For molecular modelers and researchers, organizing complex molecular structures can often feel like an overwhelming challenge. When working on integrative molecular design in SAMSON, the Folder attribute space in the Node Specification Language (NSL) offers an efficient, powerful way to categorize and query molecular structures based on numerous predefined attributes. This blog post walks you through key Folder attributes and how they can streamline your work.
What Are Folder Attributes?
The Folder attribute space (short name: f) focuses exclusively on folder nodes in SAMSON. It allows users to retrieve specific molecular structures by querying properties such as the number of atoms, formal charges, or even structural models within the folder. These attributes provide insights into the folder contents without requiring you to manually inspect each structure.
Inherited Attributes
Before delving into folder-specific attributes, it’s helpful to note that folders also inherit attributes from the Node attribute space. Here’s a glimpse:
- Visibility: Query whether the folder is visible (
f.v) or hidden (f.h). - Selection: Access folder selection states using
f.selected. - Ownership: Find out if the folder “ownsMaterial” with
f.om.
Folder-Specific Attributes at a Glance
Folder-specific attributes address some of the most pressing pain points for modelers by making queries granular and defining key properties:
1. Counting Molecular Components
Use attributes to count various atomic and structural elements in a folder, such as:
- Number of atoms:
f.nat - Number of carbons:
f.nC - Number of residues:
f.nr - Number of structural models:
f.nsm
For example, if you need to locate folders containing fewer than 1000 atoms, you can use:
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f.nat < 1000 |
Or, find folders with the number of residues in a specific range:
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f.nr 100:120 |
2. Formal and Partial Charges
If you’re working on charged molecular species, consider using f.fc (formalCharge) or f.pc (partialCharge) to narrow down folders based on their charge properties.
Examples include:
- Folders with formal charge equal to 1:
f.fc 1. - Folders with partial charge in a range:
f.pc 1.5:2.0.
3. Structural Organization
Attributes like f.nsg (numberOfStructuralGroups) and f.nseg (numberOfSegments) allow you to manage queries based on the structural complexity of folders. For instance:
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f.nsg > 10 |
This command matches folders with more than 10 structural groups.
Why This Matters
Using these attributes empowers researchers to quickly filter and organize complex datasets. For example, imagine working with a large biomolecular assembly where manual sorting is time-consuming. By typing a simple query like f.nat < 200, you can instantly isolate relevant folders containing structures under 200 atoms.
Explore More
With Folder attributes in SAMSON, molecular modelers benefit from a highly extensible way to streamline workflows and manage their projects effectively. Explore the complete documentation on NSL Folder attributes to see the exhaustive list and examples: documentation.samson-connect.net/users/latest/nsl/folder/.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get your version today at SAMSON Connect.