If you find yourself repeating the same sequence of actions while preparing or analyzing molecular models, the difficult part is often not any single step. It is remembering every step, repeating it consistently, and making the workflow understandable to someone else—including future you.
SAMSON’s scripting and extension pathways offer two different ways to reduce that friction. The useful first question is: Do I want to automate a task, or add a capability? The answer helps you choose where to begin, without taking on more complexity than your goal requires.
When scripting is the right starting point
Start with Scripting when your goal is to automate work inside SAMSON, run Python scripts, manage packages, or embed a script or app in a document. This is the natural path for repeated procedures and scripted workflows.
Before writing a script, describe the task in plain language. What do you repeatedly do? Which parts are the same each time, and which depend on the model or question? A short outline can reveal whether the task is a good candidate for automation and gives you a simple way to check whether the script covers the intended workflow.
It can also help to separate the workflow into three parts:
- Inputs: What information or starting material does the task depend on?
- Actions: Which repeated operations would you like Python to handle?
- Outputs: What result or record do you need at the end?
This is a planning aid, not a prescribed SAMSON scripting format. It helps keep a script focused and makes it easier to explain what it is intended to do. If the workflow is meant to be reused, consider whether embedding the script or an app in a document would make it easier to keep the scripted work alongside the relevant material.
When extensions are the better fit
Not every need is a repeated sequence of actions. If you want to install additional capabilities, or you are exploring how to develop and distribute them, go to Extending SAMSON. That topic covers extension management and the path involving the Software Development Kit (SDK).
A practical distinction is: use the scripting track when you want to automate a workflow; use the extension track when your goal is to add or manage capabilities. These tracks can complement one another, but you do not need to study both immediately. If your task is only to automate, begin with scripting. If built-in capabilities already meet your needs and you are not managing extensions, you can postpone the extension material.
A small plan for getting started
- Choose one repetitive task. Keep the first goal narrow enough that you can tell whether automation helped.
- Write down the current sequence. Note the decisions and repeated actions, not just the hoped-for result.
- Follow the scripting guide. Use it to explore SAMSON’s integrated Python environment, package management, and script execution.
- Decide how the work should be reused. If others—or you at a later date—need the scripted workflow with its context, explore embedding scripts or apps in documents.
- Expand only when needed. If your goal changes from automating a task to installing or developing capabilities, continue to the extension guide.
This approach keeps the learning path tied to a real modeling need. It also makes it easier to share a useful, clearly scoped workflow instead of a collection of unexplained steps.
For related next steps, explore Simulate and analyze for scripted modeling or analysis pipelines, or Share and collaborate if you want to distribute scripted documents. To explore the complete automation and extension path, read the original documentation page.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.