When working with molecular systems, modeling becomes significantly easier if your software knows what kind of data it’s dealing with. In SAMSON, this is achieved through a smart organization system called node types. If you’re new to SAMSON or just starting to explore its more advanced features, understanding how node types work is one of the easiest ways to improve your productivity.
But what exactly is a node in SAMSON?
Nodes: The building blocks of molecular models
At its core, SAMSON uses a data structure called a graph to represent your molecular systems. Nodes are the elements (or vertices) of that graph, and they represent different objects within your scene: atoms, bonds, molecules, simulation results, graphical representations, annotations, and more.
Each node has an associated type. This is crucial, because it tells SAMSON (and you as the user) how that node behaves, what properties it contains, and how it can be interacted with. Whether you’re building a new model, analyzing interactions, or customizing visuals, knowing the node types gives you better control over your entire project.
Common node types in SAMSON
Here are some common node types you’ll frequently encounter:
- Structural nodes: atoms, bonds, residues, chains, molecules, etc. These are typically part of your system’s core structure.
- Visual models: nodes that define how structures are rendered (e.g., ball-and-stick, surfaces, ribbons).
- Simulation results: the output of simulations (e.g., energy profiles, trajectories).
- Annotations: text labels, measurement tools, etc., that help you interpret and present your systems.
- Groups: containers to organize multiple nodes logically for better navigation.
Each of these node types has properties and behaviors specific to its role. That means when you’re developing your own workflows—or even SAMSON Extensions—you can build logic that interacts with the exact kinds of nodes you need.
Power-up: filtering and selection with node types
One of the most powerful uses of node types is in selection and filtering. For instance, if you want to select only atoms involved in hydrogen bonding, or only surface nodes, knowing their types lets you script smart workflows or simply use the filter tools more effectively.
SAMSON comes with a feature called the Node Specification Language (NSL), which works closely with node types. With NSL, you can write expressions that query nodes by type, name, properties, or even relationships. It’s a great time-saver for complex selections.
Custom extensions: why node types matter even more
If you eventually move into developing your own SAMSON Extensions or automating processes, node types become indispensable. They allow your code to safely and precisely manipulate only the nodes it should, reducing bugs and making your tools more robust.
Wrap-up
Learning how SAMSON classifies and handles node types will make you a more efficient and accurate molecular modeler. It helps you interact with your systems in a structured way, improving clarity, automation potential, and overall modeling experience.
To dive deeper into node types, visit the official documentation on Node types.
Learn more about all reference pages in SAMSON.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.