If you’ve ever spent time sifting through complex molecular models, trying to isolate specific interaction types, you know how tricky it can be to filter out exactly what matters. Whether it’s identifying aromatic systems, differentiating single and double bonds, or dealing with undefined bond types in an imported structure, being able to quickly select and query bonds by type is a crucial feature for chemists, bioengineers, and materials scientists alike.
The Node Specification Language (NSL) in SAMSON offers an elegant and efficient way to handle this challenge. In particular, the bond.type attribute (short name: b.t) allows you to specify one or more types of bonds to focus on during your analysis—exactly what you need when trying to make sense of complex systems.
Why Bond Types Matter
When working with molecular models, it’s important to distinguish among the many kinds of bonds that can appear. For example:
- Single, double, and triple bonds provide insight into molecular geometry and reactivity.
- Aromatic bonds often indicate delocalized π-systems involved in interactions like stacking.
- Amide bonds are critical in peptides and proteins, and identifying them quickly helps when modeling folding or interactions.
- Dummy and undefined bonds typically arise from incomplete data or imported structures and must be identified and treated cautiously.
Using NSL to Query Bond Types
With NSL, querying bonds by type is quite simple. Here are a few useful patterns:
b.t s— selects all single bonds.b.t d— selects double bonds.b.t s,d— selects both single and double bonds.b.t ar— selects all aromatic bonds.b.t du,un— selects dummy and undefined bonds, helpful for cleaning or annotating models.
It’s important to note that bonds in your model must have their type correctly defined for this to work. If you’re importing structures or working with edited models, consider validating the types during preprocessing.
A Practical Example
Imagine you’re analyzing a protein-ligand complex and want to visualize only aromatic systems due to their relevance in π-stacking interactions. With NSL, you can simply enter b.t ar and instantly highlight all aromatic bonds. This helps you spot interaction regions quickly, without having to manually inspect each part of the model.
Alternatively, if you’ve just imported a dataset and want to clean up non-resolved entities, b.t du,un immediately shows you all bonds that are flagged as undefined or placeholders. This saves time and potential errors during simulation setup.
Matching by Type: Possible Values
Here’s an overview of the supported bond types and their associated short names in NSL:
single(s,1)double(d,2)triple(t,3)amide(am)aromatic(ar)dummy(du)undefined(un)
Want to learn more? You’ll find the complete reference in the NSL documentation, including other useful bond attributes like length, order, and customType.
Explore the full NSL bond attribute documentation here.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.