If you’re working with molecular modeling and already using SAMSON, you might often find yourself juggling different tools just to run or tweak a Python script. But did you know SAMSON has native support for Python scripting?
Whether you’re analyzing simulation data, tuning a system setup, or automating repetitive tasks, being able to run, edit, and save .py files directly inside the molecular design platform saves considerable time and effort. Here’s a quick look at how SAMSON handles Python scripting and where you might benefit the most.
The Challenge: Fragmented Workflows
Molecular modelers frequently move data between simulation software, file editors, and custom scripts. A script you wrote to analyze a trajectory might need to be run separately in a different environment, detached from the visual and modeling context you were working in.
This detachment can interrupt thought flows and cause errors, especially if you’re tweaking input files visually in SAMSON but analyzing results elsewhere. It also makes versions harder to track, particularly when sharing with collaborators.
The Simple Solution in SAMSON
SAMSON supports Python scripts directly inside its platform through integrated file handling. Here’s what that means:
- You can read Python files (i.e.,
.py). - You can write or edit them directly within SAMSON using its Code Editor.
- You can execute Python scripts right within the platform, removing the need to switch contexts.
This seamless workflow allows you to interact with molecular data visually and programmatically at the same time. For example, use models or simulation outputs from SAMSON as inputs to a script, then immediately visualize results—all in one session.
It’s also helpful for educational use. If you’re teaching or learning molecular modeling, being able to write scripts and see the effects directly in the same environment helps reinforce understanding and avoids setup roadblocks.
Common Use Cases
- Automating repetitive geometry generation or analysis tasks.
- Post-processing simulation trajectories.
- Scripting custom views or visual overlays.
- Batch processing structures in a document.
Moreover, SAMSON Documents can embed files (like scripts or data), making file sharing straightforward. You don’t just share a structure, but also the tools and logic you used to analyze it.
What about Dependencies?
Script execution is done within SAMSON’s environment. If you’re using libraries, make sure they are available or supported by your SAMSON setup. For some users, this might include writing SAMSON Extensions that bundle these requirements, which is possible using the extension development framework.
Best Practices
- Use descriptive filenames for your scripts to keep things organized inside your SAMSON Documents.
- Comment your code well—especially helpful when sharing with peers.
- If a script is critical to your project, embed it right into your SAMSON Document.
Being able to script directly where you model, visualize, and simulate helps reduce errors, improves reproducibility, and saves time. The tools are already there—you just need to start using them.
To learn more, visit the official SAMSON documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.