For molecular modelers and computational chemists, identifying specific types of bonds—like those with fractional bond orders in conjugated systems—can often involve a mix of guesswork and manual inspection. Whether you’re refining a force field, preparing a simulation, or analyzing resonance structures, this filtering step can be both time-consuming and imprecise.
Fortunately, SAMSON’s Node Specification Language (NSL) provides an elegant way to filter and manipulate bonds based on their bond order. This can significantly reduce setup time and minimize errors in molecular models. In this blog post, we’ll focus on using bond.order—or simply b.o—for smarter selection workflows.
What is bond order in NSL?
In NSL, bond.order refers to the numeric strength of a bond—usually floating-point values. These can range from whole numbers like 1 (single bond) and 2 (double bond), to fractions like 1.5, which are common in aromatic systems or between delocalized atoms.
Why it matters
Imagine analyzing aromatic rings or resonance structures. Recognizing bonds with an order of around 1.5 is essential for constructing correct models or validating predicted structures. Similarly, detecting unexpected bond orders can help debug imported data, clean up geometries, or spot issues in topology assignments.
How to search by bond order
NSL makes bond-order filtering intuitive. Here are some examples:
b.o >= 2– finds all bonds with bond order of 2 or more. Useful when focusing on double and triple bonds.b.o 1.5:3– narrows results to fractional or higher bond orders found in delocalized or conjugated systems.
Use case: Working with delocalized systems
Suppose you’re analyzing a large conjugated molecule and want to isolate all 1.5 bond order connections. Instead of visually inspecting each bond or guessing which region is conjugated, just run:
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b.o 1.5 |
This targets precisely the delocalized bonds, so you can then apply further analysis, assign parameters, or export them for documentation.
Use case: Detecting abnormal bond orders
If you’re processing molecules from an external database or a PDB file with limited bond information, it’s useful to identify improperly assigned bond orders. For example, if the topology assigns an unrealistic 3.0 order to a single bond, you might want to highlight everything with an order > 2.5:
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b.o > 2.5 |
This lets you catch and correct errors before they propagate downstream into simulation or analysis tools.
Combining filters
NSL is even more powerful when combining bond order filters with atom or bond type filters. For example, to find double or higher bonds only between carbon atoms:
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a.e C and (b.o >= 2) |
This filters bonds specifically based on atomic element and bond order, offering granular control over your selection.
Conclusion
Filtering by bond order in SAMSON’s NSL can streamline workflows, reduce manual inspection time, and increase the reliability of setup pipelines. Whether you’re investigating aromaticity or preparing structures for simulation, this functionality is worth mastering.
To learn more about the available bond attributes and examples, visit the official documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.