When modeling molecular systems, it’s often essential to distinguish between different types of chemical bonds. For instance, detecting all aromatic or amide bonds in a structure can give valuable insight into reactivity, structural stability, or conformational preferences. However, doing this manually can be time-consuming and error-prone, especially in large or complex molecules.
The Node Specification Language (NSL) in SAMSON offers a concise way to filter and manipulate molecular data through well-structured queries. One useful subset of NSL capabilities relates specifically to bonds and how to filter them based on their type. This can help modelers rapidly inspect and modify molecular models according to specific research or design needs.
Understanding bond types in NSL
NSL categorizes bond types using the bond.type attribute, which has the short name b.t. This attribute lets you match bonds based on the chemical bonding type. These types are:
single(shorthands:s,1)double(d,2)triple(t,3)amide(am)aromatic(ar)dummy(du)undefined(un)
To apply this in SAMSON, simply use a NSL query such as:
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b.t s |
This will match all single bonds in the structure. You can also target multiple bond types using a comma-separated list:
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b.t s,d |
This matches all bonds that are either single or double.
Common use cases
If you’re analyzing aromatic systems in drug-like molecules, this query will be useful:
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b.t ar |
Or perhaps you’re interested in highlighting amide bond linkages in peptides or proteins:
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b.t am |
To filter structurally ambiguous parts of a molecule, catching undefined or dummy bonds may help:
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b.t du,un |
This query is particularly useful when cleaning up imported structures or checking outputs from conversion tools.
Best practices
It’s a good idea to combine bond type queries with other attributes. For example, to find only aromatic bonds longer than 1.4 Å:
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b.t ar AND b.len > 1.4A |
But remember: the bond must already have its type defined for the bond.type filter to work. Check your structure’s metadata if you’re not getting expected results.
Conclusion
Being able to filter and identify bonds by type is a routine part of molecular modeling work. With NSL in SAMSON, you can express these queries efficiently and apply them in powerful, flexible workflows. It’s a small time investment that pays off in analysis speed and accuracy.
To learn more about how to work with bond attributes in NSL, visit the SAMSON NSL documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.