For many molecular modelers, scripting is both a blessing and a hurdle. Python unleashes the full potential of advanced modeling workflows, but coding from scratch—especially for simple, repetitive tasks—can slow down everyday work. Wouldn’t it be great to just describe what you want and have the script written for you?
The /script command in SAMSON AI offers exactly that capability—bridging natural language and Python scripting through the power of GPT-5. Instead of spending time researching function calls and writing boilerplate code for molecules, selections, or visualizations, you can now describe your intent in plain English, and SAMSON AI will suggest a complete Python script using the SAMSON API.
Common Pain Point: Writing Repetitive Scripts
Suppose you often perform tasks such as shifting atoms, computing the gyration radius, or building minimal interfaces for user input. Each time, you have to write or reuse code—while being careful not to make small syntax errors that can disrupt your workflow.
With /script, repetitive scripts like these can be created automatically:
/script select all atoms and translate them in the z direction by 1 angstrom./script compute the gyration radius of the receptor./script create a GUI that lets me enter a distance in angstrom, with a 'Move' button.
These generated scripts follow SAMSON’s Python API structure, making it easy to run, customize, or extend them later on. You can quickly build up a personal library of one-click tools that are tailored for your research needs—all originating from simple natural sentences.
Combining with Other Modules
Because these AI-generated scripts are based on Python, it’s easy to plug in other powerful libraries. Imagine combining molecular modeling with trajectory analysis, machine learning, or visualization libraries like Matplotlib or Plotly without having to spend time hand-coding the basics. You can use /script as a starting point to produce Python code blocks and connect them with your broader pipeline.
How to Access
You can open SAMSON AI via Interface > Assistant or using the keyboard shortcut Ctrl + 0 on Windows and Linux or Cmd + 0 on macOS. Once open, type /script followed by your instruction, and the AI will return a script ready to execute or tune.
Whether you’re a scripting pro looking to speed up writing templates, or you’re just beginning to explore automated modeling workflows, this command can save time and reduce friction.
To learn more about this feature and other commands in SAMSON AI, visit the official documentation page.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.