A molecular project can contain many conformations, and the ones with especially large atom counts may be hard to pick out just by browsing names. If you need to narrow the list by size, SAMSON’s Node Specification Language (NSL) lets you query paths using their number of atoms.
In NSL, the path attribute space matches only conformation nodes. Its short name is p. The attribute for atom count is numberOfAtoms, abbreviated nat, so the compact form of the query is p.nat.
Find paths above a size threshold
For a quick first pass, ask for paths with more than 100 atoms:
path.nat > 100
The short form expresses the same query:
p.nat > 100
This is useful when your immediate question is simply whether a path is larger than a chosen cutoff. The comparison is explicitly “more than 100,” so it does not mean “100 or more.” Change the number to suit the threshold you want to examine.
Focus on a range
Sometimes a cutoff is too broad: you may want to inspect paths whose atom counts fall within a particular interval. Use a colon between the two values:
path.nat 100:200
Or use the short form:
p.nat 100:200
The documentation describes this as matching paths with a number of atoms between 100 and 200. If the exact treatment of the endpoints matters for your task, check the behavior in your SAMSON workflow rather than assuming whether the limits are inclusive.
Keep the attribute spaces straight
The p prefix is more than shorthand: it identifies the path attribute space, which is restricted to conformation nodes. The atom-count query is therefore not a general search for every kind of node with a certain size. This distinction helps avoid applying a useful filter to the wrong category of object.
Path nodes also inherit some attributes from the general node attribute space. For example, you can refer to a path’s name with p.n, and the inherited selected and selectionFlag attributes are available as well. The selected attribute has no short name in the path space; the selection flag’s short name is sf. These inherited attributes are separate from nat: use the latter when your criterion is specifically the number of atoms.
A practical way to use the filter
Start with a question you can state as a count: “Which paths have more than 100 atoms?” Run p.nat > 100. If that returns a set that is too broad for your review, try a narrower interval such as p.nat 100:200. You can also use a named form, such as path.nat > 100, when readability matters more than brevity. The two forms communicate the same attribute and criterion.
This turns an otherwise visual browsing task into a clear, reusable selection expression. It is particularly handy when atom count—not the path’s name—is the information you need to sort your attention around.
For the full attribute reference and additional inherited attributes, see the SAMSON path attributes documentation.
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