No module named 'MDAnalysis.core.Selection when running pycontact

Question

No module named 'MDAnalysis.core.Selection when running pycontact

PatSoto-BioPhys opened this issue 3 years ago · 9 comments

Hi All,
Today I installed PyContact following instructions to my best (I use python 3.8, installed MDAnalysis, cloned the repository of PyContact and installed it). However, I keep on getting the error message: ModuleNotFoundError: No module named 'MDAnalysis.core.Selection'
Any hints on what might be going on and how to resolve it?

Thanks!

Patricia

Answer 1 · 2021-08-31T19:51:53.000Z

Hi!

Did you clone the most recent version of the development branch?
I fixed the problem a while ago but I have to release a new version to make it more accessible. Sorry for the inconvenience...

Answer 2 · 2021-08-31T21:00:08.000Z

Thanks for the prompt response!
I cloned the development branch (downloaded the ZIP file). The date of the files is Sep 1 2020. Is this the correct ZIP file?

Answer 3 · 2021-08-31T21:06:06.000Z

Okay, that should be right... then afterwards which command did you use to install pycontact?

Answer 4 · 2021-08-31T21:11:44.000Z

I cd to pycontact-develop
and type in:
python setup.py build_ext -i
python setup.py install

Answer 5 · 2021-09-01T05:23:22.000Z

Okay... that looks good.

If the "correct" pycontact version was installed, the code causing the error should not be present anymore...
So, maybe you installed an older version via pip or so before?

Answer 6 · 2021-09-01T18:22:35.000Z

I cd to pycontact-develop
and type in:
python setup.py build_ext -i
python setup.py install

Answer 7 · 2021-09-01T18:24:56.000Z

I uninstalled pycontact, cython PyQt5 and MDAnalysis.
Then, I reinstalled in the following order: MDAnalysis, cython, PyQt5, pycontact (development).
I get a different error message: qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "" even though it was found.
This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem.

I will tinker and see if I can figure it out. At least there is no error about MDAnalysis!

Answer 8 · 2021-09-01T18:28:24.000Z

I did:

sudo apt-get install libxcb-xinerama0

And now have a nice pycontact running. Thanks!!

Answer 9 · 2023-10-06T10:35:21.000Z

Hello friends,

Today I tried to install pycontact and it returns the same error "ModuleNotFoundError: No module named 'MDAnalysis.core.Selection'" despite guiding me from the above comments.

Steps that I followed for the installation :
1. Download the pyconctat repository "pycontact-develop.zip" (06/10/2023).
2. conda create -n pycontact python=3.8
3. conda install -c conda-forge mamba
4. mamba install -c conda-forge mdanalysis
5. pip install cython
6. pip install pycontact PyQt5

Execute also the optional commands
pip install cython PyQt5
python setup.py build_ext -i
python setup.py install

All this I executed located inside the downloaded pycontact repository.

I would appreciate any help, best regards