Finding Bonds by Type in Molecular Models: A Quick Guide to NSL

When working with complex molecular systems, it’s common to run into questions like:

  • How can I select only double and triple bonds?
  • Can I isolate aromatic bonds efficiently?
  • How do I spot undefined or dummy bonds in large structures?

These are common challenges for molecular modelers who work with large molecular datasets or imported structures. Fortunately, the Node Specification Language (NSL) in SAMSON provides powerful selection tools to help with exactly this. One such tool is the bond.type attribute (short name: b.t), which allows you to filter bonds based on their type.

Why Bond Types Matter

Different bond types often have distinct chemical behaviors. Being able to highlight or select specific bond types, like double bonds or aromatic systems, helps with:

  • Visual analysis and cleaning of imported systems
  • Preparing subsets for quantum chemical calculations
  • Understanding structure-property relationships

For example, selecting only amide bonds might help identify peptide backbones, while filtering dummy or undefined bonds helps clean up imported structures from noisy files.

How to Use bond.type in NSL

To select bonds by type, use one of the following values in the b.t attribute:

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

For instance:

  • b.t s — selects all single bonds
  • b.t d, t — selects both double and triple bonds
  • b.t ar — selects aromatic bonds
  • b.t du, un — selects all dummy and undefined bonds

This makes it extremely fast to isolate just what you’re looking for, whether you’re debugging a file or preparing a subset for analysis.

Tips and Best Practices

  • Make sure the bonds in your model have their type set. Imported files may not always include this data.
  • Use combined queries like b.t s, d to capture multiple bond types at once if needed.
  • Pair with other NSL attributes, like b.len or b.o, for advanced filtering.

Filtering by bond type is especially useful just after importing a model from an external source, such as PDB or MOL2 files, where bond type annotations might be incomplete or noisy. Instead of manually inspecting hundreds (or thousands) of bonds, a single NSL query can isolate the ones that need attention.

To view the complete documentation on bond attributes in NSL, 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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