One of the common challenges in molecular modeling is locating and selecting specific types of chemical bonds within complex molecular systems. Whether you’re filtering out unwanted linkages, setting up simulations, or analyzing structural features, the ability to target bonds precisely can save significant time and effort.
That’s where the Node Specification Language (NSL) in SAMSON comes in. With NSL, you can accurately filter and manipulate bonds based on their attributes using concise queries. Let’s take a closer look at how you can use NSL to work with bond types effectively.
Why Filter Bonds?
Molecular systems can contain thousands — or even millions — of atoms and bonds. In such systems, identifying specific bonding patterns like aromatic rings, amide linkages, or even undefined connections can be critical before running simulations, building force fields, or generating publication graphics. Instead of selecting these manually, NSL lets you use smart filters like:
b.t sfor single bondsb.t dfor double bondsb.t arfor aromatic bonds
This can be incredibly helpful when you need to, for example, extract all resonance structures (aromatic bonds), or inspect undefined or placeholder connections in a draft structure.
Bonds by Type
In NSL, the attribute bond.type (short name b.t) allows you to match variants of chemical bonds. Here are the accepted values you can use in your queries:
| Type | Shortcut(s) | Description |
|---|---|---|
single |
s, 1 |
Single bond |
double |
d, 2 |
Double bond |
triple |
t, 3 |
Triple bond |
amide |
am |
Amide bond (peptide links, for example) |
aromatic |
ar |
Aromatic bond (resonance structures) |
dummy |
du |
Non-chemical temporary bond (e.g. modeling scaffolds) |
undefined |
un |
Bonds without a defined type |
Query Examples
You don’t need to write lengthy scripts to query for different bond types — here’s how simple some common tasks can be in NSL:
- Find single bonds:
b.t s - Find single and double bonds:
b.t s,d - Find amide bonds:
b.t am - Find undefined bonds (possible modeling issues):
b.t un
To use these filters, simply paste them into the NSL-based selection tool in SAMSON. Once selected, bonds can be highlighted, visualized, modified, or exported, depending on your needs.
Use Case: Validate Structural Consistency
Imagine uploading a protein-ligand complex and finding that some linker bonds appear questionable. Instead of clicking through them one by one, you can use:
b.t un
… to instantly highlight all undefined bond types. This lets you quickly identify errors in structure import or pre-processing. Similarly, you can confirm the presence of amide bonds in a peptide backbone with:
b.t am
Conclusion
Combining the flexibility of NSL with the visual capabilities of SAMSON makes it much easier to navigate the complex world of molecular bonds. Whether you’re checking for errors or preparing your system for simulations, typing a few characters can help you focus only on what’s relevant.
Learn more about using bond attributes in NSL.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.