ModuleNotFoundError: No module named 'PharmaContacts'

[Bece00]

Hello Developer Team,

I am trying to install and run PharmD within a stable Conda/Docker environment. I have successfully resolved numerous complex dependency conflicts (Open Babel, RDKit, PLIP, CGRtools) and successfully built the Docker image with the pharmd package installed.

However, when running the main executable, I am encountering a critical missing dependency error:

Error Output:

_Traceback` (most recent call last):
File "/opt/conda/lib/python3.9/site-packages/pharmd/md2pharm.py", line 15, in
from PharmaContacts import (...)
ModuleNotFoundError: No module named 'PharmaContacts'

To complete the installation, could you please provide the new, active GitHub repository link for the PharmaContacts module, or an alternate source (e.g., PyPI package name, or the source files) that I can use?

Thank you very much for your time and assistance with this matter

[DrrDom]

Hi,
here is the repository with PharmaContacts - https://github.com/stsouko/PharmaContacts. You may try to install the module from there.

In general pharmd package is not maintained and I may suggest some other tools, which may be easier to install and use depending on your particular task.

Information about protein-ligand contacts from MD trajectories you can get by ProLIF (https://github.com/chemosim-lab/ProLIF). There is also an option to get information which atom is involved in interaction to get its coordinates and create pharmacophore features in 3D space. This may be tricky, but should be possible.

I also highly recommend CDPKit (https://github.com/molinfo-vienna/CDPKit). It is a universal package and has a lot of functionality to work with 3D pharmacophores. I did not use CDPKit with MD trajectories, but I believe this should be relatively easy. You may also ask the developers how to use it in your particular situation.

These are two continuously developing packages and therefore you can ask and quickly receive responses from the developers.