Exploring Folder Attributes with SAMSON’s Node Specification Language

For molecular modelers, navigating and organizing complex structures is often a major challenge. Wouldn’t it be helpful if you could filter and analyze structural data at a granular level—without drowning in details? SAMSON’s Node Specification Language (NSL) provides a structured way to achieve that, and one of its key capabilities involves folder attributes. Let’s explore how these attributes can simplify your workflows and enhance your productivity.

What Are Folder Attributes?

Folder attributes in SAMSON’s NSL allow you to interact with specific properties related to folder nodes. Folder nodes represent organizational levels in the structural hierarchy (like groups of molecules, atoms, or chains). These attributes empower you to filter, search, and analyze folders based on parameters such as the number of atoms, chains, or even formal charge.

Powerful Properties of Folder Nodes

SAMSON organizes folder attributes across two categories:

  • Inherited attributes: These come from the general Node attribute space and include properties like visible, selected, and name.
  • Specific folder attributes: These focus on molecular and structural characteristics like numberOfAtoms, numberOfChains, or formalCharge.

For example, let’s say you’re working with a dataset comprising multiple molecular structures. Instead of browsing manually, you can use expressions like f.nat > 500 to locate folders with more than 500 atoms!

Common Use Cases

Here are a few practical examples where folder attributes really shine:

  • Filter by formal charge: Use f.fc 6:8 to identify folders containing structures with a formal charge ranging between 6 and 8.
  • Sort by specific elements: Looking for carbon-heavy structures? Use the f.nC attribute to find folders with a large number of carbon atoms (f.nC > 10).
  • Examine structural complexity: With f.nr, you can focus on folders with a specific number of residues (f.nr 100:130).
  • Isolate molecular chains: The f.nc property lets you find folders that contain the desired number of chains (f.nc 2:4).

Simple, Yet Deep

The key to mastering folder attributes lies in their elegant simplicity. Although these attributes are easy to use, they give you tremendous flexibility and control. Here’s an example to illustrate:

  • To find structures with partial charges above 1.5, use: f.pc > 1.5.
  • Need to focus on a narrow range of partial charges? Use: f.pc 1.5:2.0.

These straightforward expressions ensure you’re always able to zero in on exactly what matters, while minimizing unnecessary distractions. Whether you’re analyzing batches of molecular data or preparing a model for a presentation, these attributes provide meaningful insights.

More About Folder Attributes

The documentation includes a full list of attributes—ranging from numberOfSegments to visible—with examples to make getting started easy. Explore the possibilities of attributes like numberOfSulfurs (f.nS < 6) or visibilityFlag to sharpen your focus on molecular datasets.

Interested? Learn more about folder attributes in the official documentation.

SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON for free at samson-connect.net.

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