When working on large and complex molecular systems, one common frustration for molecular modelers is managing visual clarity. Whether designing a nanosystem or analyzing simulation results, ensuring that only the relevant parts of the model are visible can dramatically impact both performance and understanding.
If you’ve worked with SAMSON, you might already be familiar with the Node Specification Language (NSL) that provides powerful ways to filter and interact with your molecular model through attributes. Among these, the visible attribute for PropertyModel nodes (short name: pm) stands out as a surprisingly effective tool to declutter your workspace by controlling visibility through fine-grained queries. Let’s explore how it works and why you might want to use it today.
What is pm.v Exactly?
The NSL structure for PropertyModel nodes supports an attribute called visible, accessible via pm.v. This boolean attribute simply indicates whether a given Property Model node is currently visible in the viewport. This might sound basic, but it provides a lot of filtering power when paired with NSL expressions. For instance:
pm.v: filters for nodes that are currently visible.not pm.v: filters for nodes that are hidden from view.
This is especially useful when working with complex systems where parts of it are temporarily obscured for analysis or presentation purposes.
Why Should You Care?
In an environment where hundreds (sometimes thousands) of Property Models may be associated with a molecule—describing everything from charge distributions to elastic tensors—having the ability to work only on what’s visible can be a time-saver and reduce cognitive load.
By using pm.v in conjunction with other NSL queries, you can easily write expressions like:
pm.v and pm.n "*Electrostatic*"
This will return all visible Property Models whose names contain the word “Electrostatic.” It’s a simple, elegant way to focus only on what’s currently relevant in your visual analysis.
How Is This Different From Other Visibility Options?
The pm.v attribute complements other visibility-related attributes inherited from general node behavior, including:
selectionFlag(pm.sf)visibilityFlag(pm.vf)hidden(pm.h)
While these also pertain to visibility, pm.v is practical because it tells you about the rendered state directly—whether or not it’s visible now. This may differ from the visibilityFlag, which indicates a flag value. For straightforward visibility checking, pm.v is your go-to tool.
Use Case: Batch Selection for Presentation
Imagine you’re preparing a publication and you want to isolate a small subset of visually relevant descriptors from a complex model. Using:
pm.v and pm.sf
You can identify visible property models that also have their selection flag on. This allows you to apply styling or export data from nodes that are both relevant and currently in view.
Takeaway
The pm.v attribute is a small but powerful feature in your SAMSON toolkit. It enables smarter data selection, easier scene management, and efficient workflows when combined with other attributes in the NSL.
To learn more about how visibility and other attributes work with Property Model nodes in SAMSON, visit the official documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.