For molecular modelers, understanding and handling side chain attributes is a repetitive yet essential task when analyzing and designing molecules. Whether you are selecting specific side chains, filtering nodes based on their properties, or analyzing molecular structures, the Node Specification Language (NSL) in SAMSON provides a systematic way to make these tasks efficient and reproducible.
What Are Side Chain Attributes in NSL?
Side chain attributes are part of the sideChain attribute space in SAMSON, designed specifically to work with side chain nodes in molecular structures. By querying and filtering these attributes, you can pinpoint specific structural elements or functional groups with precision. Each attribute comes with its own syntax, short names, possible values, and practical use cases.
Key Side Chain Attributes and How to Use Them
Here are some of the most useful sideChain attributes you should be aware of. These attributes inherit functionalities from broader attribute spaces such as node and structuralGroup. Below is a summary to get you started:
| Attribute Name | Description | Examples |
|---|---|---|
hasMaterial |
Returns true or false depending on whether the side chain contains material properties. |
sc.hm, not sc.hm |
name |
Filters side chains by name. Can take a string value or patterns. | sc.n "A", sc.n "L*" |
numberOfAtoms |
Counts the total number of atoms in a side chain. | sc.nat < 1000, sc.nat 100:200 |
partialCharge |
Retrieves or filters the side chain’s partial charge, using float values. | sc.pc > 1.5, sc.pc 1.5:2.0 |
visible |
Sets or queries the visibility of side chains. | sc.v, not sc.v |
Each of these attributes can be combined in NSL expressions to refine your searches, allowing you to work more effectively with large molecular datasets.
Example Use Case: Selecting Visible Side Chains With More Than 10 Carbon Atoms
Suppose you need to identify all visible side chains that contain more than 10 carbon atoms in a molecular structure. Using the attributes visible (v) and numberOfCarbons (nC), you can write the expression:
|
1 |
sc.v and sc.nC > 10 |
This simple query helps in isolating the relevant nodes without spending time manually inspecting the entire model.
Making Your Workflow Smoother
When working with SAMSON’s NSL, it’s helpful to consider that attributes from structuralGroup (e.g., formalCharge or numberOfAtoms) can also be applied to side chains. This flexibility, combined with short code representations like fc or nat, empowers you to quickly manipulate and filter molecular data.
By understanding these attributes, you can streamline molecule selection, visualize specific regions of interest, and carry out precise data analysis without excess effort.
To dive deeper into the technical details of each attribute, including additional examples and explanations, check out the full documentation on SAMSON’s side chain attributes here.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.