid_amdock.py! I got an error window "No module named PyQt5.uic.

Valdes-Tresanco-MS commented 2 years ago

You must make sure that you have PyQt5 installed in such a control environment. 

python -m pip install pyqt5
houdini69 commented 2 years ago

Tried to install AMDock and then compile pymol from the beginning in conda environnment. AMDock installation was ok. After installing dependencies (glew glm and netcdf4) compilation of pymol failed with at the end,

Traceback (most recent call last): File "/Users/xxxx/miniconda3/envs/AMDock/lib/python3.10/multiprocessing/pool.py", line 268, in del File "/Users/xxxx/miniconda3/envs/AMDock/lib/python3.10/multiprocessing/queues.py", line 377, in put File "/Users/xxxx/miniconda3/envs/AMDock/lib/python3.10/multiprocessing/connection.py", line 205, in send_bytes File "/Users/xxxx/miniconda3/envs/AMDock/lib/python3.10/multiprocessing/connection.py", line 405, in _send_bytes AttributeError: 'NoneType' object has no attribute 'pack'

What does it mean?

Valdes-Tresanco-MS commented 2 years ago

I do not have much information regarding this. I have not yet tested python 3.10 in production, so I am currently oblivious to what bugs it may have. Please tell me the specifics so I can try to reproduce the bug. macOS Version. PyMOL version and if it the open-source version

Please try using python 3.8 or 3.9 and see if you have the same problems. I will try to reproduce the problem as soon as possible.

houdini69 commented 2 years ago

macOS Version: 10.13.6 High Sierra PyMOL(TM) Molecular Graphics System, Version 2.6.0a0. Open Source version from https://github.com/schrodinger/pymol-open-source.

pymol compilation succeeded using python 3.9 with same error as previously. I can start pymol in AMDock env. However I couldn't start AMDock in AMDock env and I got AMDock Traceback (most recent call last): File "/Users/xxxx/miniconda3/envs/AMDock/bin/AMDock", line 5, in from AMDock.Docking_Program import run File "/Users/xxxx/miniconda3/envs/AMDock/lib/python3.9/site-packages/AMDock/Docking_Program.py", line 9, in from AMDock.result_tab import Results File "/Users/xxxx/miniconda3/envs/AMDock/lib/python3.9/site-packages/AMDock/result_tab.py", line 9, in from AMDock.variables import Variables File "/Users/xxxx/miniconda3/envs/AMDock/lib/python3.9/site-packages/AMDock/variables.py", line 6, in import AutoDockTools, pymol ModuleNotFoundError: No module named 'pymol'

houdini69 commented 2 years ago

Ok. I finally succeeded to properly install AMDock. I just have to use AMDock tutorial!

pillar-github commented 1 year ago

how you solve the problem: ModuleNotFoundError: No module named 'pymol'.

macOS Version: 10.13.6 High Sierra PyMOL(TM) Molecular Graphics System, Version 2.6.0a0. Open Source version from https://github.com/schrodinger/pymol-open-source.

pymol compilation succeeded using python 3.9 with same error as previously. I can start pymol in AMDock env. However I couldn't start AMDock in AMDock env and I got AMDock Traceback (most recent call last): File "/Users/xxxx/miniconda3/envs/AMDock/bin/AMDock", line 5, in from AMDock.Docking_Program import run File "/Users/xxxx/miniconda3/envs/AMDock/lib/python3.9/site-packages/AMDock/Docking_Program.py", line 9, in from AMDock.result_tab import Results File "/Users/xxxx/miniconda3/envs/AMDock/lib/python3.9/site-packages/AMDock/result_tab.py", line 9, in from AMDock.variables import Variables File "/Users/xxxx/miniconda3/envs/AMDock/lib/python3.9/site-packages/AMDock/variables.py", line 6, in import AutoDockTools, pymol ModuleNotFoundError: No module named 'pymol'

houdini69 commented 1 year ago

I had to move all builded/compiled modules (glew, glm, netcdf4, pmw, libpng, freetype, libxml2) with conda in AMDock site-packages folder (/Users/xxxxxxx/miniconda3/envs/AMDock/lib/python3.9/site-packages/ folder