A molecular project can be difficult to hand off even when the model itself is easy to share. The analysis script may live in a separate folder, input files may be scattered across a computer, and a colleague may not know which steps to run. That gap can make a workflow hard to repeat—or even hard to understand later.
SAMSON documents can hold more than molecular models: they can also embed Python scripts, folders, and other files. That creates a practical way to keep a model and the materials needed to work with it together. The document can then be shared with colleagues or students rather than sending a collection of files with uncertain relationships.
Build a shareable project in small steps
- Prepare the workflow materials. Gather the Python script and the files it needs, such as data or supporting documents. If the project uses a Python package, make a note of its name and version requirements. SAMSON documents can embed files and folders, but embedding a project folder does not, by itself, install its Python packages on another computer.
- Embed the files. Drag files or folders into SAMSON and choose to embed them when prompted. Alternatively, use Home > Embed files or Home > Embed folders. The embedded materials are stored within the document, helping keep the project together when the document is transferred.
- Make the entry point easy to find. Give the main script a clear name and include a short README or notes file describing its purpose, expected inputs, and the order of operations. You can embed these supporting files alongside the script. A concise note is especially useful when someone opens the document months later.
- Open and run the script. Double-click an embedded Python script to open it in the Code Editor. Run a script using the Run control or the Run menu, or execute code in the integrated Python Console.
Make the handoff clearer
SAMSON’s integrated Python environment includes the SAMSON Python API, a Jupyter Qt Console, and a Code Editor based on Monaco Editor. The console is useful for trying a short operation interactively; the editor is better suited to a script you want to keep and share. Both provide access to the SAMSON Python API, so the same workflow can be developed interactively and then saved as a script.
If the script needs packages beyond the environment’s installed packages, use Python Console > Edit > Manage packages… to open the Package Manager. It can install packages from PyPI by name, including version specifications such as foo==1.2.0, and it can install a valid local Python package from a path. For a shared project, record any required package names and versions in an embedded note. That gives the next person a concrete starting point instead of leaving them to guess why an import fails.
It can also help to record what the script expects and what it changes: for example, the relevant input file, the command or analysis being performed, and any settings that matter to interpreting the result. This is not a substitute for checking the workflow on the recipient’s system, but it makes the handoff more transparent and easier to troubleshoot.
Once the document is ready, share it through email, GitHub, or SAMSON Connect Documents. A recipient can open the document, inspect the embedded materials, and open the script in the Code Editor. This approach is useful for collaborative projects, teaching exercises, and research materials where the script should remain close to the molecular model it operates on.
For details about the Python Console, package management, code templates, and embedding files, see the SAMSON scripting documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.