Making Sense of Bond Types in SAMSON’s Node Specification Language (NSL)

When working with complex molecular systems, identifying specific bond types quickly can save researchers a tremendous amount of time. Whether you are filtering for hydrogen bonds, distinguishing between aromatic or single bonds, or building precise molecular queries, defining correct bond types is essential for efficient molecular modeling.

In SAMSON, the Node Specification Language (NSL) enables you to search and filter bonds based on their defined type. This blog post will explain how to use bond types in NSL queries and why this is particularly useful for molecular modelers working with large datasets or designing custom selections.

Understanding Bond Types

In SAMSON’s NSL, bond types are accessed through the bond.type attribute, shortened to b.t. Each bond is assigned a type either automatically or manually through annotation. These types include:

  • single — s or 1: single bonds
  • double — d or 2: double bonds
  • triple — t or 3: triple bonds
  • amide — am: amide bonds
  • aromatic — ar: aromatic bonds
  • dummy — du: non-standard or placeholder bonds, often used for modeling purposes
  • undefined — un: bonds with undefined type, which may occur in imported or incomplete structures

Common Use Cases

Here are a few examples of how you might use bond type filters in NSL:

  • b.t s: matches single bonds
  • b.t d: matches double bonds
  • b.t s,d: matches both single and double bonds — handy when you’re interested in strong covalent interactions
  • b.t ar: isolates aromatic bonds, useful for highlighting planar ring systems
  • b.t du,un: captures bonds that might need cleanup or further annotation

Why It Matters

If you’ve ever tried to select all aromatic bonds in a protein-ligand complex without a proper query system, you know how tedious it can be. With NSL, you can create a specific query in seconds. Searching for b.t ar immediately gives you all aromatic bonds across your entire system, regardless of size. You can then color them, label them, or export the result, depending on your workflow.

This ability becomes particularly useful in the following scenarios:

  • Preparing systems for quantum chemistry calculations: filter out dummy or undefined bonds that could cause errors
  • Teaching and visualization: highlight only single or double bonds to help explain chemical concepts
  • Model cleanup: identify improperly typed bonds

Important Notes

To use bond type filtering effectively, make sure your molecular models have proper bond typing enabled. Imported files that lack this information may require preprocessing or manual annotation in SAMSON.

To learn more about NSL’s bond type filtering and to explore the complete list of bond attributes, visit the official documentation.

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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