Repetitive work is easy to underestimate. A sequence of small actions—setting up a task, running the same operations, and checking the result—may feel manageable once. Repeating it across many molecular models, or asking a colleague to reproduce it later, is where the effort and the chance of inconsistency grow.
SAMSON’s automation and extension learning path offers two ways to address this: use Python for repeatable work inside SAMSON, or manage and develop extensions when you need additional capabilities. The first practical step is deciding which kind of problem you are trying to solve.
First, separate repetition from missing capability
If the task is possible with capabilities you already have, but requires the same sequence of actions again and again, start with Scripting. The scripting documentation covers the integrated Python environment, managing packages, running scripts, and embedding scripts or apps in documents.
If your problem is that you need to add capabilities—or you want to understand how SAMSON extensions are installed, developed, or distributed—go to Extending SAMSON. These are related paths, but they answer different questions: “How can I repeat this workflow more easily?” versus “How can I add or manage functionality?”
Turn a recurring task into a clear plan
Before writing a script, describe the task in ordinary language. What do you start with? Which actions do you repeat? What result do you need at the end? This short outline can reveal whether the work is genuinely repetitive or whether the steps change from model to model.
- Identify the repeatable part. Separate the steps you perform every time from the decisions that depend on the specific system or question.
- Choose the right learning path. For automation, reproducibility, or document-embedded Python workflows, begin with Scripting. For installing or developing new capabilities, begin with Extending SAMSON.
- Keep the workflow understandable. Give the script or embedded workflow a clear purpose, and make its expected inputs and outputs easy for another person to recognize.
- Check the result. Compare the output with what you intended to produce. Automation can reduce repeated manual work, but it does not replace scientific judgment or result checking.
- Decide how it should be shared. If the workflow should travel with a document, explore embedding scripts or apps in documents. If the goal is broader functionality, explore the extension path instead.
This is also a useful way to think about reproducibility. A repeatable workflow is more than a saved sequence of actions: someone else needs to understand what it is for and what to expect from it. SAMSON’s documentation points to document-embedded scripts and apps as one route for packaging a scripted workflow, while the extension pathway is intended for adding or distributing capabilities.
Follow only the path you need
You do not have to learn both subjects at once. If you are not writing Python or embedding scripts, you can skip Scripting for now. If built-in capabilities are sufficient and you are not managing extensions, you can skip Extending SAMSON. This keeps the learning effort aligned with the immediate problem.
For a modeling or analysis task that you want to automate, continue from scripting toward Simulate and analyze. If you want to distribute scripted documents or work with others, see Share and collaborate. For deeper references and troubleshooting, use Reference and help.
To choose your starting point and see the recommended reading order, visit the Automate and extend documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.