When working with complex molecular models, one of the most common (and sometimes frustrating) tasks is selecting specific types of atoms to analyze, visualize, or modify. Whether you’re trying to highlight aromatic rings, isolate charged atoms, or segment atoms based on their partial charge or hybridization, doing it manually is slow and error-prone.
Thankfully, SAMSON offers a powerful and flexible way to solve this: by using the Node Specification Language (NSL) and especially the atom attributes. These attributes can be combined in human-readable expressions that easily pinpoint the atoms you’re interested in.
What’s the problem?
Say you want to highlight just the aromatic carbon atoms in your system, or perhaps identify all atoms with partial charge above 1.0. If you’re dealing with large proteins, small organic molecules, or complex drug-like compounds, that can mean searching through thousands of atoms. It’s tedious to do manually — and even worse if you’re trying to automate a pipeline.
Atom Attributes Offer a Shortcut
Each atom in SAMSON can be characterized by many attributes — from basic ones like symbol, element, and mass to more specific ones like aromatic, resonance, or hybridization.
You can leverage these with short expressions. For example:
a.ar: matches all aromatic atomsa.s C and a.ar: matches only aromatic carbon atomsa.pc > 1.0: matches atoms with partial charge greater than 1.0a.hy sp2: matches atoms with SP2 hybridization
These expressions make it easy to select just the atoms you care about — even when they are deeply embedded in a large structure. The simplicity of the syntax allows both novice and expert users to build sophisticated filters quickly.
Combining Attributes for Power Users
You can combine atom attributes using logical operators like and, or, and not. This allows you to write queries like:
a.s N and a.ar: match aromatic nitrogen atomsa.fc < 0 or a.fc > 0: match atoms with any non-zero formal chargea.g tet and a.hy sp3: match atoms with tetrahedral geometry and sp3 hybridization
This means fewer mistakes, more consistent selections, and scripts or workflows that can be reused and adapted easily.
Saves Time and Scales Easily
Imagine building a script that highlights all atoms with partialCharge > 1.5 and resonance true. This is straightforward with attributes:
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1 |
a.pc > 1.5 and a.reso |
You could even export selected atoms, measure distances between these atoms, or run simulations only on selected regions. Selection becomes not an obstacle, but a tool.
Takeaway
Whether you’re inspecting functional groups, preparing input for simulations, or building analysis scripts, using NSL with atom attributes allows you to focus on what matters — the chemistry — rather than spend time on tedious selections.
You can explore the full list of atom attributes in the official documentation: NSL Atom Attributes Documentation.
✨ Mastering atom attributes truly opens the door to more efficient, precise, and enjoyable molecular modeling.
SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at https://www.samson-connect.net.