If you’ve ever worked with complex molecular systems, you probably know the frustration of having to search through large collections of molecular paths looking for the relevant ones. Whether you’re modeling conformations, analyzing structural dynamics, or filtering outputs, being able to quickly pinpoint sets of molecules based on their structural size can significantly accelerate your workflow.
Enter NSL’s path.numberOfAtoms attribute.
In SAMSON—the integrative molecular design platform—you can use the Node Specification Language (NSL) to filter, find, and manipulate different parts of your model. The path attribute space (short name: p) is dedicated to conformation nodes, and one of its most practical attributes is numberOfAtoms (short name: nat).
What’s the Use Case?
Let’s consider a practical pain: You’re simulating a protein-protein interaction and want to visualize only the subsets where a given path contains more than 100 atoms, possibly filtering noise or small by-products. Manually identifying these would be tedious and error-prone.
With NSL, you can simply write:
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p.nat > 100 |
This single line instantly selects only those paths that contain more than 100 atoms. That means no scripting, no manual counting, and no endless zooming in your molecular viewer.
Narrow Down Specific Ranges
Maybe you want a bit more specificity. You are interested in molecules with roughly mid-sized conformational paths to explore their potential behavior. NSL lets you write:
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p.nat 100:200 |
This matches all paths containing between 100 and 200 atoms—an intuitive way to dynamically change what is being analyzed or visualized, based on size constraints.
Combining with Other Attributes
The path attribute space gets even more powerful when combined with other inherited attributes such as name or selected. For example:
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p.nat > 100 and p.n "LigA*" |
This selects all conformational paths starting with the name “LigA” that contain more than 100 atoms. The pattern matching feature ("L*") lets you generalize to groups of aligned names, simplifying how you match large sets of molecules structured under standard naming conventions.
Visual Feedback and Immediate Action
The real-time feedback in SAMSON makes NSL search commands like p.nat especially useful: Select, group, modify or export in just a few clicks. Combining visibility filters and NSL queries allows for an efficient inspection of large molecular systems.
Tip
If you’re wondering whether the selected paths also obey other conditions—like whether they’ve been tagged manually or automatically—use p.selectionFlag to explore those layers too:
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p.nat > 100 and p.sf true |
Conclusion
Understanding path.numberOfAtoms can save molecular modelers hours of manual filtering. With a few keystrokes, you can work more efficiently, focus your visualizations, and prepare cleaner reports and datasets. If you regularly analyze large structures or dynamic systems, this little-known attribute can make a big difference.
To learn more about path attributes in NSL, visit the official documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON from https://www.samson-connect.net.