In molecular modeling, selecting the right set of atoms can be the difference between getting a meaningful result and spending hours troubleshooting. One common requirement is to select atoms based on their molecular geometry—for example, tetrahedral or trigonal planar geometries.
In SAMSON’s Node Specification Language (NSL), atom geometries can be used to define powerful queries that work across different molecular structures and formats.
Why Geometry-Based Queries Matter
You might need to analyze or modify all tetrahedral carbon atoms, or highlight octahedral metal complexes. Geometry isn’t always visible at a glance, especially in large biomolecules or complex inorganic assemblies. Instead of manually checking each atom, using atom.geometry in NSL can help you programmatically identify what you need.
Getting Started with atom.geometry
With NSL, the atom geometry attribute is accessed using a.g. You can match geometries by either their full name or short name. For instance:
a.g tetmatches tetrahedral atomsa.g omatches octahedral atomsa.g lmatches linear atoms
Geometry matching works only when geometry has been computed first, so ensure the structure you’re working with is analyzed beforehand in SAMSON.
Common Geometry Types
| Geometry | Short Name |
|---|---|
| Tetrahedral | tet |
| Trigonal Planar | tpl |
| Trigonal Pyramidal | tpy |
| Linear | l |
| Octahedral | o |
| Dodecahedral | d |
Examples You Can Use
- Select tetrahedral atoms:
a.g tet - Select carbon atoms with octahedral geometry:
a.s C and a.g o - Select atoms that are either linear or bent:
a.g l, b
These selections are especially useful when scripting molecule filters or building subsets for computational analysis. Geometry-based queries can be combined with other atomic properties (like symbol or hybridization) for more precise control.
Tips
- Always verify that geometry has been precomputed. Otherwise, results may come up empty.
- Combine
a.gfilters with visualization styling to quickly identify patterns across large structures. - Save frequently-used filters in your workspace to streamline your workflow.
Exploring structures through geometry reveals symmetries, potential coordination environments, and reactive sites more efficiently than eyeballing atoms one by one.
To see the full list of supported geometries and learn more, visit the documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.