When analyzing or designing molecular systems, selecting specific types of atoms quickly and precisely can save a lot of time and reduce errors. One of the frequent needs among molecular modelers is to isolate aromatic atoms across complex molecular structures. Whether you’re identifying aromatic systems in drug molecules or filtering specific atom types for simulations, doing this manually can be time-consuming and error-prone.
Fortunately, the Node Specification Language (NSL) in SAMSON offers a simple and precise way to query and match atoms based on their attributes—including aromaticity.
Why Search for Aromatic Atoms?
Aromatic atoms participate in critical chemical behavior due to delocalized π-electrons. Identifying these atoms can be essential for:
- Detecting functional groups like benzene rings in organic molecules
- Setting up force field parameters for simulations
- Targeting π-π stacking interactions in protein-ligand docking
How to Select Aromatic Atoms with NSL
In SAMSON, the atom.aromatic attribute—or shorter, a.ar—is used to match aromatic atoms.
Here are some practical examples:
a.ar: Selects all aromatic atoms in your document.a.s C and a.ar: Selects only aromatic carbon atoms.a.inRing and a.ar: Selects atoms that are both in a ring and aromatic.a.sy "C.ar"(if available): Matches based on SYBYL types, useful if you have pre-assigned atom types.
Combining a.ar with other attributes allows you to build precise and sophisticated queries. For example, you could write:
|
1 |
a.ar and a.hba |
to identify aromatic atoms that are also hydrogen bond acceptors.
Complementary Attributes
Sometimes, you’ll want to narrow aromatics further with additional filters. Here are some commonly used attributes you can combine with a.ar:
a.e: Match by element name (e.g.a.e Nitrogen)a.hp: Match polar hydrogensa.nbha: Number of bonded heavy atoms
With these combinations, your queries become more chemically meaningful and help you isolate just the right atoms for your task—whether it’s molecular painting, fragment selection, or biomolecular interaction analysis.
Advanced Tip: Build Selection Macros
Save your frequently used aromatic filters in SAMSON using selection macros or scripts to automate model preparation or property annotations.
Want to Learn More?
You can see the full set of atom attributes and filter examples in the NSL Atom Attributes documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON from https://www.samson-connect.net.