How to filter molecular bonds by length in SAMSON’s Node Specification Language

When working with molecular models, identifying bonds of specific lengths is often essential. Whether you’re analyzing structural changes, refining a force field, or creating visualizations that focus on specific bonding regimes, quickly filtering for bond lengths can save a lot of time and effort.

This is where SAMSON’s Node Specification Language (NSL) comes in handy. NSL lets you query molecular structures efficiently using a concise syntax. In this post, we’ll take a closer look at how you can use NSL to filter bonds by length, giving you control and speed in analyzing complex molecules.

Why filter by bond length?

Bonds that are too short or too long often indicate issues in your molecular models, such as incorrect geometry or problems arising from an optimization step. Conversely, selecting well-defined bond lengths can also help isolate specific interactions or prepare targeted simulations. For example:

Identifying potential hydrogen bonds or weak interactions by filtering longer bonds
Focusing on covalent bond ranges to clean up dummy or undefined links
Spotting abnormal bond stretches during conformational changes

Using `b.len` in NSL

Bond lengths in SAMSON can be queried using the b.len attribute. Unlike some software where only preset bond types are available, SAMSON allows you to define flexible numerical ranges or inequality conditions.

Here are several examples of how to use it:

b.len >= 1.5A – matches bonds with a length equal to or greater than 1.5 angstroms
b.len 1.2A:1.4A – selects bonds with lengths between 1.2 and 1.4 angstroms
b.len 0.15nm:2.1nm – works with nanometers too; here, the range is between 0.15 and 2.1 nanometers

The unit (e.g., angstroms or nanometers) must be specified in your query to make sure the filter behaves as expected. Both are supported fully within NSL.

Common pitfalls to avoid

Here are a few helpful tips to keep in mind:

Be explicit with units: b.len 1.3 is ambiguous. Write b.len 1.3A or 1.3nm for clarity.
Range syntax: Use start:end format with no spaces — spaces can break the parser.
Decimal vs integer: Even for integer-looking values, it’s safer to format bond lengths as floats (e.g., 1.0A vs 1A).

Combining with other attributes

You can also combine bond length filters with other NSL attributes to refine your selection. For instance, to find bonds with length between 1.3 and 1.5 angstroms AND of single type, you can write:

b.len 1.3A:1.5A AND b.t s

1	b.len 1.3A:1.5A AND b.t s

This level of specificity is especially useful in tasks like ligand docking, modification of active sites, or rebuilding partially resolved structures.

Wrapping up

The ability to filter molecular bonds by length with NSL is a practical strategy that saves time and helps you navigate large molecular systems more efficiently. Whether you’re debugging geometry or selecting a subset of interactions, using b.len can make your workflow smoother.

To learn more about bond attributes in NSL, visit the official documentation page: https://documentation.samson-connect.net/users/latest/nsl/bond/.

SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.