Writing Python scripts for molecular modeling can unlock advanced automation, data processing, and custom workflows in SAMSON, but for many users, the idea of starting from scratch with code is daunting. If you’ve ever felt slowed down by scripting—even though you knew it could save you time—SAMSON AI might be just what you need.
SAMSON AI is more than a chatbot—it’s a command-aware intelligent assistant integrated into the SAMSON molecular design platform. One of its standout features is the /script command, which lets you generate Python scripts using plain English instructions. Whether you’re new to scripting or want to draft more complex functions faster, this streamlines your workflow.
Why molecular modelers struggle with scripting
Many computational chemists and structural biologists face a similar pain: they know that scripting can automate tedious tasks—like selecting atoms, calculating properties, or setting up trajectories—but they either:
- Don’t have time to write the code manually
- Are unsure about specific API syntax
- Want to prototype something quickly but don’t want to leave the modeling environment
If that sounds familiar, you’re definitely not alone.
Natural language in, optimized script out
The /script command in SAMSON AI addresses these pain points by turning your natural language request into ready-to-run Python code based on the SAMSON API.
Here are some examples of what you can type in the Assistant input field:
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/script select all atoms and translate them in the z direction by 1 angstrom. |
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/script create a GUI that lets me enter a distance in angstrom, with a 'Move' button. |
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/script compute the gyration radius of the receptor. |
SAMSON AI will then generate and display structured Python code that’s tailored specifically to your request. You can review it, modify it if needed, save it, or run it directly inside SAMSON.
Combining the SAMSON API with other Python modules
Advanced users can also enhance the generated scripts by integrating them with third-party Python libraries. For instance, you could combine SAMSON API calls with NumPy for numerical analysis, matplotlib for plotting, or even machine learning toolkits for model prediction. This makes SAMSON a powerful hub not only for modeling but for data science workflows as well.
When to use SAMSON AI scripting
Here are a few situations where the scripting command can be particularly useful:
- Quick calculations (e.g. distance matrices, radii, angles)
- Batch operations over a set of molecules
- Building and refining analysis pipelines
- Prototyping user interaction via GUIs
Try it with zero setup
You don’t need to set up a development environment. Just open SAMSON AI via Interface > Assistant or use Ctrl+0 on Windows/Linux or Cmd+0 on Mac. Then type /script followed by your request and see the result instantly.
This can be a helpful tool even if you’re already comfortable writing code. Think of it as a way to:
- Speed up the first draft of a script
- Learn the correct usage of SAMSON’s API
- Explore ideas quickly
Whether you’re automating repetitive tasks or exploring complex molecular systems with code, the /script command is a practical companion.
To learn more about scripting with SAMSON AI, visit the full documentation page: https://documentation.samson-connect.net/users/latest/samson-ai/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.