Many researchers and molecular modelers benefit from integrating custom Python scripts into their molecular workflows. Whether you’re adding machine learning models, working with bioinformatics libraries, or just need a statistical package, the ability to easily install and manage Python packages matters. But managing environments outside your main platform can be tedious and error-prone, especially when transitioning between systems or collaborating with others. This is where SAMSON’s integrated Python Package Manager comes in.
Why Managing Python Packages Inside SAMSON Helps
If you’ve ever tried to set up a molecular modeling workflow that uses a mix of tools—NumPy for math, Matplotlib for graphics, Biopython for bioinformatics—you know that managing dependencies can quickly become distracting. You might switch between terminals, IDEs, and file explorers just to get one script to run. Inside SAMSON, this friction is reduced. You can search, install, upgrade, and remove packages directly from within the SAMSON interface.
Getting Started: Opening the Package Manager
To manage Python packages, simply open the Python Console via Interface > Python Console, and then go to Edit > Manage packages.... This opens the built-in Python Package Manager—a graphical interface that gives you full control over your Python environment without leaving SAMSON.
Installing Packages from PyPI
The Package Manager supports installation from PyPI. You can enter a package name directly and click Install. Familiar with pip? You can provide full pip-style arguments like:
scipy==1.9.0to install a specific versionrdkit --upgradeto get the latest versionnumpy matplotlib seabornto install multiple packages at once
Installing Local Python Packages
Need to work with code under development? You can install local packages too. Simply provide a path to a package folder (with a valid setup.py) and click Install.
Tip for developers: check the editable/develop mode box to install in edit mode (equivalent to pip install -e). This allows changes you make in source files to take effect immediately, which is useful during development.
A note for macOS users: editable packages may sometimes not reload properly after a restart. You can workaround this by switching to non-editable mode or adding the path to sys.path.
Uninstalling Packages
To remove a package—whether locally installed or from PyPI—just provide its name and click Uninstall. The interface updates the list of installed packages accordingly, helping you keep your working environment clean.
A Seamless Integration
By embedding package management directly into the SAMSON interface, you eliminate the need for external environment management tools. This keeps your modeling, scripting, and data analysis unified in one place—whether you’re adding stats libraries or full-fledged apps for molecular simulations.
Learn more about SAMSON’s scripting capabilities and Python integration in the full documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here.