Working with molecular modeling platforms can sometimes be daunting, especially when you need to manage and analyze complex structural data. If you’ve ever struggled to efficiently filter or explore folder-related attributes in SAMSON, the Folder Attributes functionality in SAMSON’s Node Specification Language (NSL) might be a perfect solution for you. This blog post elaborates how certain folder attributes can assist molecular modelers in working more efficiently.
What are Folder Attributes?
Folder attributes belong to the folder attribute space (denoted by the short name f) and are designed to match folder nodes in SAMSON. These attributes allow users to filter, organize, and query folders based on a variety of structural and contextual properties.
For example, folder attributes can give insights into properties such as the total number of atoms, molecules, chains, or even specific elements like Carbons or Oxygens in a folder. This feature is especially valuable when working with extensive molecular datasets or when you need to focus on specific structures.
Why is This Useful?
As a molecular modeler, exploring complex molecular assemblies often necessitates narrowing down your data to folders or configurations matching specific patterns. Without an efficient filtering mechanism, this process could easily become tedious and error-prone. Let’s imagine a common pain:
- You are working on a large biomolecular structure spanning several chains, residues, and atoms, but you only need folders containing molecules with a specific number of Hydrogen atoms.
- You’d like to compare molecule groups based on their formal or partial charges.
Using folder attributes in SAMSON simplifies such tasks, making it easy to express constraints and retrieve the structures you need.
Some Key Folder Attributes
Here are some of the most useful folder attributes and how to use them:
- hasMaterial (
f.hm): Checks whether a folder contains structural material. Possible values aretrueorfalse. Example:f.hm. - numberOfAtoms (
f.nat): Matches folders based on the number of atoms. Examples:f.nat > 1000(folders containing more than 1000 atoms) orf.nat 100:200(folders with 100 to 200 atoms). - numberOfCarbons (
f.nC): Specifically filters folders with a given number of Carbon atoms. Examples:f.nC < 10orf.nC 10:20. - partialCharge (
f.pc): For advanced calculations, this can filter folders by the total partial charge of molecules. Examples:f.pc 1.5:2.0. - name (
f.n): Targets folders with specific names or patterns. Example:f.n "ProteinA".
Exploring Attributes with Examples
Using NSL, you can query these attributes for precise results. For instance:
f.nat > 150: Finds folders with more than 150 atoms.f.nC 5:10: Selects folders with 5 to 10 Carbon atoms.
Such fine-grained control over folder properties allows modelers to perform targeted searches and save considerable time when analyzing data. Whether you’re working with small molecules or large biomolecular assemblies, filtering by folder attributes can be immensely helpful.
Learn More and Start Exploring
To delve deeper into folder attributes and their applications, refer to the complete documentation page on Folder Attributes here: https://documentation.samson-connect.net/users/latest/nsl/folder/.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.