When working on molecular models—whether your goal is to study protein-ligand interactions, simulate quantum properties, or simply clean up your structure—getting bond types right is essential. Unfortunately, many modelers overlook this step, which can lead to subtle but significant errors in downstream analyses.
In this post, we’ll take a careful look at how to identify and filter specific bond types using the Node Specification Language (NSL) in SAMSON. This can help you troubleshoot inconsistencies, detect unexpected bonding patterns, and refine selections for simulations or visualizations.
Why bond types matter 🚧
The type of a bond—whether it’s single, double, triple, aromatic, amide, dummy, or undefined—determines not just visual representation but also energy evaluation, geometry optimization, and reactivity prediction. For example:
- Aromatic rings modeled with single/double bond alternation can behave differently than if tagged properly as aromatic.
- Dummy bonds are often artifacts and may need cleanup in input files.
- Undefined bonds might be placeholders that block certain computations from running altogether.
Fortunately, SAMSON makes it straightforward to work with bond types using its NSL query system. Here’s how.
Selecting by bond type in NSL
The attribute bond.type, or short name b.t, allows you to filter bonds based on a well-defined set of bond types. You can use both full names and abbreviations for convenience.
Available bond types:
single(s,1)double(d,2)triple(t,3)amide(am)aromatic(ar)dummy(du)undefined(un)
Example queries
You can quickly find all bonds of a given type using the following filter expressions:
b.t s– matches single bondsb.t d– matches double bondsb.t s,d– matches both single and double bondsb.t ar– matches aromatic bondsb.t du,un– matches dummy and undefined bonds
This is particularly useful when assessing imported files where some bond types may not be correctly detected. You can now easily check and correct these before proceeding with your simulations.
Common use cases
- Cleaning up input structures: Identify undefined or dummy bonds before running optimizations.
- Selective rendering: Visualize only aromatic bonds in a polymer chain.
- Refined selections: Perform calculations only on reliable bonding frameworks.
Although this all might sound simple, a few well-crafted NSL queries can dramatically improve the reliability of your models.
To learn more about working with bond attributes in SAMSON’s Node Specification Language, visit the full documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.