When working with molecular systems, especially larger ones, organizing data becomes more than a convenience—it becomes essential. If you’ve ever found yourself clicking folder by folder to locate a model with fewer than 500 atoms, or just the right number of residues, you’re not alone.
In SAMSON, the integrative platform for molecular design, it’s now much easier to search and filter folders based on specific atomic or structural attributes. Thanks to the Node Specification Language (NSL), you can formulate precise queries that match folders containing exactly the kind of data you’re looking for.
Why this matters
Let’s say you’re dealing with a complex assembly of proteins and ligands. You might:
- Want to isolate structures from a dataset that contain fewer than 1000 atoms.
- Need to locate folders with exactly 2–4 molecular chains.
- Be analyzing different structural models and need to filter based on how many exist in each folder.
Going through each folder manually is not scalable when working with large datasets. This is where NSL and attributes like numberOfAtoms (f.nat), numberOfChains (f.nc), or numberOfStructuralGroups (f.nsg) come into play.
The essentials of folder querying
NSL attributes let you easily craft expressions for filtering. If you want folders that contain fewer than 1000 atoms:
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1 |
f.nat < 1000 |
Or folders with the number of atoms between 200 and 400:
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1 |
f.nat 200:400 |
These numeric-based filters work with many attributes specific to folders, including:
f.fc— formal chargef.nC/f.nH/f.nN/f.nO/f.nS— number of specific elements like C, H, N, O, Sf.nm— number of moleculesf.nr— number of residuesf.nsg— number of structural groups
These queries are not just useful for efficiency—they can drive your analysis. For instance, you might want to investigate only those folders where the number of Oxygens is greater than 20:
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1 |
f.nO > 20 |
Or limit your focus to systems with 3 or 4 structural models:
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1 |
f.nsm 3:4 |
Combining attributes
You can also combine filters logically. Looking for folders with fewer than 500 atoms and more than 2 residues?
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1 |
f.nat < 500 and f.nr > 2 |
Or folders that have a formal charge between 1 and 3 and contain at least one sulfur atom?
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1 |
f.fc 1:3 and f.nS > 0 |
A flexible tool for targeted exploration
Being able to search according to structural properties minimizes data overload and helps ensure consistent processing. Whether you’re setting up a simulation, selecting training data, or validating results, defining what you need upfront saves time downstream.
To learn more and explore all the folder attributes available in NSL, visit the official documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.