When working with complex molecular systems, researchers often find themselves juggling multiple representations, layers of information, and relationships between parts of their models. In SAMSON, a molecular design platform, this complexity is managed through an elegant and flexible concept: node types.
Whether you’re designing novel materials, simulating biomolecular interactions, or just exploring structural data, having a clear understanding of SAMSON’s node types can significantly improve your modeling workflow. Let’s break it down.
What is a “Node” in SAMSON?
In SAMSON, everything you work with is a node: atoms, bonds, molecular models, annotations, simulations, visual representations – they’re all nodes in a hierarchical system. This structure allows you to construct and manipulate molecular systems in a modular, nested way.
Types of Nodes
Nodes are grouped into different node types based on their roles. Some of the fundamental types include:
- Structural nodes: Atoms, residues, molecules, and groups. These represent your system’s core data.
- Visual nodes: Representations like ball-and-stick models, surfaces, or ribbons. These help you visualize what’s going on.
- Simulation nodes: Encapsulations of simulations like molecular dynamics or energy calculations.
- Annotation nodes: Labels or markers you might use to keep track of regions of interest.
- Group nodes: Allow you to hierarchically organize your molecular content, which is especially useful for large systems.
Why Node Types Matter
Understanding node types helps you:
- Filter and select content more effectively when working with large molecular systems.
- Customize your workflow by adding or modifying specific types of data without affecting others.
- Create reusable templates through smart grouping of relevant nodes.
- Streamline simulation setups by targeting only the nodes your algorithm needs (e.g., selecting only atoms for energy minimization).
Combining Node Types with the Interaction Designer and NSL
Once you’re familiar with node types, you can take advantage of SAMSON’s advanced features like the Interaction Designer or the Node Specification Language (NSL). These tools let you define complex interaction patterns or filter selections with precision, further tying back to the concept of node types.
Tips for Working with Node Types
- Use the Document View in SAMSON to explore the hierarchical structure of your node tree visually.
- Hover or right-click nodes to quickly see their type or access context-specific options.
- Search for nodes by type or name using the filtering tools built into SAMSON’s interface.
By learning how to leverage node types, you’ll navigate complex molecular systems more easily and build better models with less frustration.
📘 Learn more about node types in the official documentation.
Visit the full References section of the documentation to explore related topics.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.