A molecular modeling task often starts as a sequence of small actions: prepare a model, adjust settings, run an operation, inspect the result, and save the work. Doing that once is manageable. Repeating it across many structures—or trying to reproduce it weeks later—can become tedious and make it harder to remember exactly what was done.
Automation can help, but it is not necessary to turn every task into a software project. A useful first step is to identify which parts of your workflow are repeated and decide whether scripting or an extension is the better fit. SAMSON’s Automate and extend guide brings these paths together.
Start with the repeated task
Before writing code or installing anything, describe the job in plain language. What do you do repeatedly? Which steps need the same decisions each time, and which depend on the molecule or the question you are investigating? This simple inventory helps you focus on the part where repetition is costly, rather than trying to automate an entire process at once.
For example, you might want a more repeatable way to carry out a sequence of actions or to keep a scripted workflow with a document. If the goal is automation inside SAMSON, the documentation recommends starting with Scripting. It covers the integrated Python environment, managing packages, running scripts, and embedding scripts or apps in documents.
Use scripting when the workflow is the problem
A script is a natural place to begin when you want to reduce repeated manual work or make a procedure easier to revisit. Instead of relying only on memory, you can keep the workflow represented in a form that can be inspected and refined. Embedding scripts or apps in documents is also relevant when the workflow should travel with the document, rather than live only in a separate set of personal notes.
Think of the script as part of your scientific record, not merely a shortcut. Give it a clear purpose, keep the steps understandable, and note any choices that a future user would need to know. A workflow is more useful when another person—or you, several months later—can tell what it is intended to do and when it should be used. The documentation’s scripting track is the place to learn about the available environment and how to run and embed scripts in SAMSON.
Choose extensions when you need capabilities
Not every challenge is best solved by scripting. If your goal is to add capabilities to SAMSON, manage extensions, or explore building and distributing an extension, follow the Extending SAMSON track. It introduces extension management and the path toward the Software Development Kit (SDK) and extension development.
A practical distinction is to ask whether you are trying to automate a task you already perform, or add a capability that is not currently part of your setup. The first question points toward scripting; the second may point toward extensions. You do not need to study both tracks at once: the documentation recommends following the one that matches your immediate goal.
Make the next step small
- For automation or document-embedded Python workflows: begin with Scripting.
- For installing or developing capabilities: continue with Extending SAMSON.
- If neither is needed right now: stay with SAMSON’s built-in capabilities and return to these topics when a specific need comes up.
Once a workflow is easier to repeat, its next challenge may be scientific rather than operational. The documentation points to Simulate and analyze for scripted modeling, path generation, or analysis pipelines, and to Share and collaborate for distributing scripted documents or working with others.
To choose the right starting point and see the complete recommended path, read the Automate and extend documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.