When working with complex molecular systems, it often becomes essential to select or filter models based on specific electrostatic properties. One of the most important among these is the partial charge. Whether you’re studying charge distributions, preparing systems for simulations, or analyzing docking results, being able to rapidly isolate models based on their partial charges can save considerable time and reduce manual curation.
In this post, we dive into how the partialCharge attribute in the Node Specification Language (NSL) of SAMSON allows you to filter structural models based on their total partial charge. Spoiler: it’s more straightforward than you might think—and once you get the hang of it, it’s a huge time-saver.
Why Partial Charge Matters
Partial charges influence molecular interactions such as hydrogen bonding, salt bridge formation, and van der Waals interactions. Being able to efficiently locate molecular models within a workspace that share a specific range of partial charges can assist in tasks like:
- Identifying charged versus neutral forms of molecules
- Filtering candidate molecules in screening workflows
- Validating the result of parameterization processes
Using sm.pc to Filter on Partial Charge
In SAMSON’s NSL, the sm prefix refers to the structural model attribute space. To filter based on partial charge, you add the .pc suffix. Supported values include both exact numbers and ranges.
Here are some examples:
sm.pc 1— Selects structural models with a total partial charge of exactly 1sm.pc 1.5:2.0— Matches models with total partial charge between 1.5 and 2.0sm.pc > 1.5— Matches models with partial charge strictly greater than 1.5
When to Use It
Imagine you are working with a library of molecular structures, and you want to flag those with a partial charge potentially leading to high electrostatic interactions. With a single NSL query (e.g., sm.pc > 1.5), you could visually isolate those in the SAMSON interface.
This feature is especially useful in virtual screening, where hit lists could contain hundreds or thousands of models. Setting a filter lets you focus on subsets of molecules for downstream analysis or visualization.
Filtering Strategies
You can also combine the partialCharge filter with other NSL attributes for more refined selections. For example:
sm.pc > 1.5 and sm.nat > 50— Large molecules with higher chargessm.pc 2:4 and not sm.h— Charged models that are not hidden
Filters like these can be written directly into the NSL console or embedded into SAMSON’s automation workflows for complex screening tasks.
Learn More
This example is just one of many practical applications of NSL in SAMSON. To explore additional structural model attributes, including atom counts, visibility flags, and selection state, visit the official documentation page.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.