Making Sense of Bond Types in Molecular Models: A Filtering Guide

When you’re working with complex molecular systems, being able to selectively identify and manipulate different types of bonds can save hours of modeling time. Whether you’re performing structural analysis, preparing systems for simulations, or simply cleaning up data, bond type classification becomes essential.

In SAMSON’s Node Specification Language (NSL), you can efficiently filter and search for specific bond types using the bond.type attribute (short name: b.t). This blog post provides a practical walkthrough on how to understand and use this bond filtering feature. It’s especially useful when you’re dealing with large biomolecules or complex materials and need to target only certain bond types—like aromatic or amide bonds, for example.

What’s the problem?

Imagine you’re working on a molecule with hundreds or even thousands of bonds. You want to apply an operation (like visualization styling, measurement, or dynamics tuning) only to a subset of these bonds—say, just the aromatic ones. Manually identifying and tagging them would be highly error-prone and time-consuming.

That’s where the bond.type filter comes in: it automates this process based on predefined categories of bonds in SAMSON.

Supported bond types and filters

You can use either descriptive names or short codes to match specific types of bonds:

How to use the filter

Here are practical examples you can use in NSL to find what you need:

• b.t s matches single bonds.
• b.t d matches double bonds.
• b.t s,d matches both single and double bonds.
• b.t ar matches aromatic bonds.
• b.t du,un filters dummy and undefined bonds — useful when cleaning or debugging a model.

Since bond types must be defined to use this filter, ensure your molecular system has been properly initialized or imported with bond type information.

Visual Feedback 🔍

Use the bond type filtering along with SAMSON’s visual styling tools to get immediate graphical feedback. This makes it easier to inspect structural motifs—such as conjugated ring systems or peptide backbones—by highlighting specific bonds.

Use cases at a glance

Structural analysis: Identify aromatic systems in drug scaffolds.
Model preparation: Validate or clean undefined or dummy bonds before simulations.
Reaction mechanisms: Focus on triple bonds or amides involved in catalysis.

Filtering based on bond type isn’t just about viewing—it’s often the first step before running simulations, applying bond-specific force fields, or preparing chemical reactions.

To learn more about bond filtering and other NSL features, view the full documentation page here.

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