A molecular modeling task rarely happens just once. You may repeat the same preparation steps, run similar analyses across several structures, or need a colleague to follow the same workflow later. Repeating every action manually can take time—and makes it harder to remember exactly what you did.
SAMSON’s automation and extension resources offer two routes for reducing that friction: use Python scripting for repeatable work inside SAMSON, or manage extensions when you need additional capabilities. Choosing the right route first can save you from exploring features that do not address your immediate problem.
Start with the task you repeat
Ask yourself what you want to make easier:
- Repeating a sequence of actions? Begin with Scripting. The documentation describes an integrated Python environment, package management, script execution, and ways to embed scripts or apps in documents.
- Adding capabilities to SAMSON? Go to Extending SAMSON to learn about installing extensions and the SDK and extension-distribution path.
- Doing both? Read the scripting material first, then move on to extensions. That order provides a foundation for automation before you explore how SAMSON can be extended.
Make a workflow easier to repeat
A useful first automation target is a task you already understand and perform more than once. Before writing a script, describe the task in plain language: what do you start with, what actions do you take, and what result do you need? This simple outline helps separate a stable sequence from decisions that require your judgment.
Then consider whether the workflow should live only in your working process or be embedded in a document. The documentation identifies document-embedded scripts and apps as part of the scripting path. That option is worth exploring when the script is closely tied to a document or when you want the scripted workflow to travel with it.
Keep the first version focused. Automate one repeated task rather than trying to capture an entire research process at once. After running it, note which steps still need manual attention. That gives you a practical basis for deciding what to improve next—and helps avoid treating every scientific decision as something that should be automated.
Know when scripting is not the answer
Not every user needs Python or extensions. If your current work relies on built-in capabilities and you are not managing extensions, the extension-development path may be unnecessary. Likewise, if you are not writing Python or embedding scripts, you can skip the scripting material for now.
This distinction matters because “automation” and “adding capabilities” solve different problems. Scripting is the relevant starting point for repeatable actions and scripted workflows. Extension management is the relevant path when your goal is to install or develop additional capabilities. Following the path that matches your need makes the learning process more direct.
Choose your next step
For Python automation or a reproducible scripted workflow, start with Scripting. For installing or developing new capabilities, continue to Extending SAMSON. If your scripted work leads into modeling or analysis, the Simulate and analyze guide is a related next stop; for sharing scripted documents, see Share and collaborate.
For the full learning path, visit the Automate and extend documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.