Generating Python scripts for molecular modeling tasks can be time-consuming, especially when switching between documentation, scripting environments, and the visual platform. If you’ve ever wished you could just describe what you want in plain English and get a working script instantly, SAMSON AI might save you a lot of time.
SAMSON AI, available in the Professional plan of the SAMSON platform, includes a powerful /script command that lets you generate Python code by simply typing what you want to do. Instead of writing boilerplate code, you can focus on designing, analyzing, and understanding molecular systems.
Common frustration: scripting friction
Many researchers and students in molecular design regularly write small Python scripts to automate repetitive tasks or run analyses. But even simple actions—like selecting atoms or translating structures—can require multiple steps: checking function names, learning the API, debugging syntax, etc.
With SAMSON AI’s /script command, you type a description of your intent, and the assistant writes the corresponding Python code that uses the SAMSON Python API.
How it works
To generate a script, open the SAMSON AI Assistant (via Interface > Assistant or the Ctrl+0 shortcut on Windows/Linux or Cmd+0 on Mac), and type a prompt prefixed by /script.
Some examples:
/script select all atoms and translate them in the z direction by 1 angstrom./script create a GUI that lets me enter a distance in angstrom, with a 'Move' button./script compute the gyration radius of the receptor.
In each case, SAMSON AI will return Python code tailored to SAMSON’s scripting environment. You can even combine generated scripts with standard scientific Python libraries, such as NumPy or scikit-learn, for advanced processing or machine learning tasks.
What can you generate?
Here are a few ideas to get you started:
- Automate repetitive tasks like residue selection or geometry analysis.
- Create custom graphical user interfaces for your workflows.
- Build script templates for your students or lab members.
- Combine molecular data with external datasets using Pandas.
A simple boost for teaching and learning
Because the assistant explains the code it’s generating, students new to molecular scripting can learn Python in context. It also helps when experimenting with new APIs: you don’t need to memorize everything—just ask for examples.
Limitations to be aware of
While SAMSON AI provides functional scripts in most cases, it’s still worth reviewing the generated code carefully. Results may vary depending on the prompt clarity. And some advanced features might still require manual adjustment or deeper API knowledge.
Where to go from here
If you’re tired of searching through documentation or starting every script from scratch, /script can make your life easier. It lowers the barrier to automating and accelerating your molecular modeling workflows, while giving you space to focus on science.
To learn more about scripting and other SAMSON AI features, visit the SAMSON AI documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON here.