For molecular modelers working with complex structures and data, managing folders effectively can significantly streamline the design process. SAMSON, the integrative molecular design platform, provides a robust and intuitive system for working with folder attributes through its Node Specification Language (NSL). This article explains key folder attributes, their use cases, and the power they bring to your molecular modeling workflows.
What Are Folder Attributes?
Folder attributes in SAMSON’s NSL are properties associated with folder nodes that contain structural and molecular data. They allow you to query, filter, or categorize data easily, enabling precise targeting of specific molecular structures based on predefined attributes. From general visibility settings to advanced criteria like atom counts, these attributes open up new possibilities for managing your molecular data.
Examples of Powerful Folder Attributes
Let’s explore some of the most useful folder attributes and highlight real-world applications for each:
1. Formal Charge (f.fc)
The folder.formalCharge attribute helps you identify folders with structures having a specific total formal charge. This is essential for understanding the electronic properties of your systems. For example:
f.fc 1: Matches folders with structures having a formal charge of 1.f.fc 6:8: Filters folders where the formal charge falls between 6 and 8.
This is particularly useful when analyzing charged molecular systems or verifying ionic states during simulations.
2. Number of Atoms (f.nat)
The folder.numberOfAtoms attribute is essential for organizing large datasets based on structural complexity. Here are two common examples:
f.nat > 100: Selects folders containing over 100 atoms.f.nat 100:200: Filters folders with atom counts between 100 and 200.
By employing this attribute, you can focus on folders that meet specific complexity requirements for further analysis or simulation.
3. Visibility and Selection
SAMSON provides intuitive flags to manage the visibility and selection status of folders:
folder.visible (f.v): Easily includes or excludes folders from your current view.folder.selectionFlag (f.sf): Toggles whether a folder is selected for specific operations.
These attributes help keep your workspace clean and organized when dealing with multi-level molecular structures.
4. Number of Molecules (f.nm)
If you need to focus on folders containing a specific number of molecular entities, the folder.numberOfMolecules attribute is for you. For example:
f.nm < 3: Matches folders with fewer than three molecules.f.nm 2:4: Filters folders containing between two and four molecules.
This kind of filtering is invaluable when working on supramolecular assemblies or specific molecular aggregates.
Seamless Customization and Filtering
The examples above represent just a fraction of the possibilities. Advanced users can combine multiple attributes to construct incredibly detailed queries. For instance, combining f.nH (number of Hydrogen atoms) with f.v (visibility) enables fine control over data filtering, making visualization and simulation preparation more precise. Additionally, the short names for attributes allow simple commands for quick workflows.
To learn about all the available attributes and maximize your productivity, visit the full documentation at SAMSON Folder Attributes Documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON and explore its powerful features, including folder attributes, from SAMSON Connect.