If you’ve ever worked with complex molecular datasets that contain multiple conformations, you already know how time-consuming it can be to manually search for specific conformers that meet certain structural criteria. One common task for molecular modelers is to identify conformations with a specific number of atoms—either because a simulation or computational method requires it, or just to group subsets of conformations for comparison.
Fortunately, SAMSON provides a simple and powerful way to do this using the Node Specification Language (NSL). In this post, we’ll explore how you can utilize the numberOfAtoms attribute to filter conformations efficiently.
Understanding conformation.numberOfAtoms
In SAMSON’s NSL, the numberOfAtoms attribute belongs specifically to the conformation attribute space, which means it only applies to conformation nodes. The shared short name for this attribute is co.nat.
This attribute is extremely useful when you want to:
- Filter out conformations that are too small or too large for your purposes.
- Prepare a subset of conformers for simulation or structural comparison.
- Validate consistency across a dataset by checking atom counts.
Example Syntax
Here are a few practical NSL queries using numberOfAtoms:
co.nat > 100: Selects all conformations with more than 100 atoms.co.nat 100:200: Selects conformations with atom counts between 100 and 200 (inclusive).
These filters can be combined with other NSL attributes to refine your selection even further. For example, if you want conformations with more than 100 atoms that are currently selected, you could use:
|
1 |
co.nat > 100 and co.selected |
Why It Matters
Being able to construct quick queries like this provides several benefits:
- Speed: No need to click through lists or visualizations manually.
- Reproducibility: You can save and share queries with collaborators.
- Scalability: Works just as well with 10 conformers as with 10,000.
Let’s say you’re preparing input files for a simulation that only accepts molecules with exactly 150 atoms. Instead of manually counting atoms or writing scripts, you can simply type:
|
1 |
co.nat 150 |
And instantly get exactly what you need.
Explore Further
The co.nat attribute is just one of many attributes available in SAMSON’s Node Specification Language. You can also filter by name, selection flags, and more. This makes NSL a powerful companion in data-heavy molecular modeling workflows.
To learn more about conformation attributes in NSL, visit the original documentation: https://documentation.samson-connect.net/users/latest/nsl/conformation/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.