Reproducibility and automation are essential in molecular modeling, yet many modelers struggle when it comes to managing Python environments. Switching between systems, sharing workflows, or simply setting up dependencies for simulations or AI-based modeling can often lead to frustrating environment errors or version mismatches.
This is where SAMSON’s integrated Python Package Manager can make a real difference. Instead of relying on external terminals or hoping your environment is set up correctly, you can install, update, and remove Python packages directly inside SAMSON. Let’s walk through how this works—and how it simplifies your modeling life.
Built-in pip—No Terminal Required
Whether you’re using packages from PyPI or developing your own custom tools, SAMSON lets you handle everything within a dedicated GUI. Navigate to Python Console > Edit > Manage packages… and you’ll open the Python Package Manager.
From here, you can inspect installed packages, specify versions, and pass arguments just like with pip. For example:
scikit-learn==1.2.0installs a specific version.pandas --upgradeupgrades to the latest.numpy>=1.18.0ensures a minimum version.
This integration ensures that your modeling scripts always have the exact dependencies you need, avoiding surprises when something breaks due to mismatched versions.
Local Development? No Problem.
Working on your own tools or collaborating on private packages? You can install local Python packages using the same GUI. Simply provide the path, and SAMSON installs it as a package.
Even more useful: you can check the editable/develop mode (similar to pip install -e) to link the package directly to its source directory. Any changes made to your source code are immediately reflected in SAMSON—perfect for iterative development!
Note: For stable usage, especially on macOS, revert to non-editable installation if you hit compatibility issues.
No More Cleaning Scripts Between Machines
Because SAMSON supports Universal File Embedding, you can embed entire Python apps—including the scripts and supporting modules—inside SAMSON documents. This means your scripts and their dependencies travel with your project. Share workflows with colleagues or students as a single file—everything included.
This self-contained approach greatly reduces the effort required to reproduce experiments or prepare interactive teaching materials. Your teammates get exactly what you developed—no additional setup required.
Managing and running Python packages is often one of the hidden difficulties that slow down productive workflows. SAMSON makes this process intuitive and accessible for both experienced developers and newcomers in computational molecular design.
To explore more scripting features, visit the official SAMSON scripting documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here.