Simplifying Path Selection with Path Attributes in SAMSON

For molecular modelers, effectively selecting and analyzing molecular conformations can be a daunting task. When working with large systems or exploring conformations, the ability to efficiently identify specific paths is essential. This blog post dives into SAMSON’s path attributes in the Node Specification Language (NSL), a powerful and precise tool for refining your molecular design workflow.

What Are Path Attributes?

Path attributes in SAMSON are part of the path attribute space in the Node Specification Language (NSL). They allow you to filter and select paths (conformation nodes) based on specific properties. This feature is indispensable when handling complex molecular datasets, as it quickly narrows down your selection based on the criteria you need.

Inherited and Specific Attributes

Path attributes in NSL are divided into two categories:

  • Inherited Attributes: These are general attributes applicable across nodes, such as name, selected, and selectionFlag.
  • Path-Specific Attribute: The numberOfAtoms attribute is unique to paths and enables selection based on the number of atoms in a path.

Using the numberOfAtoms Attribute

The numberOfAtoms attribute (short name: p.nat) deserves special attention. It allows users to filter paths based on the number of atoms they contain. This is especially useful when working with structures where the size of a path is a determining factor.

Here are some examples of how this works:

  • Match paths with more than 100 atoms: path.nat > 100 (short version: p.nat > 100).
  • Match paths with between 100 and 200 atoms: path.nat 100:200 (short version: p.nat 100:200).

These expressions make it straightforward to identify paths of interest, whether you’re focusing on larger molecular segments or specific ranges of conformation sizes.

A Real Example: Selecting Based on Attributes

Imagine working on a molecular system with hundreds of conformations, and your analysis requires isolating paths with specific atom counts. Instead of manually identifying these paths, you can use the NSL expressions:

  • To identify paths with exactly 150 atoms: p.nat 150.
  • To exclude smaller paths, find paths with atom counts greater than 300: p.nat > 300.

This simplifies the task significantly, reducing manual effort and increasing focus on the next steps of the analysis.

Combining Attributes for Advanced Selection

Path attributes are even more powerful when combined with inherited attributes like name. For example:

  • Select paths with a name starting with “L” and between 50 to 100 atoms: p.n "L*" and p.nat 50:100.
  • Find paths that are both selected and have more than 200 atoms: p.selected and p.nat > 200.

This capability ensures that molecular modelers can create highly tailored queries, saving time and improving accuracy in their workflows.

Learn More

SAMSON’s path attributes provide molecular modelers with intuitive and precise tools for path selection. By mastering these attributes, you can streamline your workflows, accelerate discoveries, and make better use of SAMSON’s integrative design platform. To explore all the features and examples in detail, visit the official documentation page: Path Attributes in NSL.

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

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