Molecular modeling often involves managing and analyzing complex structures. Keeping track of annotations and specific characteristics to highlight relevant portions of the model is essential for clarity and precision. SAMSON’s Node Specification Language (NSL) provides a structured way to achieve this, and today we’ll explore note attributes—a feature designed to interact with specific note nodes in your project.
What Are Note Attributes?
Note attributes are part of the note attribute space, referred to by the short form nt. These attributes apply specifically to note nodes in SAMSON and are a subset of broader attributes shared across other node types. Whether you are filtering, tagging, or organizing annotations in your molecular model, these attributes ensure flexibility and precision.
Key Note Attributes
Here’s a breakdown of some key note attributes you can start using in SAMSON:
| Attribute | Short Name | Values | Examples |
|---|---|---|---|
| hidden | h |
true, false |
nt.h, not nt.h |
| name | n |
Strings in quotes | nt.n "Example" |
| visible | v |
true, false |
nt.v, not nt.v |
Examples of Usage
Let’s look at a few practical examples:
- Filtering Visible Notes: To identify or manipulate only visible note nodes, use
nt.v. Similarly, to exclude visible notes, usenot nt.v. - Tagging Notes with Names: If you’ve assigned names to specific annotations, filter them with
nt.n "Name". You can even use wildcards likent.n "L*"to capture all notes starting with “L.” - Highlighting Hidden Notes: To find hidden note nodes within the attribute space, utilize
nt.hor exclude them using its negation,not nt.h.
Integrating Notes into Complex Workflows
By systematically categorizing notes with visibility flags (nt.v), selection flags (nt.sf), or using logical operators like and, or, you can create advanced filtering workflows. These workflows are especially useful when dealing with layered data, such as annotations across molecules in a biophysical simulation. Using these attributes ensures you can navigate efficiently without overwhelming complexity.
Conclusion
SAMSON’s note attributes in the NSL are designed to enhance your molecular modeling experience through efficient organization and control over annotations. Whether you’re analyzing structures, tagging annotations, or refining visual outputs, these attributes offer clarity and precision.
To explore the topic in more depth, visit the official documentation at https://documentation.samson-connect.net/users/latest/nsl/note/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.