Unpacking Folder Attributes in SAMSON for Molecular Modeling

For molecular modelers working on complex systems, efficiently organizing and navigating molecular structures is critical. One of SAMSON’s powerful features is its folder attribute space in the Node Specification Language (NSL), designed to optimize how folder nodes are specified and queried. In this blog post, we’ll dive into the folder attributes and how they can be used to streamline your work when managing molecular structures.

What Are Folder Attributes?

Folder attributes in SAMSON are essentially ways to query and work with specific properties of folder nodes containing molecular structures. By using these attributes, you can easily filter, group, or analyze molecular data without laborious manual steps. These attributes are identified by short names for convenience, and you can use them to match folder nodes based on properties such as the number of atoms, molecular contents, visibility settings, and more.

Key Inherited Folder Attributes

Some of the folder attributes are inherited from the general node attribute space. Here are a few that are commonly used:

  • visible (f.v): Checks if the folder is visible in the workspace. For example, f.v matches visible folders, while not f.v matches non-visible ones.
  • name (f.n): Matches folders by their names using strings. For example, f.n "Ligand" matches folders named “Ligand” while f.n "Lig*" uses wildcard patterns.
  • ownsMaterial (f.om): Matches folders that own materials—they contain primary molecular data rather than referencing other nodes.

These inherited attributes offer essential flexibility for common tasks like toggling visibility or identifying folders by name.

Specific Folder Attributes: Going Beyond the Basics

Folder nodes also come with unique attributes tailored for molecular modeling, enabling users to query specific molecular properties. Here are some key examples:

  • numberOfAtoms (f.nat): Allows you to filter folders based on the total number of atoms in their structures. For instance, f.nat > 100 matches folders containing more than 100 atoms, and f.nat 100:200 matches structures containing between 100 and 200 atoms.
  • numberOfCarbons (f.nC): Matches folders with a specified number of carbon atoms. Similar to atom counts, you can specify exact numbers or ranges, e.g., f.nC < 10.
  • numberOfChains (f.nc): This attribute is invaluable for working with proteins or macromolecules. A query like f.nc 2:4 matches folders with two to four chains.
  • formalCharge (f.fc): Matches folders based on the total formal charge of their structures. For instance, f.fc 6:8 matches folders whose structures have a formal charge between 6 and 8.

With these attributes, tasks like exploring the composition of molecular components or searching for specific configurations become faster and more reliable.

Why Use Folder Attributes?

Imagine you’re modeling a biomolecular complex and need to quickly identify and analyze all folders containing structures with:

  • More than 500 atoms.
  • At least one chain.
  • A specific name (e.g., “Ligand A”).

With SAMSON’s NSL folder attributes, you can perform this structured query in seconds. Simply enter the query string into the filter, analyze the results, and focus your attention on the relevant sections of your project.

Learn More

For more details on folder attributes and to explore additional features, visit the official documentation here.

Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get started with SAMSON today by visiting SAMSON Connect.

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