For many molecular modelers, scripting in Python has become a core part of their workflow. Whether you’re automating analyses, performing simulations, or applying data science tools, access to Python packages is essential.
But managing packages—especially across different environments—can be frustrating. Switching between your terminal and your visual platform, ensuring the right versions are installed, keeping things synced… it disrupts your focus, adds complexity, and can lead to version conflicts or broken environments.
If you’re using SAMSON, there’s a simpler way. You don’t need to jump between tools. SAMSON integrates a built-in Python Package Manager right inside its interface, so you can manage everything without leaving your modeling environment.
Where to Find It
Within the Python Console, go to Edit > Manage packages… to open the Python Package Manager. This gives you quick access to a visual interface for checking what’s installed, adding new packages, or uninstalling those you no longer need.
Installing Packages (from PyPI)
In the Package Manager window, all you have to do is type the name of the package you need and click Install. It supports standard pip syntax, so you can:
- Specify versions (e.g.,
scikit-learn==1.2.2) - Install multiple packages at once (e.g.,
numpy pandas matplotlib) - Use pip flags like
--upgrade
Installing Local Packages
Working on a custom module or integrating a collaborator’s code? SAMSON allows you to install local packages too. Just provide the path to the package (with a valid setup.py) and click Install.
If you’re modifying the code regularly, you can opt for the editable/develop mode (pip install -e style), so your changes are reflected immediately without reinstalling. This is especially helpful for iterative development during plugin or tool design.
Uninstalling Packages
Just type the name of the package and click Uninstall. It works for both PyPI and local packages.
Why It Matters
Managing packages from within your modeling environment reduces friction. You stay in the flow of your research, manage dependencies visually, and avoid context-switching that can break your concentration. With SAMSON, molecular modelers can script and build with the full flexibility of Python, while integrating essential tools like NumPy, PyTorch, BioPython, Scikit-learn, and more directly into their simulations.
Whether you’re doing AI-assisted structural biology, tweaking visualizations, or developing your own extensions, managing Python packages inside SAMSON helps keep things tidy and time-efficient.
To learn more about installing and managing packages in SAMSON, visit the official documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.