Filtering Bonds by Type Made Easy with NSL

If you’ve ever struggled to select specific kinds of chemical bonds when modeling molecules — for example, only double bonds or aromatic ones — you’re not alone. Whether you’re refining a complex molecule or preparing input data for simulations, isolating bond types efficiently is essential for many tasks in computational chemistry and molecular design.

Fortunately, SAMSON’s Node Specification Language (NSL) offers a simple, readable way to specify exactly which bonds you want to work with — and avoid tedious manual filtering. In this post, we’ll explore how to select bonds by type using NSL so you can focus more on your science and less on repetitive clicks.

Why Bond Type Matters 🧬

In many molecular modeling tasks, different bond types (single, double, triple, aromatic, etc.) have distinct chemical or mechanical roles. Being able to select and analyze them separately can help with:

• Setting up forcefield parameters
• Identifying reactive centers
• Designing targeted fragment modifications
• Creating visual filters for large biological structures

How to Select Bonds by Type in NSL

In NSL, the bond.type attribute is your entry point. It allows you to filter the molecular bond nodes by a predefined set of chemical types.

Here are the supported types and their short codes:

Common Usage Examples

These NSL expressions will help you get started immediately:

• b.t s selects all single bonds
• b.t d selects all double bonds
• b.t ar selects all aromatic bonds
• b.t du,un selects all dummy or undefined bonds, useful for cleaning things up
• b.t s,d selects all single and double bonds

This flexibility allows you to quickly focus on meaningful molecular interactions relevant to your research.

Helpful Tips

• Make sure bond types have been defined in the molecular structure — otherwise they won’t be matched.
• You can combine bond type filters with other filters (e.g., length or custom type) for even more precise selection.

Learn more about bond attributes and the NSL.

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