One common pain point for molecular modelers is managing the many files associated with a project—molecular structures, Python scripts, input/output files, figures, research papers, and other resources. These files often get scattered across folders, complicating versioning, backups, collaboration, and reproducibility.
SAMSON, the integrative platform for molecular modeling and design, provides a helpful solution: Universal File Embedding. This feature allows users to embed any files or folders directly within a molecular document. The result? A truly self-contained document that travels with everything you need.
📦 What Is Universal File Embedding?
In SAMSON, a document is the central container for all molecular data, including atoms, bonds, models, and simulations. With Universal File Embedding, this container can now include:
- Python scripts or entire Python-based apps
- Input/output files for simulations
- PDFs of research papers
- Figures, datasets, and more
This approach ensures everything is stored in one place and can be shared, opened, and reproduced fully on another computer—even when offline.
📁 How to Embed Files and Folders
Embedding is straightforward. There are two ways to do it:
- Drag & Drop: Simply drag a file or folder into the SAMSON interface. SAMSON will prompt you to choose whether to embed it.
- Menu Selection: Use
Home > Embed filesorHome > Embed foldersfrom the main menu.
Once embedded, files and directories are listed in the internal structure of the document. This means the next time someone opens the document—even on a different system—all the embedded content is still there and ready to use.
💡 A Real-World Use Case
Imagine you’re building a molecular model and writing a Python script that performs a custom analysis. You also generate a plot and save it as an image file. Perhaps you’re referencing a recent paper, and you want to include the PDF for convenience.
With SAMSON, you can embed all of these directly within the project document. When you’re ready to share your model with your collaborator, one file is all you need to send. There’s no need to worry about missing files or broken paths.
🔁 Working Across Systems
Because documents with embedded data are self-contained, they’re perfect for collaboration. You can share them through SAMSON Connect, external drives, or any storage solution. All collaborators can retrieve the full molecular project exactly as it was, with no links to chase or dependencies to manually install.
📂 Organize and Document Your Work
Embedding also encourages better project documentation. You can include:
- README files with descriptions of what the project includes
- Scripts used for preprocessing or postprocessing
- Parameter files for simulations
When you later revisit a project—or hand it off to someone else—it becomes easier to understand and replicate.
Learn more about file embedding and other document features in SAMSON on the official documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.