Efficient Folder Filtering Using Node Specification Language in SAMSON

Molecular modelers often face the challenge of navigating complex molecular structures and their attributes in sophisticated design platforms like SAMSON. How can one effortlessly filter folders by criteria such as the number of atoms, molecules, or even specific elements? The Node Specification Language (NSL) in SAMSON provides an elegant solution to this pain point through its rich set of folder attributes. Here’s how these attributes can make your workflow smoother and more efficient.

An Introduction to Folder Attribute Space

The NSL folder attribute space in SAMSON is designed specifically to match folder nodes. This attribute space allows users to filter and query the contents of molecular structures with precision. It includes inherited general attributes from the node attribute space and additional folder-specific attributes.

Unlock the Power of Folder-Specific Attributes

When working with vast molecular datasets, being able to filter folders based on specific criteria can save you a significant amount of time. Some folder-specific attributes include:

  • formalCharge: Matches folders with a specific total formal charge. Expressions like f.fc 6:8 target folders with charges between 6 and 8.
  • numberOfAtoms: Filters on atom count with expressions like f.nat > 100, simplifying work with larger molecular structures.
  • numberOfChains: For filtering folders by the number of structural chains. Expressions like f.nc 2:4 are particularly helpful for multimolecular systems.
  • numberOfHydrogens, numberOfCarbons, numberOfNitrogens, etc.: These attributes allow atom-specific filtering. For example, f.nH < 10 targets folders with fewer than 10 hydrogens.

Use Cases: Time-Saving and Precision

Let’s explore a couple of practical examples:

  • Hydrogen Filtering: Working on a reaction involving hydrogen donors? Query folders using f.nH 5:15 to quickly find structures with 5 to 15 hydrogens.
  • Charge-Specific Systems: If you’re investigating specific charge behaviors, use f.fc > 0 to locate positively charged systems and streamline your analysis.
  • Custom Atom Ranges: When preparing large-scale simulations, ensure your folder satisfies the required atom range with f.nat 100:1000.

Inheritable Attributes for Enhanced Flexibility

Folders in SAMSON also inherit general attributes from nodes, such as:

  • visible: Quickly filter folders with f.v to include only visible items.
  • selected: Target selected structures using expressions like f.selected.
  • hidden: Exclude hidden folders from your queries with not f.h.

These high-level attributes further enhance the flexibility and granularity of your queries.

Learn and Optimize

To take full advantage of the folder attributes in SAMSON and integrate them into your workflow, head over to the official documentation at Folder Attributes in SAMSON. It includes comprehensive explanations, practical examples, and the full list of available attributes.

SAMSON and all SAMSON Extensions are free for non-commercial use. Get started today by downloading SAMSON from SAMSON Connect.

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