Easily Read, Write, and Run Python Scripts Inside SAMSON

Python scripting has become essential for many in the scientific computing world—especially molecular modelers who often need to automate tasks, analyze data, or build custom tools. If you use SAMSON, the integrative molecular design platform, the good news is: Python scripts are fully supported and natively integrated.

Whether you’re writing a quick script to parse data, customizing an analysis method, or prototyping a new visualization, SAMSON lets you go from idea to implementation—all without leaving the application.

Why Python in SAMSON?

In many workflows, scientists write Python scripts externally and then bring the output into a modeling tool. This context-switching can slow things down and lead to errors. SAMSON removes this friction by embedding Python support directly in the interface.

In practical terms, this means you can:

  • Open and edit .py files within SAMSON itself
  • Run scripts in the context of your current molecular model or simulation
  • Embed Python scripts inside SAMSON Documents, preserving the full context of your work

This setup is particularly useful for teaching, collaboration, or long-term projects where keeping code and data together creates clarity.

What Is Supported?

You can both read, save, and execute Python files in SAMSON. Python files support the standard .py extension. You’ll do all of this directly in SAMSON’s Code Editor.

Here’s a simple example: suppose you want to compute the center of mass of a molecule and color atoms by distance from the center. You could write and run that script in SAMSON, and immediately see the result applied to the active structure.

Moreover, if you’re sharing your SAMSON Document, your embedded script goes along with it. No extra export, no chasing someone for the external code they used. Everything travels together.

When and Why You Might Use This

Here are a few example situations where Python scripting in SAMSON is particularly handy:

  • Processing data from a molecular dynamics simulation automatically
  • Batch-modifying large sets of molecules with custom logic
  • Quick prototyping of analysis tools before developing full extensions
  • Teaching Python scripting for molecular modeling in classroom settings

Writing scripts in SAMSON doesn’t require setup outside the platform—it’s there when you install SAMSON. All you need is your modeling project and your Python ideas.

How to Get Started

To get started with Python scripting in SAMSON:

  1. Open a SAMSON Document with molecular structures or simulations.
  2. Go to the Code Editor (found in the SAMSON interface settings).
  3. Create or open a .py file.
  4. Edit and run your code with immediate feedback on results.
  5. Embed the script in the SAMSON Document to store or share it alongside your work.

If you’ve used Python scripting in other tools before, the integration in SAMSON feels natural. If you’re new to scripting, having a consistent and visual feedback loop can make the learning curve much less steep.

Ready to explore? The Python Scripting in SAMSON documentation provides examples and detailed guides to help you move forward.

To learn more about supported formats and capabilities in SAMSON, visit the official documentation page.

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

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