When working with large molecular datasets, especially during simulations or conformational analyses, it often becomes crucial to filter and identify specific conformations based on simple yet decisive properties like the number of atoms. If you’re building workflows in SAMSON, the integrative molecular design platform, there’s an efficient way to do this using the Node Specification Language (NSL).
Imagine you have a molecular system with hundreds (or thousands) of conformations—each potentially containing a different number of atoms due to molecular flexibility, modifications, or solvation. Skimming through each manually to find relevant subsets is not only time-consuming but can also lead to oversight and errors.
What is the co.nat attribute?
In NSL, the conformation.numberOfAtoms attribute (short form: co.nat) is specifically designed to work with conformation nodes. This attribute matches conformations based on the number of atoms, allowing users to conveniently filter out unneeded data and focus on structures that meet specific criteria.
Examples: Targeting atom counts precisely
co.nat > 100— selects conformations that have more than 100 atoms.co.nat 100:200— selects conformations with a number of atoms between 100 and 200.
Using these queries, you can quickly tailor your selection to match whatever size scale is relevant to your research or modeling task.
Why does this matter?
The number of atoms often correlates with the size or complexity of a conformation, and being able to group or isolate conformations based on this metric can simplify:
- Running simulations only on structures within a desired complexity range
- Extracting manageable data subsets for analysis or visualization
- Identifying outlier conformations that might indicate mis-labeled or corrupted files
This functionality is particularly valuable for researchers working with conformational ensembles from molecular dynamics, docking experiments, or dataset-driven screening pipelines.
Combining filters for more control
While co.nat focuses on atom counts, it can be combined with other attributes inherited from the generic node space. For instance:
co.nat > 200 and co.selected— select conformations with more than 200 atoms that are also currently selected.co.nat < 150 and not co.selectionFlag— select smaller conformations that haven’t been flagged.
These combinations are useful when building more sophisticated queries for iterative analysis or preparing datasets for exporting to other tools.
Check the full conformation attributes documentation for more examples and integration tips.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here.