Taming Complex Molecular Structures with Atom Filters in SAMSON

When dealing with large macromolecules, molecular modelers often need to isolate specific types of atoms quickly. Whether you’re setting up a simulation, visualizing specific regions, or analyzing properties, being able to filter atoms precisely can save hours of manual work. This is where SAMSON’s Node Specification Language (NSL) becomes incredibly helpful.

In this post, we’ll explore how to effectively use atom attributes in NSL to filter atoms based on characteristics like hybridization, aromaticity, geometry, and electronegativity. If you’ve ever struggled to select, say, all SP2-hybridized atoms in a protein backbone, or only non-polar hydrogens, this is for you.

Use Case 1: Selecting SP2-Hybridized Carbons

If you’re analyzing aromatic systems or unsaturated functional groups, SP2-hybridized carbons are typically of interest.

You can select them in NSL using:

This matches carbon atoms with SP2 hybridization. For an additional condition like resonance (e.g., for delocalized pi systems), extend the query:

Use Case 2: Finding Aromatic Atoms

Aromatic atoms are commonly targeted in drug design and quantum chemistry. To identify them:

To go further and select only aromatic nitrogen atoms, for example:

Use Case 3: Filter by Electronegativity

Atoms with high electronegativity often play crucial roles in intermolecular interactions. To find atoms with electronegativity above 2.5:

To select atoms in a specific range:

This is handy for analyzing polar regions or hydrogen bonding interfaces.

Use Case 4: Selecting All Polar Hydrogens

Polar hydrogens participate in hydrogen bonding, which drives many macromolecular interactions. Select them with:

To exclude hydrogens bound to carbon (i.e., non-polar):

Use Case 5: Geometry-Based Selection

Looking to isolate atoms in trigonal planar geometry?

This corresponds to geometries like those found in carbon-carbon double bonds. You can also combine this with specific atoms:

Why This Matters

Being able to filter atoms precisely isn’t just convenient—it’s essential when building molecular dynamics simulations, configuring force fields, or interpreting 3D structures. Imagine reducing a 10,000-atom scene to just 15 atoms with specific features, instantly.

All filters in SAMSON’s NSL use intuitive short names (e.g., a.s for symbol, a.hy for hybridization), making it easier to build queries and experiment. This also integrates well with scripting and batch analysis.

You’ll find a comprehensive reference to all atom attributes—including formal charges, oxidation states, and even metal subcategories—along with examples, in the official SAMSON documentation.

Learn more in the documentation.

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