When working on large-scale molecular simulations or datasets, it’s often useful to filter and select models based on specific criteria—like partial charge. Whether you’re preparing input for a simulation, cleaning up a library of structures, or simply exploring patterns across molecules, being able to query models by charge properties can save a lot of time and make your workflows cleaner.
In the SAMSON integrative molecular design platform, the Node Specification Language (NSL) lets you query structural models with precision. One particularly practical attribute for researchers is partialCharge, which allows you to examine or filter structural models based on their total partial charge.
Why search by partial charge?
- Simulation readiness: Ensuring systems are neutral before running simulations is often critical.
- Data exploration: Quickly inspect or group molecules with high or low partial charges.
- Material selection: In materials science, filtering by partial charge might help identify specific catalysts or surfaces.
How to query partial charge with NSL
The structuralModel.partialCharge (short name: sm.pc) attribute can be used to match models depending on the total partial charge value. You can use numeric comparisons or even specify a range of values. Here are a few useful examples:
|
1 |
sm.pc > 1.5 |
This line matches all structural models with a partial charge greater than 1.5.
|
1 |
sm.pc 1.5:2.0 |
This one matches models where the total partial charge is between 1.5 and 2.0 (inclusive).
|
1 |
sm.pc -1:1 |
If you want electrically neutral or nearly neutral models, this line selects partial charges between -1 and 1.
Visual workflow example
Once you’ve selected such models inside SAMSON using the appropriate NSL query, you can combine this selection with materials, visibility flags, or even graph-based searches. Because queries like sm.pc are evaluated per structural model, your selections are fast and decoupled from atom-by-atom inspection.
It’s particularly powerful in large projects involving a database of molecules where you may want to extract just those molecules with extreme or interesting charging behavior.
Bonus tip
If you regularly need to monitor electrostatic features of your molecular models, consider creating a preset NSL filter with sm.pc conditions, pair it with visualization settings (e.g., color-code by charge), and reuse it throughout your projects!
To learn more about partial charge filtering, including the precise syntax and additional examples, visit the official documentation page: https://documentation.samson-connect.net/users/latest/nsl/structuralModel/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download the platform at https://www.samson-connect.net.