For molecular modelers working with the SAMSON platform, understanding the path attribute space in the Node Specification Language (NSL) can greatly streamline workflows, especially when focusing on conformation nodes. This blog post aims to shed light on these attributes, providing a clear breakdown of their usage and examples of their application.
What Are Path Attributes?
Path attributes belong to the path attribute space (short name: p), specifically designed for targeting conformation nodes in molecular modeling tasks. Whether you’re filtering nodes or defining specific node properties, these attributes offer precision and flexibility in shaping how you engage with your molecular designs.
Inherited Attributes from the Node Attribute Space
Several attributes come from the general node attribute space. Below is an overview of these inherited attributes:
| Attribute name | Short name | Possible values | Examples |
|---|---|---|---|
| name | n |
strings in quotes | p.n "A"p.n "L*" |
| selected | true, false |
p.selectednot p.selected |
|
| selectionFlag | sf |
true, false |
p.sf falsep.sf |
Specific Path Attributes
In addition to inherited attributes, the path attribute space includes specific features that help in working directly with conformation nodes. The key attribute in this category is:
| Attribute name | Short name | Possible values | Examples |
|---|---|---|---|
| numberOfAtoms | nat |
integers | p.nat > 100p.n 100:200 |
The numberOfAtoms attribute (short name p.nat) allows you to target paths with a specific number of atoms. For example:
p.nat > 100: matches paths with more than 100 atoms.p.nat 100:200: matches paths with atom counts between 100 and 200.
Practical Applications for Molecular Designers
Imagine working with large molecular assemblies where specific conformational states need to be analyzed or filtered. Path attributes provide the precision and filtering capabilities required for such tasks. For instance, using p.selected, you can easily isolate nodes that were previously tagged as selected during your workflow. Meanwhile, p.nat can help identify conformation paths based on the number of atoms they contain—ideal for refining your modeling steps or preparing analysis data.
Learn More
Interested in diving deeper into the technical details? Visit the official Path Attributes documentation to explore more examples and see how this powerful feature can enrich your molecular modeling.
SAMSON and all SAMSON Extensions are free for non-commercial use. To get started, download SAMSON at https://www.samson-connect.net.