Working on complex molecular systems often means juggling numerous structural models, molecules, and folders. As projects grow—especially in materials science, drug discovery, or macromolecular modeling—identifying the right subset of data can become time-consuming and error-prone.
This is where the Node Specification Language (NSL) in SAMSON can be especially helpful. By using folder attributes like numberOfAtoms (f.nat), modelers can quickly filter folders with specific structural characteristics, making their workflows much more efficient.
When You’re Drowning in Structures
Many molecular modelers working in collaborative or long-term projects end up with SAMSON documents containing dozens (or hundreds) of folders, each containing atoms, molecules, or coarse-grained representations.
Imagine you imported several molecule libraries and now need to identify all structures with a number of atoms between 100 and 200—perhaps to select medium-sized ligands, filter by molecular complexity, or simply isolate a subset suitable for a particular algorithm or simulation.
This is where folder-level filters in NSL save time.
Introducing: f.nat (Number of Atoms)
The f.nat attribute lets you filter folders based on how many atoms they contain. This is especially helpful when your folders contain disparate structures and you’re interested only in those meeting specific size criteria.
Examples:
f.nat > 100— matches folders with more than 100 atomsf.nat 100:200— matches folders with atoms between 100 and 200
These expressions are typed directly into the NSL filter bar within SAMSON’s selection or search tools.
Use Case: Pre-selecting Candidates for Binding Simulations 🧪
Say you’re screening a database for potential ligands and only want ligands of a certain size—small enough for binding but large enough to provide diversity. By applying f.nat 150:400, you immediately narrow down to relevant candidates. This allows you to prepare simulations faster and avoid testing unsuitable structures.
Quick Tip: Combine with Other Folder Attributes
f.nat works best when combined with other NSL expressions. For instance, you could find visible folders with a medium-size ligand as follows:
|
1 |
f.v true and f.nat 150:400 |
This further limits your selection to only currently visible folders within the SAMSON interface.
Visual Example
Above: A visual from the SAMSON documentation showing how molecular selections can be filtered and refined, step by step.
Conclusion
When your molecular data grows in size and complexity, navigation becomes a challenge. Filtering folders using attributes like f.nat for number of atoms offers a precise and efficient way to regain clarity and control—accelerating workflows and keeping your focus on the molecules that matter most.
To learn more about folder-level attributes in the Node Specification Language (NSL), visit the full documentation: https://documentation.samson-connect.net/users/latest/nsl/folder/
SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at https://www.samson-connect.net