Turning a SMILES string into a reliable 3D molecular structure can often feel more complicated than it needs to be. If you frequently work with virtual screening, molecular docking, or QSAR modeling, you’ve likely spent too much time juggling between scripts, file formats, and errors in structure generation. This is a common pain point in cheminformatics workflows. Fortunately, SAMSON’s SMILES Manager offers a simpler way.
Within SAMSON, the RDKit-based SMILES Manager extension makes it straightforward to convert one or several SMILES strings into 3D molecular models in just a few clicks.
Importing SMILES
You can import SMILES from standard .smi or .txt files. The most typical format includes the SMILES code followed by a molecule name:
|
1 2 |
COc1cc(CNC(CCCCC=CC(C)C)C(F)(F)F)ccc1O Mol2 |
Once imported, the extension will automatically display the molecule’s 2D depiction, and if the SMILES is invalid, it will flag an issue with a placeholder error image.
Visual Feedback Before You Export
Each molecule in the table shows a live-updated 2D image. You can double-click to open it in a larger viewer, compare multiple molecules at once, and even zoom in or out on complex molecules. The benefit here is clear: you get instant feedback about the chemical structure you’re about to work with, and can catch errors before they propagate into your simulations.
One-Click 3D Generation
To generate a 3D structure, simply select the molecule(s) in your table and go to the Export menu. Click on Selected SMILES string to Document. This will automatically generate the 3D representations and insert them in your active SAMSON document for further analysis or export.
If you prefer, you can also right-click on an individual molecule to generate its 3D structure directly, or use the option in the enlarged view window of the molecule.
Use Cases
- Quickly screen a compound library and build 3D geometries for docking studies.
- Start from a list of SMILES and instantly visualize or validate molecules during virtual screening campaigns.
- Generate input structures for property prediction pipelines or machine learning workflows.
The ability to go from text-based representations of structures to fully rendered 3D molecules and directly include them in your modeling environment can save significant time and reduce potential conversion errors.
Learn More
If you’re interested in improving your structure generation workflow, the SMILES Manager in SAMSON provides a tightly integrated, visual, and easy-to-use solution. You can read the full tutorial here: Using the RDKit SMILES Manager in SAMSON.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.