Quickly Identify Bonds by Type in Your Molecular Models

When working with complex molecular structures, it’s often necessary to inspect or refine specific bond types, such as identifying only the aromatic bonds in a protein-ligand complex or checking for unusual bond patterns in generated conformers. This task, usually time-consuming with conventional approaches, becomes much more efficient using SAMSON’s Node Specification Language (NSL).

In this post, we go into the practical use of the bond.type attribute in NSL to filter and select specific kinds of bonds in your molecular models. This is especially useful if you’re building or analyzing molecular structures and need precise control over the types of bonds your queries match.

Overview of bond.type

The bond.type attribute, accessible using the short name b.t, allows you to match specific categories of bonds. These can be:

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

This means you can quickly identify and select specific bond types without manually analyzing them one by one in a viewer. It’s a major time-saver when validating models or preparing molecules for simulation.

Common use cases

🧪 Check For Unusual Bonds

Sometimes, imported structures contain undefined or dummy bonds. With NSL, it’s straightforward to filter these out for closer inspection:

  • bond.type dummy or b.t du
  • bond.type undefined or b.t un

🧬 Focus on Aromatic Systems

If your goal is to analyze conjugated systems or aromatic rings, use:

  • bond.type aromatic or b.t ar

This lets you isolate pi systems quickly and explore charge delocalization or substitution patterns.

🔍 Isolate Backbone Bond Types

For cleaner visualization or computation, some workflows need to hide everything but covalent single or double bonds. You can express that with:

  • b.t s,d

This reveals all single and double bonds, filtering out triple, aromatic, or less conventional types.

Syntax Tips

NSL provides both long-form and short-form syntax. For example:

  • bond.type single ⇨ b.t s
  • bond.type dummy, undefined ⇨ b.t du,un

This makes it easy to write compact and readable queries as you get used to the notation.

Important Note on Compatibility

For bond.type queries to work, bond types must be defined in your model. Ensure that your structure contains interpreted chemical typing, which is typically handled during molecule import or construction in SAMSON.

Conclusion

Using bond.type in NSL can significantly speed up the way you navigate and analyze complex molecular systems. Whether you’re optimizing a structure, spotting defects, or visualizing key functional groups, these queries help streamline the process and reduce manual overhead.

For more information and examples of bond attributes in NSL, check out the full documentation at SAMSON Bond Attributes 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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