When analyzing molecular structures, it’s easy to get lost in atoms and forget that the bonds connecting them are just as critical. Bond types strongly influence molecular behavior, from conformations to reaction mechanisms. Yet, many modelers ignore this during search and filtering workflows. If you’ve ever wondered how to programmatically distinguish single, double, or even aromatic bonds in your selections, there’s a useful feature in the Node Specification Language (NSL) that you might not be using: bond.type.
NSL is the powerful query system built into SAMSON, used to find and operate on nodes in molecular models. And in the bond attribute space (abbreviated b), the b.t query lets you filter based on bond types with surprising flexibility and simplicity.
When Identifying the Right Bond Matters
Let’s say you’re modeling a catalytic site and need to differentiate between single and double bonds near a substrate. Or you’re designing a ligand and want to target only aromatic bonds for stacking interactions. Even a small mistake in ignoring bond types can affect energy calculations or lead to incorrect functional group identification.
This is where queries like:
b.t s– matches single bondsb.t d– matches double bondsb.t ar– matches aromatic bondsb.t du,un– matches dummy and undefined bonds, great for spotting incomplete models
come in very handy. You can use these in combination with atom-level queries to pinpoint exactly what you’re looking for in complex molecular systems.
Shorthand for Clarity and Speed
One elegant feature of NSL is its use of short forms. If typing bond.type aromatic feels cumbersome, you can simply write b.t ar. There are multiple shorthand mappings:
- single:
s,1 - double:
d,2 - triple:
t,3 - amide:
am
This means you can chain types together in concise queries: b.t s,d,ar gets you single, double and aromatic bonds in one line.
A Quick Workflow Tip
Use b.t to combine visual inspection and scripting. For instance, run a query like b.t ar to find all aromatic bonds, and visually inspect how SAMSON highlights them in the molecular model. This reveals ring systems instantly, especially helpful in molecular docking or drug design workflows.
Prevent Errors, Prioritize Insights
When working at scale or scripting, users often forget that undefined or dummy bonds may creep into models – especially after import from external databases or homology modeling. Try running:
|
1 |
b.t du,un |
to catch and review these. It can save time and prevent downstream issues in simulations or documentation.
You can find more details on how to use b.t and explore other bond attributes in the full documentation page: NSL Bond Attributes Documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at www.samson-connect.net.