Python scripting has become a go-to tool in computational chemistry and molecular modeling due to its flexibility and ease of use. But managing, editing, and executing scripts while visualizing complex systems can sometimes be less than seamless, especially when moving between code editors and simulation platforms. If you’re a user of SAMSON, this is one area where the platform quietly makes your life easier—and it’s worth exploring how.
One platform, many formats
SAMSON provides out-of-the-box support for Python scripting. It allows users to:
- Open
.pyscripts for inspection and editing, - Save modified or new scripts,
- Execute them directly within the application, eliminating the need to juggle between windows or external script runners.
All of this is handled within SAMSON’s built-in Code Editor, which supports any non-binary text file. This makes it easy to develop custom scripts for tasks such as automation, analysis, and visualization—all within the same platform where the molecular models are managed and explored.
Why this matters
Running a simple Python script to automate selections or calculate geometric parameters might not seem like much, until you find yourself copy-pasting coordinates between tools, importing/exporting data repeatedly, or debugging scripts outside the context they’re supposed to run in.
By allowing users to both view molecules and run scripts on them in one space, SAMSON merges the modeling workflow and the scripting workflow. If you’re a researcher or student developing your own protocols or learning by scripting, this integration saves both time and effort.
Format support at a glance
Python scripts in SAMSON use the standard .py format. They can be read, written, and executed, just like this:
| File type | Description | Read | Write | Execute |
|---|---|---|---|---|
| PY | Python scripts | ✓ | ✓ | ✓ |
You can also embed these scripts directly into SAMSON Documents, alongside molecular data. This makes it easy to share reproducible workflows with collaborators, where you don’t just send data—you send both the data and the logic used to analyze it.
What about dependencies?
SAMSON’s scripting interface is designed to work within its own Python ecosystem. This environment is tailored to tasks in molecular modeling and simulation. If your workflow depends on external Python packages, be sure to consult the official Python scripting documentation for tips on environment configuration and best practices.
Conclusion
For those conducting molecular modeling, integrating Python scripting into the workflow is rarely optional—it’s necessary. SAMSON lowers the barrier to doing this by embedding scripting directly into the platform. Whether you’re automating inspections, custom visualizations, or analyses, SAMSON allows you to do it efficiently and without switching contexts.
To learn more about working with Python scripts and supported file formats in SAMSON, visit the official documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.