Installing and Editing Local Python Packages Inside SAMSON

Many molecular modelers and computational chemists have their own Python packages—for custom simulations, analysis pipelines, or even neural networks for property prediction. But using them often means jumping between development environments, terminal sessions, and structured molecule viewers. What if everything could happen in one place?

In SAMSON, the integrative molecular design platform, you can develop, install, and test local Python packages—within the same environment where you model molecules. Here’s how it works, and why it can save you time.

Installing Local Python Packages in SAMSON

Working with a local Python package in SAMSON involves just a few steps. Whatever your package does—analyzing trajectories, calculating descriptors, or controlling visualization—you can install it inside SAMSON using the built-in Python package manager.

Open the Python Console via Interface > Python Console, then choose Edit > Manage packages…. SAMSON’s intuitive GUI will offer a clear window where you can manage packages directly:

To install a local package:

• Enter the path to the local package directory.
• Ensure the package contains a valid setup.py file.
• Click Install.

Editable Installation: Develop and Test Simultaneously

One of the most useful features is the ability to install a package in editable mode (like pip install -e .), so any changes you make to your source code are instantly reflected in SAMSON—no need to reinstall after every tweak.

This is particularly helpful when you’re iteratively developing code and want to keep testing with molecular models. Whether you’re debugging an energy calculation or modifying a graph-based molecule classifier, every change is there instantly.

To install in editable/develop mode, just check the corresponding option in the package manager window before clicking Install.

Attention macOS users:

Editable packages might need a manual workaround on some macOS systems. If the package doesn’t load automatically on the next launch, try installing in non-editable mode or double-check sys.path.

Why This Matters

If your modeling workflow currently involves switching between Jupyter notebooks, scripting consoles, and a molecular viewer, this approach can centralize everything. Package development, simulation scripting, results visualization—all happen in SAMSON. It minimizes interruption and maximizes productivity, particularly during prototyping or teaching.

By making local package installation and editing seamless, SAMSON empowers researchers and educators to not just use tools—but to build and iterate on them, all within a molecular design platform.

To learn more, visit the SAMSON Scripting Documentation.

SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.