As molecular modelers, we frequently compile complex projects involving not only molecular structures but also simulation scripts, datasets, papers, and custom tools. When it’s time to share our work with collaborators or transfer it to another machine, juggling all these components can quickly become a problem. Missing files, broken paths, and inconsistent versions can make reproducibility a challenge.
SAMSON, the integrative platform for molecular design, offers a practical solution: Universal File Embedding. This feature lets you embed any file or folder directly inside your SAMSON document, making your entire project self-contained. Whether you’re moving your project between computers or collaborating with others, all necessary elements travel with the document, avoiding headaches and delays.
Drag and Drop Simplicity
Embedding files and folders in your project is straightforward. Simply drag-and-drop one or more files or folders into the SAMSON interface. You’ll be asked whether you’d like to embed them. If you want even more control, use:
- Home > Embed files
- Home > Embed folders
You can embed a range of useful items — Python scripts, machine learning models, CSV datasets, figures, PDFs, or even entire app folders. This empowers you to bundle everything that’s part of your molecular workflow or publication package in one place.
What Happens Under the Hood?
Once embedded, these files are stored within the SAMSON Document. There’s no need to manage separate folders or make sure external dependencies are transferred correctly. When you save the document, everything stays in it — much like a zip archive, but visible and accessible natively in SAMSON.
Why It Matters
This becomes especially useful when you’re:
- Publishing supplementary material alongside a molecular design
- Sharing complex simulation setups with remote collaborators
- Running workflows on a cluster or external machine
- Teaching and packaging educational content
By making files integral to the document, it ensures the recipient receives exactly what you intended, with no broken links or missing assets.
Example: Embedding a Script
Say you’re developing a Python script for conformational analysis. Instead of placing it in a shared drive or emailing it separately, just drag it into SAMSON, embed it, and save the document. It’s now preserved alongside your molecular data.
This approach is also compatible with embedding entire projects or codebases, as development scales.
Conclusion
Universal File Embedding in SAMSON is a simple yet effective way to keep your molecular modeling projects organized, portable, and collaborative. It reduces friction, supports reproducibility, and brings peace of mind when working across systems or with teams.
Learn more about embedding and managing files in SAMSON here: https://documentation.samson-connect.net/users/latest/loading-molecules/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.