For molecular modelers, identifying and customizing specific paths within a molecular structure can often be challenging. The path attribute space in SAMSON’s Node Specification Language (NSL) offers an elegant solution for pinpointing and analyzing elements within conformation nodes. Whether you want to filter paths by the number of atoms they contain or toggle selection flags efficiently, knowing these attributes can significantly enhance your modeling workflow. Let’s dive into some of the key path attributes and their practical applications.
What are Path Attributes?
The path attribute space, identified by the short name p, is designed to work specifically with conformation nodes in SAMSON. Through these attributes, you can query paths based on the number of atoms, their names, or even their selection states.
In addition to attributes specific to path, this space inherits a few attributes from the more general node attribute space. These include:
- name (
n): Matches paths based on their names. - selected: Matches if a path is selected. The selection state can be toggled dynamically.
- selectionFlag (
sf): Matches paths based on boolean selection flags.
Filtering Paths by the Number of Atoms
One of the most powerful features of the path attribute space is its ability to filter paths by the number of atoms they contain. The numberOfAtoms attribute (short name: nat) provides a highly practical way to include or exclude paths based on atom count thresholds.
Example 1: Paths with More Than 100 Atoms
If you’re working on a structure and need to analyze only the larger conformation paths, you can use an expression like:
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p.nat > 100 |
This will match all paths with more than 100 atoms. It’s perfect for narrowing down complex models to focus on regions of greater interest.
Example 2: Paths Within a Range
To find paths with an atom count that lies between 100 and 200, use:
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p.nat 100:200 |
This flexibility is particularly useful when working with structural models that exhibit variability in the number of atoms across different paths.
Practical Use of Selection Attributes
In addition to atom counts, toggling selection-related attributes can help streamline workflows. The selected attribute allows you to match paths based on whether they are currently selected:
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p.selected</code> or <code>not p.selected |
The selectionFlag attribute (sf) operates similarly, but with an added bonus of associating boolean flags to refine selections further.
Why Use Path Attributes?
By mastering these path attributes, you can drastically optimize your workflow when working with large or complex molecular structures. These attributes provide granular control over conformation nodes, making it easier to identify, filter, and manipulate parts of your models without manually navigating through large volumes of data.
To explore all the options and stay precise in your queries, visit the full documentation on path attributes: https://documentation.samson-connect.net/users/latest/nsl/path/
SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at https://www.samson-connect.net.