Simplifying Molecule Management: Understand File Attributes in SAMSON’s NSL

When working on molecular design, managing complex sets of molecular data effectively is a key challenge. If you are using SAMSON, the integrative molecular design platform, the “file” attribute space in the NSL (Node Specification Language) provides a powerful way to specify and manage file nodes associated with your projects. This guide will walk you through what you need to know about file attributes, how to use them, and why they matter.

What Are File Attributes?

File attributes in NSL correspond to specific characteristics and actions that affect “file nodes” in SAMSON. These file nodes typically represent file-specific elements in your molecular modeling workspace. Whether you’re organizing your data or running queries, leveraging these attributes can streamline operations. The “file” attribute space is denoted with the short name fi, making expressions concise and easier to use.

Key Attributes to Know

  • Name (n): This attribute refers to the name of a file node. You can use it for string-based queries, making it easier to locate specific files. Example expressions include fi.n "A" to match a name exactly or fi.n "L*" to match names with a certain pattern.
  • Selected: This boolean attribute indicates whether a file node is selected or not. Use fi.selected for queries targeting selected nodes, or not fi.selected to exclude them.
  • SelectionFlag (sf): This boolean attribute allows you to set or check custom selection flags on file nodes. Example expressions include fi.sf false to specifically exclude nodes with selection flags or fi.sf to include them.

Practical Applications

These attributes aren’t just abstract concepts—they bring real utility to daily workflows:

  • Quickly filter and retrieve file nodes by their names using targeted expressions.
  • Organize your workspace efficiently by setting custom parameters for selected files or groups of files.
  • Visualize only the nodes of interest in your models by toggling selection flags.

For instance, using fi.n "L*", you can instantly identify all file nodes starting with the letter “L”—saving significant time in larger projects.

Using Attributes in Context

Since file attributes in NSL inherit from generic node attributes, they integrate seamlessly into broader workflows. However, some notable differences exist: for example, while the file attribute “selected” functions similarly to its node counterpart, it does not have a short name like s.

Why This Matters

Organizing data thoughtfully is critical when working in molecular design. Mismanaged or overwhelming file structures can lead to errors, interruptions, and loss of time. By getting familiar with SAMSON’s file attributes in NSL, you can unlock a streamlined, precise way to manage data and focus on the science behind your projects.

To explore the full potential of file attributes and see more examples, refer to the original documentation: https://documentation.samson-connect.net/users/latest/nsl/file/.

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

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