As a molecular modeler, one of the most common challenges is efficiently managing and analyzing the hierarchical structures that define molecular systems. Understanding folder attributes in SAMSON’s Node Specification Language (NSL) can help solve this problem by providing an expressive way to pinpoint folder-level properties within your molecular projects.
SAMSON’s folder attributes simplify the process of querying and managing nodes, especially when working on complex molecular structures like proteins, large assemblies, or multimeric systems. Whether you’re organizing structural models or filtering components based on atom composition, learning to use these attributes can significantly boost your productivity.
What Are Folder Attributes?
Folder attributes belong to the folder attribute space in NSL. This attribute space is designed specifically for working with folder nodes in SAMSON. Folders often serve as containers holding molecular datasets, making these attributes essential for specifying folder-level queries and expressions.
Here’s a quick breakdown of what you can do with folder attributes:
- Match folders based on the number of atoms, chains, hydrogens, carbons, or other specific elemental counts.
- Query folders by their visibility, material ownership, or structural properties like residues, segments, or structural models.
- Filter folders based on formal or partial charges, enabling searches for specific ionized or charged regions in structures.
Key Examples and Use Cases
Using folder attributes can transform how you work with molecular assemblies. Below are several practical examples showcasing how to use folder attributes in SAMSON:
1. Selecting Folders by the Number of Atoms
If you want to find folders containing molecular structures with a specific number of atoms, you can use the f.nat attribute:
f.nat > 100: Matches folders with more than 100 atoms.f.nat 100:200: Matches folders with an atom count between 100 and 200.
2. Filtering Based on Visibility
Manage the visual clarity of your molecular models with the f.v (visible) attribute:
f.v: Matches folders that are currently visible in the interface.not f.v: Matches hidden folders.
3. Organizing by Element Counts
Imagine you’re interested in finding molecular systems based on specific compositions, such as carbon or oxygen counts. These can be quickly filtered using attributes like f.nC (numberOfCarbons) or f.nO (numberOfOxygens):
f.nC < 10: Matches folders with fewer than 10 carbon atoms.f.nO 10:20: Matches folders containing between 10 and 20 oxygen atoms.
4. Identifying Charged Systems
When working with charged systems, charges play a critical role. Use f.fc (formalCharge) or f.pc (partialCharge) to query charged folders:
f.fc 1: Matches folders with a total formal charge of +1.f.pc 1.5:2.0: Matches folders with a total partial charge between 1.5 and 2.0.
Why Use Folder Attributes?
Folder attributes allow greater control in navigating complex molecular repositories. Here are some of their benefits:
- Simplify hierarchical management for large molecular systems.
- Save time by using precise queries instead of manual searches.
- Ensure reproducibility by embedding clear filtering rules in NSL expressions.
Conclusion
Folder attributes in SAMSON open the door to more refined querying and organization of molecular assemblies. Once mastered, these tools streamline your workflow and help you get precise insights into your data, faster.
To explore each folder attribute in detail, refer to the official documentation page: https://documentation.samson-connect.net/users/latest/nsl/folder/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here: https://www.samson-connect.net.