Molecular modeling often demands precise control over what is displayed or hidden in visual outputs. Whether you’re preparing figures for publication, creating complex simulations, or organizing large datasets, fine-tuning visibility attributes can make your workflow smoother and results more impactful. This blog post explores how SAMSON’s Node Specification Language (NSL) leverages presentation attributes to help you master visibility settings.
The Presentation Attribute Space
The presentation attribute space in NSL (short name: pr) is the toolset designed specifically for dealing with visibility-related attributes in presentation nodes. You can think of this as a language to dictate what appears, disappears, or is highlighted in your molecular model without affecting the underlying data.
Key Attributes for Visibility Control
Below are the key attributes available in the presentation space that allow you to control visibility and emphasis:
hidden(h): Use this to completely hide or show a node. For example:pr.h– checks if a node is hidden.not pr.h– checks if a node is visible.visibilityFlag(vf): This allows you to toggle a visibility flag, which can work in tandem withhidden. Examples:pr.vf– checks if the visibility flag is true.pr.vf false– sets the flag to false, effectively “hiding” the node when used appropriately.visible(v): Toggles the “visible” status of nodes. Examples include:pr.v– verifies visibility.not pr.v– verifies invisibility.
Why You Need this Control
Imagine working on a highly detailed molecular design project where certain molecular components are not immediately relevant. Using attributes like hidden or visible, you can declutter your workspace to focus on what truly matters. Similarly, for presentations, finely tuned visibility settings ensure that your visuals are clear and non-distracting.
Additional Tips
All these attributes can be combined with logical operators in NSL to form powerful expressions. For example:
pr.h and not pr.vf– finds nodes that are hidden and do not have their visibility flag set.pr.v and pr.vf– focuses on nodes that are visible and marked with a visibility flag.
Mastering these attributes can significantly enhance your molecular modeling workflow by offering intuitive control over the display of intricate systems.
To explore the full documentation on presentation attributes, including more examples and attribute details, please visit SAMSON’s official documentation page on presenation attributes.
SAMSON and all SAMSON Extensions are free for non-commercial use. To get started, download SAMSON here.