For molecular modelers, scripting with Python opens the door to automation, customization, and integration with other tools. But juggling between software environments often creates unnecessary friction. If you want to edit and run your Python scripts in the same environment where you design molecular systems, SAMSON might simplify your life.
SAMSON is a molecular design platform that supports Python scripting directly through its built-in Code Editor. Whether you’re creating analysis tools, setting up workflows, or modifying simulation parameters, working with Python inside SAMSON can help you streamline your process.
đź“‚ Supported File Format: PY
SAMSON supports Python scripts through the standard .py file format. It allows you to:
- Read Python scripts directly into the Code Editor
- Write new scripts or save modifications
- Execute scripts natively through the integrated scripting interface
This means you don’t have to leave SAMSON to validate or iterate on a script—everything happens within the same platform.
🛠️ Typical Use Cases
- Custom visualization: Write scripts to automate labeling, coloring, or geometry updates for specific types of molecules.
- Batch operations: Process multiple structures, convert formats, or apply filters in a loop—directly in SAMSON.
- Interfacing with other tools: Use Python to load data from external sources, modify it within SAMSON, and save results for further use.
đź“‹ Simple Example
If you’re new to scripting in SAMSON, here’s a minimal example that selects all water molecules:
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# Sample Python script in SAMSON import samson as sn system = sn.getActiveDocument() for node in system.getNodes(): if node.getName() == "H2O": node.select() |
Run this script in the Code Editor, and it will highlight all water molecules in your document. You can modify this logic to target any specific atom type, residue, or feature.
Using Python directly in SAMSON saves time you might otherwise spend exporting data to another editor or debugging across multiple environments. Having a single space where you import molecular models, develop code, and visualize results helps reduce context switching and make your workflow smoother.
🚀 Starting with Scripting
To learn how to write and run Python in SAMSON, browse the dedicated Python Scripting documentation. It includes syntax guidance, API references, and tips for integration across SAMSON Extensions.
For more details on supported formats for Python and other file types, refer to the full documentation on supported formats.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.