Mastering Side Chain Attributes in SAMSON’s Node Specification Language

For molecular modelers working with complex systems, understanding and manipulating side chain attributes can be a vital step to streamline analyses and simulations. In SAMSON’s Node Specification Language (NSL), side chain nodes hold a wealth of attributes that allow precise and targeted control over molecular structures. This blog post explores these attributes, their meanings, and how to use them effectively for your modeling needs.

Why Side Chain Attributes Matter

Side chain attributes in SAMSON make it easier to filter, select, or modify specific side chain nodes in molecular models. Whether you are analyzing a protein structure or working with coarse-grained simulations, these attributes help you efficiently query and manipulate components of your model.

These attributes are part of the sideChain attribute space (short name: s) and include both node-level and group-level attributes available through inheritance. The diverse set of attributes can represent visibility, chemical composition, formal charges, and much more.

Exploring the Key Attributes

Below, we will delve into some of the most important side chain attributes and what they enable:

  • hasMaterial (sc.hm): Boolean attribute indicating whether a side chain node has material.
  • name (sc.n): Allows querying side chain nodes by their names. For example, sc.n "L*" selects nodes whose names start with ‘L’.
  • numberOfAtoms (sc.nat): Integer attribute that specifies the number of atoms in a side chain. For instance, sc.nat < 100 filters side chains with fewer than 100 atoms.
  • numberOfCarbons (sc.nC): Indicates the number of carbon atoms. Use expressions like sc.nC 10:20 to define a range.
  • partialCharge (sc.pc): Float attribute for partial charges. For example, sc.pc > 1.5 selects side chains with a partial charge greater than 1.5.

Other attributes, such as hidden (visibility), selected, numberOfHydrogens, and numberOfSulfurs, can also provide valuable information for specific use cases.

Practical Examples

To give you a hands-on perspective, here’s how some of these attributes can be used in queries:

  • Filter visible side chains: sc.v
  • Select side chains with a name starting with “A”: sc.n "A"
  • Identify side chains with more than 20 hydrogens: sc.nH > 20
  • Exclude side chains without material: not sc.hm

By combining multiple attributes in a single query, you can refine your selections even further for specific analyses. For example, sc.nH > 10 and sc.v retrieves all visible side chains with more than 10 hydrogens.

Learning More

This is merely an introduction to the capabilities of side chain attributes in SAMSON’s Node Specification Language. By mastering these attributes, you can enhance your workflows and make precise adjustments to your molecular design processes.

Explore the full side chain attribute reference and more examples on SAMSON’s official documentation page at https://documentation.samson-connect.net/users/latest/nsl/sideChain/.

Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can download and start using SAMSON from https://www.samson-connect.net.

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