When you’re working with complex molecular structures, isolating specific types of chemical bonds can be critical for both analysis and visualization. Whether you’re identifying aromatic interactions, highlighting hydrogen bond patterns, or preparing data for simulation, having a fast and flexible way to select bonds by type is incredibly helpful.
This is where SAMSON’s Node Specification Language (NSL) can save a lot of time. In this post, we explore one of NSL’s practical features: selecting bonds by their type using the bond.type attribute.
Why Filter by Bond Type?
As a molecular modeler or structural biologist, there are many situations where you might want to focus on one category of bond:
- Highlight amide bonds involved in peptide linkages.
- Exclude dummy bonds when counting interactions or computing energies.
- Isolate aromatic systems to analyze π-stacking effects.
- Compare geometries of single versus double bonds.
The bond.type attribute (shortcut: b.t) lets you do all of this with concise NSL queries.
Bond Type Reference
Here are the supported bond types you can use in your queries:
| Type | Shorthand | Description |
|---|---|---|
single |
s, 1 |
Single bond |
double |
d, 2 |
Double bond |
triple |
t, 3 |
Triple bond |
amide |
am |
Amide bond (common in peptides) |
aromatic |
ar |
Aromatic bond |
dummy |
du |
Dummy bond (used for modeling or placeholders) |
undefined |
un |
Bond with undefined type |
Common Queries and Use Cases
You can combine bond types to craft powerful filters:
b.t s→ Selects all single bonds.b.t d,t→ Selects all double AND triple bonds.b.t ar→ Selects aromatic bonds, useful for studying phenyl rings or conjugated systems.b.t du,un→ Excludes structural artifacts or uncharacterized bonds from chemical analysis.
Note: For this attribute to work as expected, the bond must have its type defined in the molecular data.
When to Use This Functionality
This selection feature is especially handy in workflows like:
- Preparing visualizations that highlight important structural elements.
- Running selective simulations (e.g., freezing aromatic rings).
- Calculating bond energy for specific groups of bonds.
- Exporting cleaner datasets with only chemically meaningful interactions.
These targeted selections help reduce noise and improve workflow clarity.
To learn more and explore other bond properties you can use for selection (like length or order), visit the full documentation page here: https://documentation.samson-connect.net/users/latest/nsl/bond/
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.