In molecular modeling, a small task can become a large source of friction when you have to repeat it across structures, documents, or analysis sessions. Repeating the same sequence by hand is not only tedious; it also makes it easier to miss a step or do the same work differently next time.
One way to address this is to separate your work into two questions: Can I automate this task inside SAMSON? And, if so, how will I make the workflow easy to reuse? SAMSON’s scripting resources are the place to start for Python automation, while its extension resources cover adding capabilities and exploring extension development.
Start with the task you repeat
Before writing a script, describe the repeated work in plain language. For example: what do you do first, what information do you use, and what result do you need at the end? Keep the description focused on the steps you actually repeat. This helps distinguish a suitable automation task from a larger modeling question that may need a different approach.
Then decide whether the immediate goal is automation or added functionality. If you want to automate work inside SAMSON, begin with Scripting. If you want to install extensions or understand the SDK and extension distribution path, go to Extending SAMSON. You do not need to follow both tracks when only one matches your goal.
Think beyond a one-off script
A script is most useful when you can understand and reuse it later. A practical habit is to write down its purpose, the inputs it expects, and the result it is intended to produce. Keep the workflow’s assumptions visible, especially when it depends on particular data or packages. That context can save time when you return to the work after a break or share it with a collaborator.
SAMSON’s documentation describes an integrated Python environment, package management, running scripts, and embedding scripts or apps in documents. These are useful parts of a broader reproducibility strategy: instead of treating automation as an isolated code fragment, consider how the script and its context will travel with the molecular design work. If another person needs to understand or rerun the workflow, an embedded script or app may be a relevant option to explore.
There is no need to automate everything at once. Start with one repeated, well-defined task. Check that the result matches what you expect, and make the purpose and assumptions clear before relying on it for repeated work. The documentation is the place to learn the available SAMSON scripting and package-management workflow; this article does not assume particular commands or APIs.
Know when an extension is the better path
Not every need is a scripting problem. If your goal is to add capabilities to SAMSON, manage extensions, or explore how extensions are developed and distributed, follow the extension track instead. Keeping this distinction in mind helps you choose a useful next step without spending time on a workflow that does not match your goal.
In short: use scripting as your starting point for repetitive Python work and document-embedded workflows; use the extension path when your goal is to add or develop capabilities. When your scripted modeling leads into path generation or analysis pipelines, the Simulate and analyze guide may be a relevant next stop. For sharing scripted documents or collaborating around them, see Share and collaborate.
For the full overview and links to both tracks, visit Automate and extend.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.