For molecular modelers, managing and analyzing complex molecular structures efficiently is essential. If you’ve ever wondered how to focus on specific segments of your structure or manipulate them effectively, this post is for you. SAMSON’s segment attributes in the Node Specification Language (NSL) offer a powerful set of tools to streamline these tasks.
What Are Segment Attributes?
Segment attributes allow you to specify, query, and manipulate segments of molecular models. In SAMSON, a segment refers to a collection of residues, structural groups, or atoms grouped together logically. By mastering segment attributes, you can filter, select, or customize molecular data efficiently—saving time and reducing errors.
The segment attribute space is denoted by the prefix s, and it supports both inherited attributes and segment-specific attributes. Let’s break this down to understand the key elements.
Inherited Attributes
Many segment attributes are inherited from node or structuralGroup attribute spaces. For example:
hasMaterial (short name: hm): Checks whether segments have material (e.g.,s.hm).name (short name: n): Matches segments by their name (e.g.,s.n "A").numberOfAtoms (short name: nat): Matches based on atom counts (e.g.,s.nat < 100).numberOfHydrogens (short name: nH): Filters by hydrogen atom counts (e.g.,s.nH 10:20).visibilityFlag (short name: vf): Determines the visibility of a segment (s.vf true).
Each of these provides a way to target and refine a group of segments to focus your modeling tasks.
Segment-Specific Attributes
In addition to inherited attributes, NSL provides some attributes unique to segments:
numberOfResidues(short name: nr): Targets segments based on residue count. For example:s.nr > 100: Selects segments with more than 100 residues.s.nr 100:130: Matches segments with residue counts between 100 and 130.numberOfStructuralGroups(short name: nsg): Filters segments based on structural group counts. For instance:s.nsg > 10: Targets segments with structural groups exceeding 10.s.nsg 10:13: Matches segments with 10–13 structural groups.
How Can Segment Attributes Help You?
Segment attributes are a molecular modeler’s essential toolkit for:
- Selective filtering: For instance, you might want to isolate segments with a specific material using
s.hm true. - Precise customization: Refine your analysis by targeting specific residue or structural group counts (
s.nr,s.nsg). - Visibility toggles: Focus on visible or hidden segments to declutter your workspace (
s.v,s.h).
By leveraging these attributes, you can simplify your workflows, perform targeted modifications, and analyze specific portions of your molecular structure more efficiently.
Examples to Try
If you’d like to get started, here are a couple of practical examples:
- Find segments with residue counts greater than 100 by typing:
s.nr > 100. - List hidden segments with:
not s.v.
These intuitive syntax operations allow for precise filtering and analysis in your molecular modeling tasks.
For detailed descriptions and even more use cases of each segment attribute, visit the official documentation page.
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