When designing molecular models, especially with large systems or during polymer and conformational studies, you may want to quickly isolate and inspect paths that meet specific structural criteria. One common need is identifying paths based on the number of atoms they contain. Whether you are confirming structural hypotheses or simply filtering for meaningful molecular segments, manually searching through your model is time-consuming and error-prone.
Enter the numberOfAtoms attribute in the Node Specification Language (NSL) of SAMSON. This feature helps streamline your workflow by programmatically selecting paths that meet your atom count conditions—in seconds. Here’s how it works.
What is the p.nat Attribute?
Each molecular path in SAMSON can be examined with a variety of attributes. When you’re working specifically with paths (as opposed to atoms or residues), you can make use of the path attribute space. The p.nat attribute (short for path.numberOfAtoms) is a powerful way to filter paths based on how many atoms they include.
Why It Matters
Suppose you’re analyzing a conformational ensemble or working with hierarchical molecular structures that involve hundreds or thousands of paths. If you’re looking for paths that, for example, represent fragments of a molecule above or below a certain threshold in size, p.nat will save you a significant amount of time.
Real-World Examples
Let’s explore a few practical uses of this attribute, assuming you are in an environment where NSL expressions can be entered in SAMSON’s selection interface.
p.nat > 100: Selects all paths containing more than 100 atoms.p.nat 100:200: Selects paths with an atom count between 100 and 200.
These queries can be combined with other NSL expressions to build even more specific selections. For example, you could combine atom count with selection status or name patterns if needed.
Tips for Use
- Start simple: Try filtering by only one criterion first (e.g.,
p.nat > 150). - Use ranges when you’re not sure about exact values, especially for large dynamic systems.
- Combine with spatial queries or structural metadata to get more nuanced selections.
By leveraging p.nat, you avoid visual scanning and manual selection of paths, reducing both errors and time spent on routine operations. This can be particularly helpful for tasks such as filtering out noisy fragments in a simulation result or preparing input for a follow-up analysis step.
To learn more about path attributes in SAMSON, including selected and selectionFlag, visit the full documentation at https://documentation.samson-connect.net/users/latest/nsl/path/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.