Choosing the Right Bond Types in Molecular Queries with NSL

When working with large molecular systems in SAMSON, the integrative molecular design platform, a common challenge many modelers face is how to quickly filter or select specific kinds of bonds—especially in hybrid systems or during structural validation. Whether checking for aromaticity, spotting undefined connections, or isolating double bonds in reactive centers, being able to identify bond types precisely is essential.

This is where NSL (Node Specification Language) helps. NSL allows you to create queries to filter nodes in your molecular model, including atoms and bonds, using human-readable syntax. The bond.type attribute (short name: b.t) in NSL makes it easy to select bonds by their chemical type. This post introduces how to effectively use this attribute to simplify your workflows and reduce modeling errors.

What Is bond.type?

The bond.type attribute lets you filter bonds by their category, such as single, double, triple, aromatic, dummy, etc. This filter is useful when preparing a system for simulations, inspecting structures from experimental data, or teaching concepts related to bonding.

Here are the possible bond types and their shorthand values in NSL:

Useful Examples

Here are a few examples of how you might use this in practice:

• b.t s — Selects all single bonds
• b.t d — Selects all double bonds
• b.t s,d — Selects both single and double bonds
• b.t ar — Selects aromatic bonds, useful for ring system detection
• b.t du,un — Identifies bonds that might need attention before a simulation

Why is this helpful? For one, it’s a fast way to detect anomalies. For example, spotting dummy (du) or undefined (un) bond types lets you clean up imported structures before simulation. And you can write these filters inline in your selection tools or scripts without needing to write new code.

When to Use This

• During structure import: Check for unexpected bond types in newly imported molecules.
• Before energy minimization: Ensure no undefined or dummy bonds are present.
• Teaching: Explore different types of bonding using simple NSL queries in a classroom setting.
• Model validation: Visualize all aromatic or amide bonds in a peptide chain quickly.

Combined with other NSL filters such as bond.length (b.len) or bond.order (b.o), the bond.type filter becomes even more powerful.

To learn more about NSL and bond-selecting options, you can visit the official documentation: https://documentation.samson-connect.net/users/latest/nsl/bond/

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