When working on large, detailed molecular models in SAMSON, keeping track of annotations and organizational elements becomes essential. That’s where note nodes come in. These nodes allow molecular modelers to embed comments, labels, or other textual information directly into the data graph. But did you know there’s a dedicated set of note attributes that can help you query and control these notes more effectively?
In this article, we’ll look into how to better manage and filter note nodes using the note attribute space in SAMSON’s Node Specification Language (NSL), so you can organize models more clearly and query them more precisely when building complex molecular systems.
What Are Note Attributes?
The note attribute space (short name: nt) applies specifically to note nodes — these are useful for labeling parts of your molecular model. Whether you’re identifying areas to revisit, flagging alternative conformations, or listing hypotheses, note nodes offer flexibility.
Some useful queries you can perform on note attributes include checking whether a note is visible, selected, or has a specific name.
Filtering with Note Attributes: Examples
Below is a table summarizing available note attributes and example queries you can use:
| Attribute | Short name | Sample queries |
|---|---|---|
hidden |
h |
nt.h, not nt.h |
name |
n |
nt.n "HydrophobicPatch", nt.n "TODO*" |
selected |
(no short name) | nt.selected, not nt.selected |
selectionFlag |
sf |
nt.sf, nt.sf false |
visibilityFlag |
vf |
nt.vf, nt.vf false |
visible |
v |
nt.v, not nt.v |
When Does This Help in Practice?
Let’s say you’ve used dozens of notes within your protein-ligand system to outline docking poses, mark energy calculations, or highlight water bridges. Over time, some of these notes may be turned invisible or become hidden. Searching through them manually gets tedious — even more so when these notes are nested in different parts of your model hierarchy.
Using NSL, a query like nt.n "Pose*" and not nt.v instantly lets you retrieve all note nodes related to poses that are currently invisible. Similarly, not nt.h finds all notes that aren’t hidden, regardless of where they’re located in the model tree.
A Tip on Querying Selected Notes
Unlike other node spaces, the selected attribute in note nodes does not have a short name. So instead of typing nt.s, make sure to use nt.selected. This small difference can save you debugging time when filters don’t behave as expected.
Conclusion
In complex molecular modeling projects, organization matters. Learning how to use the nt attribute space to filter and manage note nodes helps keep your workspace clean and your thinking clear. These tools are there to support your process — especially when your system includes hundreds of nodes.
To learn more, visit the original documentation page here: https://documentation.samson-connect.net/users/latest/nsl/note/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.