Installing Python Packages in SAMSON: What You Need to Know

Integrative molecular modeling often benefits significantly from using Python packages—whether it’s for data science, simulation, machine learning, or visualization. But managing packages in scientific platforms can often be a frustrating task, especially when setting up environments or dealing with dependencies. If you’ve ever wished for a smoother way to incorporate Python’s power directly into your molecular modeling workflow, this post is for you.

SAMSON, the integrative platform for molecular design, provides built-in tools that help you manage Python packages directly within its interface. From accessing pip functionality to managing local packages, this integrated approach streamlines your workflow so you can stay focused on science—not setup.

Accessing the Package Manager

To begin, open the Python Console from Interface > Python Console, and then go to Edit > Manage packages.... This will bring up SAMSON’s Python Package Manager.

Manage packages...

This interface provides a clear list of installed Python packages and their respective versions. From here, you can easily install or uninstall packages as needed.

Installing Packages from PyPI

If the package you need is available on PyPI, you’re in luck — just type the package name, and click Install. SAMSON uses pip in the backend, so you can also:

  • Install specific versions (e.g., numpy==1.23.5).
  • Set version constraints (e.g., matplotlib>=3.0.0).
  • Use pip flags (e.g., pandas --upgrade).

Package Manager: install a Python package

Installing Local Packages

Need to work from a local package or your own Python project? That’s handled just as easily. Simply provide the path and click Install. You can also use the editable/develop mode, which functions like pip install -e, so any changes you make to the local source files are automatically recognized.

Package Manager: install a local Python package

Note: If you’re not actively modifying the package against its source, it’s best not to use editable mode to avoid unnecessary issues — especially on macOS, where editable installations might fail to load after restart.

Uninstalling Packages

Cleaning things up is just as quick. Type the package name into the manager’s interface and hit Uninstall. Whether the package was from PyPI or installed locally, the interface takes care of the rest.

Why This Matters

In many platforms, integrating external scripts and packages means managing separate virtual environments or fiddling with terminal commands. SAMSON makes it easy: the whole process is done through the GUI, integrated directly into the platform used for molecular modeling, simulation, and analysis.

This is particularly helpful for molecular modelers integrating machine learning pipelines, custom force fields, or advanced data visualization tools. Whether you’re a professor setting up interactive student notebooks, or a researcher developing a custom set of tools for molecular docking analysis, streamlined package management saves time and hassle.

To learn more about scripting capabilities in SAMSON: https://documentation.samson-connect.net/users/latest/scripting/

SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here.

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