When building or analyzing molecular systems, researchers often have to manage highly complex structures composed of atoms, residues, chains, groups, and all sorts of simulation elements. Managing these efficiently is critical to working with large or dynamic molecular models. That’s where the concept of node types in SAMSON becomes useful — and even essential.
This blog post breaks down what node types are in SAMSON, how they relate to the molecular systems you’re working with, and why understanding them can streamline your modeling and analysis workflows.
Understanding Node Types
In SAMSON, almost everything is a node. Atoms, bonds, molecules, simulation results, 3D representations, annotations — all of these are nodes. A node type is simply a classification indicating what a node represents. This system allows SAMSON to organize complex molecular models within a clean, structured node hierarchy called the Document Graph.
Examples of node types in SAMSON include:
- Structural nodes (e.g., atoms, groups, chains)
- Visual nodes (e.g., molecular representations, materials)
- Simulation nodes (e.g., trajectories, constraints)
- Interaction nodes (e.g., external fields, constraints)
Each node is part of this tree-like structure that makes it possible to add, remove, manipulate, or even programmatically access model elements with precision.
Why This Matters to Molecular Modelers
Modeling often involves working with massive datasets, such as protein-ligand complexes, multi-scale systems, or molecular dynamics simulations. Without a hierarchical and type-based system, it would be frustrating to manage these structures effectively.
For example, say you want to highlight only the ligand in a protein-ligand complex. Understanding the node types helps you navigate the structure: you can select all atoms with the property isLigand == true, or traverse the Document Graph to extract just the branch corresponding to the ligand node types.
Moreover, when scripting SAMSON or using the Node Specification Language (NSL), knowing node types becomes a powerful tool. NSL allows you to select, filter, or apply operations based on node types efficiently and consistently.
Using Node Types with SAMSON Extensions
Many SAMSON Apps and Editors leverage node types to work on specific node classes. For example, a visualization editor might apply a special rendering style to only nodes of type Atom or Molecule.
Node-aware apps make operations safer and more efficient. You won’t mistakenly apply a simulation constraint to an annotation, or visualize a note as if it were a molecular structure.
Advanced Tip: Creating Custom Node Types
If you’re developing your own SAMSON Extensions (yes, that’s possible!), the node type concept gives you a clean way to define your own data structures — whether you are storing machine learning predictions, custom forces, or volumetric fields. Each can be registered as a new node type, complete with your own behaviors and data.
Conclusion
Mastering node types in SAMSON will help you make sense of large molecular systems, automate tasks more effectively, and develop or apply more powerful modeling workflows.
To learn more about node types and how they behave in SAMSON, visit the official documentation or explore the full SAMSON Reference section.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.