For molecular modelers, effective organization of molecular models can be a vital yet challenging aspect of their workflow. Knowing how to group and filter your data within the SAMSON platform with precision can drastically improve efficiency. One of the powerful tools SAMSON provides is the ability to leverage folder attributes. These attributes help users manage, categorize, and query their structural data effortlessly. In this post, we’ll explore how to use folder attributes to optimize your molecular modeling projects.
What Are Folder Attributes?
In SAMSON, folders represent nodes that can contain structures such as molecules, chains, or atoms. Folder attributes are properties that allow you to filter and interact with these nodes based on specific characteristics. There are two types of folder attributes:
- Inherited attributes: These come from the general node specification and are applicable to multiple entities including folders. For example, attributes like
hidden,visible, andselected. - Folder-specific attributes: These are unique to folders and offer advanced ways to query based on molecular properties such as the number of atoms, formal charge, or the presence of specific chemical elements such as hydrogens or oxygens.
Using Folder Attributes in Practice
Let’s illustrate how these folder attributes can help molecular modelers. Consider a scenario where you need to isolate folders representing molecular systems with specific features, such as a range of formal charges or atom counts.
Filtering by Atom Count
The numberOfAtoms attribute (short name: nat) enables you to select folders containing a particular number of atoms. It offers not only precision but also ease of use. Here’s how you can use it:
f.nat > 100: Matches folders where the number of atoms exceeds 100.f.nat 100:200: Matches folders where the number of atoms is between 100 and 200.
Filtering by Formal Charge
If your work involves focusing on molecules with specific charge conditions, the formalCharge attribute (short name: fc) is a great tool. Examples include:
f.fc 1: Matches folders with structures having a total formal charge of 1.f.fc 6:8: Matches folders with structures having a formal charge between 6 and 8.
Advanced Queries: Element-Specific Counts
When modeling or analyzing chemical systems, identifying specific atomic compositions is essential. Some folder-specific attributes allow you to count specific elements, such as:
numberOfHydrogens(nH): Filters folders based on the number of hydrogen atoms. Example:f.nH 10:20.numberOfCarbons(nC): Allows filtering by carbon atom count.numberOfNitrogens(nN): Filters by nitrogen atom count.
By combining these filters, modelers can quickly narrow down datasets to those that meet specific criteria, saving time and reducing complexity.
Take Control of Your Molecular Data
With these folder attributes, molecular modelers can gain significant control over their projects. Whether managing large datasets, preparing for simulations, or analyzing structures, these attributes enable efficient and precise workflows. Best of all, these tools are built-in and easy to integrate into everyday tasks.
To learn more about folder attributes and how they can improve your modeling process, visit the SAMSON documentation here: SAMSON folder attributes documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at SAMSON Connect.