Clarifying Molecular Chaos: How to Filter by Bond Type in SAMSON’s NSL

One of the recurring pain points in molecular modeling is organizing or selecting specific interaction types within large and complex molecular systems. When you’re analyzing a protein-ligand complex, a polymer, or a crystalline structure, being able to isolate particular types of chemical bonds — such as single, double, aromatic, or even undefined ones — can make all the difference during analysis, visualization, or simulation setup.

This is where the Node Specification Language (NSL) in SAMSON provides very precise and flexible tools. In this article, we’ll look specifically at how to filter and match bonds based on their type using the b.t shorthand attribute – a simple yet powerful feature that many newer users overlook. This can save you significant time by automating what would otherwise involve manual selection or scripting.

Understanding Bond Type Filters

Within the SAMSON NSL bond attribute space (b), the b.t attribute lets you focus on bonds of a specific type. Here’s a breakdown of the types and their corresponding short names:

  • single – s, 1
  • double – d, 2
  • triple – t, 3
  • amide – am
  • aromatic – ar
  • dummy – du
  • undefined – un

This syntax allows you to write concise queries such as:

  • b.t s – to select single bonds
  • b.t s,d – to select both single and double bonds
  • b.t ar – to isolate aromatic bonds
  • b.t du,un – to investigate bonds that are either placeholders or not yet assigned

Why This Matters

Say you’re refining a docking pose and want to ensure hydrogen atoms are connected via single bonds only. Or, you’re preparing a forcefield assignment and need to flag undefined or dummy bonds. Having rapid, textual access to bond types enables efficient filtering — without guesswork or visual inspection.

In visualization workflows, this helps with color-coding specific bond types. During setup for quantum simulations, dummy or undefined bonds can be excluded or flagged in seconds. When working with large models such as small-molecule libraries or periodic systems, text-based filtering offers precision and reproducibility.

Extra Tip: Combining with Other Filters

Want to select all aromatic bonds longer than 1.3 angstroms? Combine attributes! Here’s a sample NSL query:

This selects all aromatic bonds exceeding the specified length, perfect for investigations of delocalization or unusual conformations.

Conclusion

Although simple, the b.t bond type filter in NSL is a precise way to take control of your molecular datasets. Whether you’re troubleshooting, visualizing, or preparing your system for computation, understanding and applying bond type filters will streamline your molecular modeling workflows.

To learn more and explore additional bond attributes such as order, length, and customType, please visit the SAMSON documentation page on bond attributes: https://documentation.samson-connect.net/users/latest/nsl/bond/

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

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