Master Folder-Level Insights with SAMSON’s NSL Attributes

Molecular modelers often find themselves managing complex molecular datasets, trying to streamline workflows and extract specific information efficiently. SAMSON’s Node Specification Language (NSL) offers an invaluable toolset to help modelers refine their queries and navigate data structures efficiently. One particularly powerful feature is the “folder” attribute space, which allows users to work directly with folders and their associated properties. This blog post explores how to leverage these folder attributes for improved molecular modeling productivity.

The Value of Folder Attribute Space

The folder attribute space in NSL enables users to specify and retrieve information at the folder level. Folders are useful for grouping molecular data (e.g., molecules, atoms, residues) and these attributes allow targeted queries based on specific properties.

The folder attribute space, denoted with the short name f, includes both inherited attributes (from the node) and folder-specific attributes. These attributes support operations as simple as checking visibility to as detailed as filtering folders by the number of atoms or complex charge metrics. By employing these attributes, modelers can avoid manually sorting through cumbersome datasets and automate a wide array of data management tasks.

How It Works: Key Attributes

Here is an overview of some key attributes within the folder attribute space:

  • hasMaterial (short name: hm): Determines if a folder contains material-related data. Example: f.hm will match folders where material is present.
  • name (short name: n): Matches folders by name. This is helpful for filtering based on naming conventions. Example: f.n "L*" matches folders named with an initial “L”.
  • visible (short name: v): Helps select folders based on visibility status. Useful for workflows where hidden data might need to be toggled or batch-processed.

Folder-Specific Attributes for Advanced Filters

Going beyond inherited attributes, folder-specific attributes unlock more detailed insights. For instance:

  • formalCharge (short name: fc): Filters folders based on the total formal charge of structures. Example: f.fc 6:8 matches folders with a formal charge between 6 and 8.
  • numberOfAtoms (short name: nat): Matches folders with a specific count of atoms. Example: f.nat > 100 selects folders where structures contain over 100 atoms.
  • numberOfMolecules (short name: nm): Narrows down folders by their molecule count. Example: f.nm 2:4 matches folders containing between 2 and 4 molecules.

The folder attribute space even extends to other molecule-specific metrics, such as numberOfCarbons (nC), numberOfHydrogens (nH), or numberOfResidues (nr), ensuring precision in database navigation.

Expression Examples

Let’s look at how these attributes can help solve real needs:

  • f.nr > 130: Find all folders containing structures with more than 130 residues.
  • f.pc 1.5:2.0: Select folders where total partial charges are in the range of 1.5 to 2.0.
  • f.nc 2:4 and f.hm: Identify folders with 2-4 chains that also have associated material data.

Streamline Your Workflow

SAMSON’s folder-related NSL attributes empower molecular modelers to unlock greater efficiency and precision when managing their data. By combining inherited and folder-specific attributes, users can run tailored queries, ensuring quicker discoveries and fewer errors.

To dive deeper into the folder attribute space and see more examples, visit the original documentation page: https://documentation.samson-connect.net/users/latest/nsl/folder/

SAMSON and all SAMSON Extensions are free for non-commercial use. Download SAMSON at SAMSON Connect.

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