How to Easily Identify Ring Atoms in Molecular Structures Using NSL

Understanding ring systems in molecular models is essential when analyzing aromaticity, molecular rigidity, or designing pharmacophores. But manually detecting whether an atom belongs to a ring—and, if so, what type—can be time-consuming. This is where the Node Specification Language (NSL) provided in SAMSON comes in handy. One particularly helpful feature of NSL is its ability to filter atoms based on their ring membership—and even the size of those rings—using the inRing and ringSize attributes.

Let’s say you’re working on a structure with multiple cyclic substructures, and you want to:

• Highlight all atoms that are part of any ring
• Select atoms in 5- or 6-membered rings only
• Analyze the chemical environment of ring atoms

Here’s how you can do all that with simple NSL queries.

Find atoms inside any ring

To select atoms that belong to any ring, you can simply use:

This expression filters out all atoms not participating in rings. It’s useful when you want to isolate the rigid core of a molecule or highlight cyclic behavior in a system.

Find atoms in rings of specific sizes

If your analysis is sensitive to ring size (e.g., differences between aromatic 6-membered rings and non-aromatic 5-membered ones), NSL allows this via the ringSize attribute:

This expression selects atoms that lie in either 5- or 6-membered rings. It’s concise and enables precise annotation or filtering in your models.

A few notes:

• If an atom lies in two rings of different sizes, the ringSize attribute returns the smaller size.
• Atoms in fused rings (like in polycyclic aromatic hydrocarbons) can still be identified correctly.

Combine with other atom attributes

The real power of NSL shows when you combine these with other filters. For example, identify all aromatic carbon atoms in 6-membered rings:

This allows you to isolate the precise atoms relevant to π-systems or identify reactive sites within specific ring structures.

Why this matters

Ring structures are fundamental in almost every domain of molecular modeling—organic synthesis, drug design, materials science. Being able to query them efficiently within your modeling software saves time and ensures reproducibility. Whether you’re searching for cyclopentane rings or flagging ring strain in small cyclic compounds, NSL makes this fast and scriptable.

✅ No need to eyeball structures
✅ Works in combination with other attributes like geometry, hybridization, or element
✅ Filters apply instantly in the SAMSON workspace

You can learn more about all atom attributes here.

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