For computational chemists and molecular modelers, screening structural groups based on charge is often key to understanding reactivity, electrostatics, or guiding docking simulations. But quickly identifying molecular groups based on total partial charge in a large system can be cumbersome — unless you’re using the Node Specification Language (NSL) in SAMSON.
The partialCharge attribute in the structuralGroup attribute space solves this problem. With a single line in SAMSON’s search interface, you can immediately isolate structural groups of interest by their partial charge, whether you’re modeling ligand binding, studying charge localization, or building a database of charged groups.
What Is a Structural Group’s Partial Charge?
In SAMSON, a structural group can represent any meaningful subset of a molecular structure — a ligand, subunit, or domain. Each such group may have a partialCharge, representing the sum of individual atomic charges within the group. This aggregate charge is useful when analyzing overall molecular behavior, electrostatic interactions, or ionization states.
Using sg.pc to Filter by Partial Charge
The partialCharge attribute (short name: pc) belongs to the structuralGroup attribute space, so you refer to it using sg.pc. This attribute accepts floating-point numbers and intervals as values.
Here are some useful examples:
sg.pc 1matches all structural groups with an exact partial charge of 1.sg.pc > 1.5matches structural groups with a partial charge greater than 1.5.sg.pc 1.5:2.0matches groups with partial charges between 1.5 and 2.0 (inclusive).
Use these expressions in SAMSON’s NSL search bar to instantly list and highlight all matching structural groups in your current molecular session.
Why This Matters
Let’s say you’re performing a molecular dynamics simulation and want to flag regions with high charge density. Or perhaps you’re building a library of ligands with partial charges between 0.5 and 1.5. Rather than manually checking or writing custom scripts, you can use sg.pc in seconds to find relevant molecules.
Combining sg.pc with other attributes further expands your control. For example:
|
1 |
sg.pc 1.5:2.0 and sg.nat > 50 |
This expression filters structural groups with partial charges between 1.5 and 2.0 AND more than 50 atoms — very useful when looking at charged macromolecular sites.
Beyond Partial Charge
The structuralGroup attribute space offers many other filters you can mix and match with sg.pc, including:
sg.fc(formal charge)sg.nC,sg.nH,sg.nO(number of Carbon, Hydrogen, Oxygen atoms)sg.id(structure ID)
Pairing these lets you build highly specific queries. It’s like applying SQL-style database filtering to your 3D molecular models.
Partial charges are often not uniformly distributed, and being able to isolate segments based on their charge composition allows researchers to more effectively prototype, analyze, and visualize potential molecules. Thanks to NSL, this is now much easier in SAMSON.
To learn more about partial charge queries and other attributes in the NSL for structural groups, refer to the official documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.