When you’re inspecting or designing molecular systems, it’s easy to overlook how deeply bond types influence molecular behavior. Whether you are analyzing a drug molecule, building a polymer, or examining a crystal structure, the type of bond—single, double, aromatic, and so on—determines important chemical properties. But how do you effectively filter or extract the exact bond types you’re looking for, especially in large molecular systems?
That’s where the Node Specification Language (NSL) in SAMSON becomes incredibly handy. If you’re dealing with complex systems and only want to focus on, say, double bonds or aromatic connections, NSL lets you query and isolate them in seconds.
Why bond types matter
Bonds determine geometry, reactivity, and even the dynamics of molecular interactions. For instance:
- Single bonds (like in alkanes) allow free rotation, affecting molecular flexibility.
- Double/triple bonds are more rigid, influencing planarity and reactivity.
- Aromatic bonds indicate delocalized electrons, common in biologically active compounds.
- Amide bonds are backbone linkages in peptides, influencing protein structure.
With NSL in SAMSON, rather than visually scanning (and possibly missing things), you can use keyword searches to target exactly what you need, and that’s a huge time-saver when working on real research projects.
How to query bond types using NSL
In NSL, the attribute for bond type is bond.type, and can be shortened to b.t. Supported bond types and their codes include:
| Bond Type | Short Code(s) |
|---|---|
| Single | s, 1 |
| Double | d, 2 |
| Triple | t, 3 |
| Amide | am |
| Aromatic | ar |
| Dummy | du |
| Undefined | un |
Examples:
b.t s: Finds all single bondsb.t d,t: Finds double and triple bondsb.t ar: Isolates all aromatic bondsb.t du,un: Highlights dummy or undefined bonds, useful for checking incomplete structures
This keyword system gives you much more control over your model visualization and analysis. You can combine it with other bond attributes (like distance or order) for precise querying. For example:
|
1 |
b.t s & b.len > 1.5A |
This matches all single bonds that are longer than 1.5 angstroms—a useful check when analyzing strained or distorted structures.
Why this matters in daily work
Whether you’re screening a reaction pathway or validating a molecular mechanism, quickly highlighting just one or two types of bonds simplifies model inspection and shortens your feedback loop. If you use bond types cleverly, you can also isolate regions of interest, check parameterizations, or even find anomalies before simulation.
And since the NSL search is integrated directly into SAMSON’s visual interface, you can immediately see results on complex models with thousands of atoms. You can also export selected bonds for further analysis.
To learn more about matching bonds by type—and other attributes like length or order—check the full documentation page: Bond attributes in NSL.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here: https://www.samson-connect.net.