Simplifying File Attributes in SAMSON’s Node Specification Language

Molecular modeling often involves managing complex data structures, and keeping track of files can become cumbersome. If you’re using SAMSON—the integrative molecular design platform—and working with its Node Specification Language (NSL), understanding file attributes can save you a significant amount of time and effort. This post explains how file attributes work in NSL, focusing on making your modeling workflow more efficient.

What Are File Attributes?

File attributes in SAMSON’s NSL are part of a specialized attribute space named file, with the short name fi, designed exclusively to match file nodes. These attributes allow you to query and manage file nodes effectively.

Let’s break down the core file attributes:

1. name Attribute

The name attribute (short name: n) is inherited from the general node attribute space. It allows you to specify or query file nodes based on their names, using quoted strings. For example:

  • fi.n "A": Matches file nodes with the exact name “A”.
  • fi.n "L*": Matches file nodes whose names begin with “L”.

Matching nodes by name is especially valuable when searching for specific files in large molecular models.

2. selected Attribute

This attribute allows you to check whether a file node is selected. It accepts Boolean values (true or false). Examples:

  • fi.selected: Matches file nodes currently selected.
  • not fi.selected: Matches file nodes that are not selected.

While selected behaves similarly to node.selected, it does not include a short name like s, simplifying its use.

3. selectionFlag Attribute

The selectionFlag attribute (short name: sf) is another Boolean attribute. It is often used to assign or query custom selection statuses within file nodes. For example:

  • fi.sf false: Matches file nodes where the selectionFlag is false.
  • fi.sf: Matches file nodes with a selectionFlag set to true.

This is particularly useful for tracking specific subsets of file nodes during a modeling session.

Why File Attributes Matter

Efficiently organizing and querying file nodes can significantly streamline tasks like managing simulation input/output or grouping data for analysis. With these attributes, you can easily control node behavior, focusing only on the nodes you need to work with, and avoid wasting time manually sorting through the hierarchy.

Examples in Action

Here are a couple of practical examples to inspire your workflow:

  • fi.n "Structure_A" and fi.selected: Filters for file nodes with the name “Structure_A” that are also selected.
  • not fi.sf and fi.n "Results*.csv": Matches unflagged file nodes with names starting with “Results” and ending in “.csv”.

With such expressions, you can pinpoint exactly what you need in seconds.

Learn More

This is just an overview of how you can leverage file attributes in SAMSON’s Node Specification Language. By mastering these features, you can boost your productivity and make your molecular modeling tasks smoother. To dive deeper into the capabilities of file attributes, check out the full documentation page.

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

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