Mastering Segment Attributes for Efficient Molecular Modeling

As a molecular modeler, you may have found yourself navigating through complex datasets or structuring your model in ways that require precise and nuanced control over your nodes and segments. Understanding how to use segment attributes effectively can save you valuable time and provide clarity when working on intricate molecular design tasks.

The segment attribute space, abbreviated as s, allows you to interact specifically with segment nodes in your molecular modeling tasks. This blog post explores the main categories of attributes—those inherited from nodes, inherited from structural groups, and unique to segments—and how you can leverage them to make your work more efficient and streamlined.

Making Sense of Segment Attributes

The segment attribute space includes a wide range of capabilities, from determining visibility to counting specific element atoms in a segment. Let’s delve into the different segments and their practical applications:

Attributes Inherited from Nodes

Even though these attributes originate from the node attribute space, they are equally useful for segment nodes. For example:

  • hasMaterial (s.hm): Quickly filter segments based on whether or not they have associated material.
  • hidden (s.h) and visible (s.v): Control the visibility or exclusion of segments in your molecular model efficiently.
  • name (s.n): Search or match segments by name. Examples include s.n "A" or using wildcards like s.n "L*".
  • ownsMaterial (s.om): Check if the segment owns specific material.

Attributes Inherited from Structural Groups

The flexibility grows when attributes from structural groups are applied. Examples include:

  • numberOfAtoms (s.nat): Get integer values for atom counts, such as s.nat < 1000 or within a range like s.nat 100:200.
  • numberOfCarbons (s.nC), numberOfHydrogens (s.nH), and similar attributes for other elements: Quickly analyze the elemental composition with commands like s.nC 10:20.
  • partialCharge (s.pc): Examine or filter segments based on their charge metrics (e.g., s.pc > 1.5).

Attributes Unique to Segments

For more specialized tasks, the segment attribute space equips users with unique options, notably:

  • numberOfResidues (s.nr): Define or search for segments based on residue count. Example: s.nr > 100.
  • numberOfStructuralGroups (s.nsg): Segment nodes can also be filtered based on the structural group count, for instance, s.nsg 10:12.

Tips for Practical Usage

These attributes allow you to fine-tune your queries and operations greatly. For instance, analyzing the visibility of segments with s.v, debugging your structure using numberOfAtoms to identify improperly defined nodes, or selecting a subset of your model based on its formalCharge can significantly improve modeling workflows.

The possibilities with these segment attributes are vast, and their flexibility means you can tailor your modeling process to your exact needs. They empower you to focus on science and design rather than getting bogged down in tedious attribute filtering.

Learn and Explore More

To gain deeper insight and explore the extensive attribute possibilities, check out the complete documentation page: Segment Attributes Documentation.

SAMSON and all SAMSON Extensions are free for non-commercial use. Visit SAMSON Connect to download and get started today.

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