As a molecular modeler, have you ever struggled to manage the visibility or selection status of specific objects in complex molecular designs? If so, the presentation attributes feature in SAMSON’s Node Specification Language (NSL) might be precisely what you need to make your workflows more efficient. Let’s dive into how these attributes can simplify your modeling by giving you precise control.
What are Presentation Attributes?
Presentation attributes belong to the presentation attribute space in NSL, often referred to with the shorthand pr. These attributes apply specifically to presentation nodes, which control how objects in your molecular modeling project are visually presented or selected. They can help you manage display states, names, and selection indicators for enhanced control and clarity.
Key Attributes You Should Know
Let’s look at some impactful attributes from the presentation space:
- Hidden: Controls whether a node is hidden from view. Its shorthand is
hand it acceptstrueorfalseas values (e.g.,pr.h). - Name: Lets you assign or search for nodes by a specific name. The short name is
n, and names should be strings in quotes (e.g.,pr.n "Protein_A"). - Selected: Indicates whether a node is selected. You can write it directly as
pr.selected, but note that it does not have a shorthand form. - SelectionFlag: Acts as an indicator for flagged selections, with a shorthand
sf(e.g.,pr.sf false). - VisibilityFlag: Enforces visibility properties of nodes. Its shorthand is
vf(e.g.,pr.vf). - Visible: A straightforward boolean (true/false) that manages whether a node is visible or not. Short name:
v.
Application Examples
The best way to understand these attributes is through practical examples. Suppose you want to hide all nodes that aren’t selected:
|
1 |
not pr.selected |
Or, if you want to identify nodes by name, the following might help:
|
1 |
pr.n "Ligand_1" |
Wildcard search is also available, such as:
|
1 |
pr.n "Lig*" |
Improve Your Molecular Modeling Workflow
When dealing with complex molecular models, managing visibility and selection is crucial for clarity and efficiency. The presentation attributes in NSL enable you to specify parameters with precision, reducing clutter and saving time. Whether you’re focusing on a protein-ligand interaction or filtering out unnecessary components, these attributes streamline your process.
To learn more about presentation attributes and explore their full potential, visit the official documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.