Whether you’re analyzing molecular dynamics, building neural network models for protein folding, or integrating your own Python toolkits, managing your Python packages efficiently is essential.
Unfortunately, for many computational scientists, package installation can be frustrating. Switching between environments, worrying about dependencies, and ensuring compatibility within specific platforms often becomes a blocking point in the research workflow.
Good news: SAMSON users have it easier than most. 🧬
SAMSON integrates a built-in Python Package Manager that allows molecular modelers and developers to install, uninstall, and manage Python packages directly from within the SAMSON interface—no need to go back and forth between terminals or juggle conda environments.
Where to Find the Package Manager
To access the package manager, open the Python Console in SAMSON, and go to:
- Edit > Manage packages…
This will bring up the Python Package Manager window from which you can manage all your Python modules.
Installing Packages with One Click
To install any Python module:
- Type the name of the package (just like you’d do in pip)
- Click Install
You can also:
- Specify versions (e.g.,
scikit-learn==1.2) - Use pip flags (e.g.,
matplotlib --upgrade) - Install multiple packages at once by entering a space-separated list
Installing Local Packages
Working with custom code? In SAMSON, you can also install local packages that contain a setup.py file.
- Provide the local folder path in the input field
- Click Install
If you’re developing the package and want your edits to reflect immediately, use the editable/develop mode (equivalent to pip install -e).
Note: On some macOS systems, editable mode may not persist across sessions. If an imported module doesn’t work after restarting SAMSON, try installing it in standard (non-editable) mode instead.
Uninstalling Packages
Need to clean up or troubleshoot a package?
Simply type the package name in the manager and click Uninstall. That works for packages installed either from PyPI or locally.
Why This Matters
SAMSON’s Python environment lowers the barrier between scientific intuition and executable code. By embedding tools like pip directly into its interface, it allows researchers and educators to:
- Quickly prepare environments for simulations and machine learning
- Install visualization or bioinformatics tools without system-level access
- Maintain self-contained sessions for teaching, sharing, or documenting reproducible scientific workflows
If you’re used to fighting with terminals or dealing with broken environments, this streamlined interface can bring welcome simplicity—and perhaps reduce the cognitive load just enough to focus on what really matters: research.
To learn more, check the full documentation on SAMSON scripting.
SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON from samson-connect.net.