Understanding Side Chain Attributes in SAMSON’s NSL

Molecular modelers often grapple with the challenge of efficiently specifying and querying structural components within molecular systems. When working on side chains, understanding the available attributes in SAMSON’s Node Specification Language (NSL) can greatly streamline your interactions with molecular models. This blog post provides an overview of these attributes, focusing on side chain nodes.

The Role of Side Chain Attributes

In NSL, side chain attributes are organized within the sideChain attribute space. This allows modelers to precisely identify and manipulate side chain nodes, saving valuable time in molecular analysis and design. Furthermore, these attributes support short name identifiers, making query construction concise and straightforward.

Key Attributes for Side Chains

To illustrate, below are some key attributes available for side chain nodes, inheriting from either the node or the structuralGroup attribute spaces:

  • Visibility and Selection: Attributes like visible (v) and selected define whether a side chain is visible or selected in your molecular model. For example, sc.v queries whether a side chain is visible.
  • Atom Information: Attributes like numberOfAtoms (nat) and numberOfCarbons (nC) help you evaluate the atomic composition of the side chain. For instance, sc.nat < 1000 finds side chains with fewer than 1000 atoms.
  • Charge Details: Use attributes like partialCharge (pc) and formalCharge (fc) to assess charge properties. For example,
    sc.pc > 1.5 identifies side chains with a partial charge greater than 1.5.

Practical Examples

Here are a few practical use cases demonstrating query possibilities with the NSL side chain attributes:

  1. Finding Hidden Nodes: Locate side chain nodes that are hidden using not sc.h. On the flip side, sc.h lets you find those that are visible.
  2. Specific Atom Ranges: If you’re interested in side chains with a specific number of atoms, try sc.nat 100:200 to identify side chains with 100 to 200 atoms.
  3. Charge Distribution Insights: Evaluate side chains with a formal charge in the range of 6 to 8 with sc.fc 6:8.

Taking It Further

By leveraging these attributes, molecular modelers can create expressive queries to pinpoint exactly what they need in molecular models. This reduces the time spent on locating specific structures and allows for better focus on advanced modeling tasks.

For a detailed reference on side chain attributes, including additional examples, head over to the official documentation page.

SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON from here.

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