For molecular modelers, filtering and querying molecular data efficiently is often a significant challenge. Searching vast datasets for specific conformations can take more time than actually analyzing results. SAMSON’s Node Specification Language (NSL) offers a powerful solution to this by letting you effectively define and search for specific conformations using attributes from its conformation attribute space. In this post, we’ll explore some of these attributes and how they simplify your workflow.
What Are Conformation Attributes?
Conformation attributes belong to the conformation attribute space, referred to by the short name co. The aim is to match conformation nodes and provide detailed filtering capabilities. These attributes can be inherited from the broader node attribute space or be specific to conformations. Below, we’ll delve into some key examples.
Example 1: Filtering by Number of Atoms
If you’re working with large molecular structures and need to focus on conformations with a specific number of atoms, the numberOfAtoms attribute can be immensely useful. Introduced with the short name co.nat, it allows you to filter conformations based on the number of atoms they contain.
For instance:
co.nat > 100matches all conformations with more than 100 atoms.co.nat 100:200matches conformations with atom counts between 100 and 200.
This feature saves you from manual selection and lets you work efficiently with large datasets.
Example 2: Matching by Selection Attributes
Two frequently used attributes, selected and selectionFlag (short name: sf), help you work with selected nodes in your dataset. While selected checks whether a node is selected (true or false), selectionFlag provides even more streamlined queries for specific nodes.
Example queries include:
co.selected: Match all selected conformation nodes.not co.selected: Match unselected conformation nodes.co.sf false: Match conformations with aselectionFlagset tofalse.
Both attributes allow you to dynamically isolate and modify specific subsets of your data without repetitive manual inputs.
Additional Customization: Naming Conformations
To track specific conformations in your datasets, use the name attribute (short name: co.n), which supports strings. For instance:
co.n "A": Matches conformations named A.co.n "L*": Matches all conformations with names starting with L.
This feature not only organizes your data but makes future queries quicker and more precise.
Why These Attributes Are Essential
From simplifying atom count filters to leveraging selection attributes, NSL’s conformation-based attributes empower molecular modelers to quickly find necessary information in comprehensive datasets. By reducing manual filtering and adding flexibility to workflows, these tools steer your focus back to insightful molecular analysis.
For detailed documentation and more examples, visit this page.
SAMSON and all SAMSON Extensions are free for non-commercial use. Download SAMSON at www.samson-connect.net.