A Quick Way to Find Charged Molecules in Your Molecular Models

When working on complex molecular systems, especially in computational drug design or materials science, one common task is identifying and isolating charged structural models within large datasets. Whether you’re verifying protonation states or selecting compounds for ion-binding studies, efficiently filtering models based on total charge is essential.

The Node Specification Language (NSL) in SAMSON offers a concise way to do this through the formalCharge and partialCharge attributes in the structuralModel attribute space. Let’s explore how you can use these NSL attributes to instantly sift through your models for chemically relevant charge states.

Formal vs. Partial Charge

Before going into syntax, it’s helpful to distinguish between two key attributes:

• formalCharge: The total integer formal charge of the model—this is useful when working with ionization states, salts, or charged species.
• partialCharge: A floating point approximation of total partial charges often derived from quantum or empirical methods—helpful for guiding electrostatic interactions or docking workflows.

Querying Charged Models in NSL

In NSL, structural model attributes are accessed via the sm prefix. Here’s how to find structural models by charge:

Find positively charged models

This will match all structural models with a formal charge greater than zero. You could also search for a specific charge:

Select models within a formal charge range

This syntax matches models with formal charges ranging from -1 to +1, including neutral species—useful when broadening your criteria to include near-neutral molecules.

Filter by partial charge

This finds models where the total partial charge is between 1.5 and 2.0. Unlike formal charges, partial charges can be non-integer values, providing more flexibility when exploring polarization behavior.

Combine with Model Attributes

Charge filtering becomes even more powerful when combined with other model properties. For example, to find charged molecules with fewer than 500 atoms:

Or to restrict to visible models in your current SAMSON workspace:

Why Use FormalCharge in Your Workflow?

Here are a few common situations where using sm.fc simplifies your modeling tasks:

• Pre-screening molecular datasets for metal complexes or ionic species
• Filtering out uncharged ligands during electrostatic interaction studies
• Cleaning large imported models by identifying incorrectly protonated components

Identifying charged structures quickly helps you focus only on the models relevant to the type of physical or chemical interactions that matter in your work.

You can explore more details and examples in the NSL documentation for structural models: https://documentation.samson-connect.net/users/latest/nsl/structuralModel/

Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at https://www.samson-connect.net.