When analyzing or designing molecular systems, one of the common challenges faced by computational chemists and molecular modelers is identifying specific bond types across large and complex structures. Whether it’s searching for aromatic rings, locating all amide bonds in a protein backbone, or filtering dummy bonds from an imported structure, being able to selectively match bond types is essential for accurate modeling, simulation, or modification.
If you’re using the SAMSON platform, there’s good news: bond type filters are built into the Node Specification Language (NSL), allowing you to make precise selections using intuitive, text-based queries.
Why Bond Types Matter
Bond types carry important chemical meaning. A single vs. double bond could affect a molecule’s geometry, reactivity, or even its spectroscopic properties. In some cases, misidentified or undefined bonds can lead to miscalculations or incorrect visualizations.
With NSL, you can precisely select bonds based on their type and use these filters to automate selections, refine visualizations or prepare simulations with suitable constraints.
Supported Bond Types in NSL
In NSL, each recognized bond type has a corresponding keyword and shortcut.
| Type | Short forms | Description |
|---|---|---|
single |
s, 1 |
Single covalent bond |
double |
d, 2 |
Double covalent bond |
triple |
t, 3 |
Triple covalent bond |
amide |
am |
Amide bond (common in proteins) |
aromatic |
ar |
Bonds in aromatic systems |
dummy |
du |
Placeholder or special bonds |
undefined |
un |
Bonds with unspecified types |
Writing Queries for Bond Type Selection
You can use the bond.type attribute (short version: b.t) to match bonds of particular types. Here are some examples of how it works in practice:
bond.type single(orb.t s): selects all single bonds.bond.type single, double(orb.t s,d): selects both single and double bonds — a common query when cleaning up ring structures.bond.type dummy, undefined(orb.t du,un): helps locate problematic bonds in imported structures you may want to fix or delete.
These queries help you explore your structures with much more precision, without having to manually click or inspect hundreds of bonds visually.
Use Cases Where This Helps
- Structure validation: Quickly locate undefined or dummy bonds from imported files for cleaning.
- Fragment detection: Identify aromatic systems or amide linkages for specific molecular motifs.
- Simulation control: Select bonds by type to freeze or constrain them during molecular dynamics simulations.
A Note on Bond Definitions
Keep in mind that these queries work only if bond types are defined in your data. Some imported files (like certain PDBs) may not include all bond types. Tools within SAMSON or SAMSON Extensions may be needed to assign or correct them.
To try using bond type selection, open the NSL filter field in SAMSON’s selection panel and enter one of the queries above.
Learn more in the complete documentation: https://documentation.samson-connect.net/users/latest/nsl/bond/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.