Molecular modelers often face challenges when it comes to efficiently analyzing and selecting specific molecular properties during their design processes. Understanding the attributes of side chains in SAMSON’s Node Specification Language (NSL) can streamline this process, offering clarity and actionable insights.
What Are Side Chain Attributes?
Side chain attributes in SAMSON refer to a specific attribute space that applies exclusively to side chain nodes in your molecular models. These attributes, grouped under the sideChain namespace (short name: s), help molecular modelers identify and work with relevant molecular fragments effectively.
For example, if you are analyzing a protein, the side chains can carry crucial information such as visibility, material ownership, or the number of contained atoms. Knowing how to access and use these attributes can save time and enhance accuracy in molecular design.
Essential Side Chain Attributes
Here’s a quick overview of some key side chain attributes, their short names, possible values, and examples of how to access them:
| Attribute Name | Short Name | Possible Values | Examples |
|---|---|---|---|
| hasMaterial | hm |
true, false |
sc.hmnot sc.hm |
| hidden | h |
true, false |
sc.hnot sc.h |
| name | n |
Strings in quotes | sc.n "A"sc.n "L*" |
| numberOfAtoms | nat |
Integers | sc.nat < 1000sc.nat 100:200 |
| partialCharge | pc |
Floats | sc.pc > 1.5sc.pc 1.5:2.0 |
These attributes allow fine-grained control to query and filter side chains in your molecular structure, whether you’re evaluating interaction regions or detailing a specific structural group.
Inherited Attributes and What They Mean
Some side chain attributes are inherited from broader attribute spaces, such as node or structuralGroup. For example:
selected(fromnode): Indicates whether the side chain is currently selected.formCharge(fromstructuralGroup): Specifies the formal charge on the side chain.numberOfCarbons(fromstructuralGroup): Represents the number of carbon atoms in the side chain.
By leveraging both the namespace-specific and inherited attributes, users can conduct advanced searches and operations. For instance, you might want to identify side chains with a specific partial charge range or those that contain a given number of hydrogen atoms.
Practical Examples
The real power of side chain attributes lies in applying them to your molecular models. For example:
sc.vf false: Filters out all side chains whose visibility flag is set tofalse.sc.nat > 20: Identifies side chains containing more than 20 atoms.sc.n "L*": Matches side chains whose name starts with “L”.
These examples highlight how flexible and powerful SAMSON’s NSL is when it comes to querying complex molecular models.
Conclusion
The ability to target side chain-specific attributes within molecular models is a valuable feature for researchers and molecular designers, offering a streamlined approach to model analysis. To dive deeper into the side chain attribute space and its capabilities, please visit the official documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON here.