For molecular modelers, efficiently querying and analyzing molecular structures can often be a daunting task. This is particularly true when working with side chains, where properties like material ownership, atom counts, and visibility play a significant role in model refinement and interpretation. If this sounds familiar, SAMSON’s Node Specification Language (NSL) might just become your new go-to tool. This blog post focuses specifically on side chain attributes in NSL, helping you navigate through their possibilities and practical uses.
Mapping Out the Side Chain Attribute Space
Side chain attributes in NSL are defined under the sideChain attribute space. This space—shortened in expressions as s—is specifically tailored to model and inspect side chain nodes. Additionally, attributes within the sideChain space inherit features from both the node and structuralGroup attribute spaces. Let’s explore key attributes and how they can make your life easier.
Key Side Chain Attributes and Their Applications
Here is a list of essential attributes available in the sideChain space, their shorthand, and their practical applications:
| Attribute | Shorthand | Application |
|---|---|---|
| hasMaterial | hm |
Determine if the side chain contains a material. |
| name | n |
Filter side chains by name. For instance, sc.n "A" filters for side chain names starting with ‘A.’ |
| numberOfAtoms | nat |
Specify ranges to search for side chains with a particular number of atoms. For example, sc.nat < 1000. |
| partialCharge | pc |
Identify parts of your structure with specific ranges of partial charges, useful in electrostatic calculations. |
| visible | v |
Toggle visibility or query visibility status (sc.v or not sc.v). |
Efficient Filtering: Examples in Action
Here are some practical examples of how you can use side chain attributes in NSL:
- To locate side chains that are visible and possess material, write:
sc.v and sc.hm. - If you’re interested in side chains containing fewer than ten carbon atoms, you can specify:
sc.nC < 10. - To exclude side chains with a partial charge greater than 1.5, filter with:
not sc.pc > 1.5.
Why This Matters
By leveraging side chain attributes in NSL, modelers save time, create more focused queries, and achieve better insights into their molecular systems. Whether you’re filtering by visibility or analyzing the composition of side chains, these tools give you precise control without overwhelming complexity.
For the full documentation, examples, and advanced use cases, visit the official documentation page on Side Chain Attributes in SAMSON.
SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON today at www.samson-connect.net.