Mastering Segment Attributes for Molecular Modelling

Molecular modeling involves interacting with highly complex data about molecular structures. Efficiently processing that data often involves selecting and manipulating specific components of a model, such as molecular segments. In the SAMSON molecular design platform, segment attributes are key to refining your workflows and streamlining analysis. Let’s explore how segment attributes can help you in molecular modeling and simplify your tasks.

What are Segment Attributes?

Segment attributes are part of the Node Specification Language (NSL) in SAMSON, designed to provide precise querying capabilities for molecular segments. These attributes allow you to filter, find, and manipulate molecular segments based on various parameters, like the number of atoms, residues, or structural groups they contain. Mastering these attributes can save you significant time and effort when working on complex molecular structures.

Inherited and Specific Attributes

Segment attributes inherit properties from other attribute spaces, such as node or structuralGroup. However, the segment attribute space also includes properties unique to segments, making it a focal point for targeting molecular segments directly. These attributes are used with short names that simplify writing queries and make scripting efficient.

Examples of Attributes:

  • Inherited:
    • numberOfAtoms (s.nat) – Allows you to query segments with a specified number of atoms, such as s.nat < 1000.
    • visibilityFlag (s.vf) – Filters visible or hidden segments by querying their visibility status.
  • Specific:
    • numberOfResidues (s.nr) – Matches segments with a specific number of residues. For example, s.nr > 100 will find segments with more than 100 residues.
    • numberOfStructuralGroups (s.nsg) – Targets segments based on their structural groups, such as s.nsg 10:20 to filter segments with 10 to 20 groups.

Why Segment Attributes Matter

Imagine you are working with a large molecular model containing thousands of atoms and residues. Manually identifying specific regions for analysis would be labor-intensive and prone to errors. Segment attributes provide a way to automate these operations with concise queries:

  • Find all segments containing a certain number of residues (e.g., s.nr > 130).
  • Filter segments that are visible with s.v or hidden using not s.v.
  • Identify segments owning material using s.om.

These capabilities ensure that you can focus on essential tasks without being bogged down by lengthy manual processes.

Practical Usage Examples

Here are examples of how segment attributes can help you efficiently analyze molecular models:

  • To isolate large segments with many atoms, use: s.nat > 500.
  • To study only visible regions of your model, filter by visibility with: s.v.
  • To analyze segments with a specific residue count, use: s.nr 50:100.

Queries like these enable you to tailor your focus to exact regions, saving time and effort while enhancing accuracy.

To explore the full range of segment attributes and see detailed examples, visit the official SAMSON 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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