When a molecular project contains many conformations, it can be hard to find the ones that are useful for a particular task. A large set may include structures with very different sizes, and manually inspecting each one is a slow way to narrow the list. If the number of atoms is the criterion that matters, SAMSON’s Node Specification Language (NSL) provides a direct filter.
Filter by a minimum size
Conformation nodes have a numberOfAtoms attribute, abbreviated nat. To match conformations containing more than 100 atoms, use:
co.nat > 100
The longer form is conformation.nat > 100. The short prefix co refers to the conformation attribute space, which matches conformation nodes. This distinction matters: the query is about the atom count of a conformation, not a request to match individual atoms.
Search within a size range
Sometimes “larger than a threshold” is too broad. For example, you may want to focus on conformations with between 100 and 200 atoms. The range form is:
co.nat 100:200
This is a compact way to express a bounded search. It can be useful when you want to reduce a crowded set to a more manageable group before inspecting names or other properties. The documented attribute accepts integer values, so use whole-number atom counts in these expressions.
A practical way to use the filter
- Decide what size boundary is meaningful. Choose a minimum count if you want to exclude smaller conformations, or a range if you need a narrower band.
- Write the query using the conformation prefix. For instance, use
co.nat > 100for a minimum-size filter orco.nat 100:200for a range. - Review the matched conformations in context. Atom count is a useful first sorting criterion, but it does not by itself tell you whether a conformation is chemically appropriate for your next step. Treat it as a way to narrow the search, then assess the candidates using the information relevant to your project.
What the query does—and does not say
A count-based expression answers a specific question: how many atoms are in the conformation? It does not describe the conformation’s name, quality, or scientific suitability. Two conformations with the same atom count can still be different in ways that matter to your analysis. Keeping the query focused makes its result easier to interpret and helps avoid treating a simple size filter as a complete comparison.
The conformation attribute space also inherits general node attributes, including selected and selectionFlag. These are separate from numberOfAtoms: the atom-count query filters by a numeric property, while the inherited attributes concern node selection state. For example, the documented selection-flag short name is sf; the selected attribute has no short name in this space.
For the full attribute reference and additional syntax details, see the SAMSON conformation attributes documentation.
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