How to Filter Bond Types When Exploring Complex Molecular Structures

When working with complex molecular systems, quickly isolating and understanding specific bond types can help molecular modelers streamline their workflow. Whether you’re refining a force field, analyzing a molecule’s geometry, or preparing a system for simulation, being able to identify and select only double bonds, aromatic bonds, or any other bond category is often crucial.

In the NSL of SAMSON, this task becomes very efficient and readable. The bond.type attribute, abbreviated as b.t, allows users to query nodes based on the types of bonds they represent, using both full and short notations.

Why Filter by Bond Type?

  • Structural analysis: Determine how many double or aromatic bonds a molecule contains, for electronic or resonance studies.
  • Search specificity: Focus domain-specific queries on only relevant bonds when searching for patterns (e.g. amide bonds in peptide design).
  • Simulations: Prepare targeted visualizations or force-field assignments.

Supported Bond Types in NSL

Here are the bond types you can filter in SAMSON, along with their short aliases:

Type Short forms Description
single s, 1 Single bond
double d, 2 Double bond
triple t, 3 Triple bond
amide am Amide bond
aromatic ar Aromatic bond
dummy du Dummy bond (placeholder)
undefined un Undefined bond type

Usage Examples

To isolate specific bond types, you can write simple commands in NSL.

  • b.t s matches all single bonds
  • b.t d matches all double bonds
  • b.t s,d matches both single and double bonds
  • b.t ar matches only aromatic bonds
  • b.t du,un matches dummy and undefined bonds, which may require editing or manual review

Tips

  • Always make sure the bond type has been defined. Otherwise, type-based filters won’t match your node even if the bond is present.
  • You can combine type-based queries with other bond attributes for more refined results (length, order, etc.).
  • Use short names to make your queries more compact: b.t s is equivalent to bond.type single.

Efficient bond type filtering doesn’t just help organize your molecular structure—it can also reveal patterns, potential issues, and key features depending on what you’re focusing on. Whether you’re editing a complex molecule or reverse-engineering a biochemical pathway, it pays off to leverage this kind of precision.

To learn more about bond attribute filtering in NSL, visit the full documentation page: 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.

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