Managing Note Attributes in SAMSON’s Node Specification Language

For molecular modelers using SAMSON, managing annotations and metadata within complex molecular structures can be a critical aspect of keeping your workflow organized and efficient. With SAMSON’s Node Specification Language (NSL), note attributes provide a dedicated space for handling such annotations. Whether you want to hide certain elements, name specific nodes, or toggle visibility flags, this blog post introduces key concepts to streamline your work with note attributes.

What are note attributes?

Note attributes belong to the note attribute space (short name: nt). They are designed exclusively for note nodes within your molecular system. If you’re working with molecular models where notes are used to annotate your data, these attributes help you navigate, filter, and organize them effectively.

Key note attributes

Below are some of the most useful attributes available in the note attribute space:

  • hidden (h): A Boolean attribute that determines whether a note is hidden (true) or visible (false).
    Example expressions:
    nt.h, not nt.h
  • name (n): This attribute matches the name of a note. You can filter notes by their names using regular expressions.
    Example expressions:
    nt.n "Note1", nt.n "Experiment*"
  • selected: Indicates whether a note is currently selected in the molecular model. This attribute does not have a short name.
    Example expressions:
    nt.selected, not nt.selected
  • selectionFlag (sf): Toggles the selection status of a note.
    Example expressions:
    nt.sf true, nt.sf false
  • visibilityFlag (vf): Determines whether a note is flagged as visible.
    Example expressions:
    nt.vf, nt.vf false
  • visible (v): A Boolean attribute that shows whether the note is currently visible. It is tightly linked to the hidden attribute.
    Example expressions:
    nt.v, not nt.v

When to use these attributes?

If you often annotate molecular structures or datasets in SAMSON (e.g., tagging specific residues, leaving experimental notes, or marking nodes for later review), these attributes allow you to filter and manipulate note nodes programmatically. For instance:

  • Use hidden to temporarily declutter your workspace by hiding specific notes.
  • Use name to target notes with specific labels when performing operations such as bulk selection.
  • Leverage selectionFlag or visibilityFlag for advanced scenarios where you need fine-grained control over which notes are visible or active during analysis.

Example visualization from the documentation:

The table below is derived from the documentation and showcases how attributes, short names, and expressions are mapped:

Table example for note attributes

Conclusion

Managing attributes for note nodes can be pivotal for an effective molecular modeling workflow. By mastering these features, you can stay more organized and accomplish tasks more efficiently. To dive deeper into the technical details and learn about other attributes, visit the official SAMSON documentation page.

Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Download SAMSON today at https://www.samson-connect.net.

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