As a molecular modeler, organizing and manipulating complex molecular systems efficiently can be challenging. Key to addressing this challenge is understanding and leveraging folder attributes in SAMSON’s Node Specification Language (NSL). Folder attributes offer a streamlined way to access, filter, and interact with folder nodes in molecular datasets. Let’s explore how these attributes can enhance your modeling workflows.
What Are Folder Attributes?
Folders in SAMSON are pivotal structures that can contain molecular models or other data. Depending on the nature of your work, you may need to filter folders based on their visibility, specific atomic characteristics, or molecular organization. Folder attributes make this possible by providing precise properties and selectors for folder nodes using NSL.
In NSL, folder attributes reside in the folder attribute space, with f as their short name. These attributes can filter or query folders based on inherited node attributes as well as folder-specific attributes.
How Can Folder Attributes Solve Molecular Modeling Challenges?
Let’s consider a common issue: You’re working with a dataset containing both visible and hidden structures. Distinguishing between them manually can be time-intensive. NSL’s visible (f.v) and hidden (f.h) attributes allow you to retrieve only the visible folders or ensure that hidden ones are excluded from operations with simple expressions like:
f.v: Matches visible folders.not f.h: Matches folders that are not hidden.
Similarly, you might want to identify folders with a specific number of chains or atoms. Folder attributes like numberOfChains (f.nc) and numberOfAtoms (f.nat) make this effortless. For instance:
f.nat > 100: Matches folders containing more than 100 atoms.f.nc 2:4: Matches folders where the number of chains is between 2 and 4.
Each attribute comes with its dedicated range of possible values—for example, integers for numberOfChains and numberOfAtoms, or true/false for visible or hidden.
Commonly Used Folder Attributes
Here are some commonly used folder attributes and their descriptions:
| Attribute | Short Name | Description |
|---|---|---|
visible |
v |
Indicates if a folder is visible. |
numberOfAtoms |
nat |
Matches folders by the specific number of atoms inside. |
numberOfChains |
nc |
Filters folders based on the number of chains. |
formalCharge |
fc |
Matches folders with specific formal charges. |
ownsMaterial |
om |
Indicates whether a folder owns material content. |
Make Your Workflows Smarter
Combining folder attributes enables advanced queries and flexible data management. For instance, you can filter folders with complex criteria like identifying those containing more than 200 atoms and visible molecules simultaneously using expressions such as:
f.nat > 200 and f.v
This level of precision allows molecular modelers to manage their datasets consistently and ensures workflow efficiency when working on multi-structure systems or large simulations.
To delve deeper into folder attributes and how to fully integrate them into your modeling activities, check out the official SAMSON documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON here.