For molecular modelers, efficiently categorizing and analyzing structural data is often a recurring challenge. This is especially true when dealing with folders containing collections of molecular structures, chains, or segments. Thankfully, SAMSON’s Node Specification Language (NSL) offers a suite of folder attributes to streamline these tasks. This blog post explores the most practical features of folder attributes, empowering users to specify, filter, and query molecular folders with ease.
What Are Folder Attributes?
Folder attributes in NSL allow you to specify properties related to folders in your molecular system. These attributes unlock functionality to match folders based on criteria such as the number of atoms, chains, or specific chemical elements in the folder’s structures. These attributes are formalized under the attribute space folder (short name: f).
Inherited Attributes: A Quick Overview
Some attributes in the folder space come from the more general node space and allow basic queries like visibility (f.visible), material ownership (f.ownsMaterial), or folder name (f.name, values as strings). For example:
f.h: Matches folders that are hidden.f.hm: Checks whether folders have material (trueorfalse).f.n: Matches folders based on their names, allowing wildcards likef.n "L*".
Specific Attributes for Detailed Queries
The folder attribute space offers more advanced properties for specifying molecular data. For instance, you can dive into essential structural features such as the count of chains, molecules, atoms, or specific elements in the folder. This allows you to target highly specific folders in your molecular system.
1. Number of Atoms (numberOfAtoms, f.nat)
If you need to identify folders based on the total number of atoms, f.nat is your go-to attribute. For example:
f.nat > 100: Matches folders with more than 100 atoms.f.nat 100:200: Matches folders containing between 100 and 200 atoms.
2. Number of Chains (numberOfChains, f.nc)
When working with proteins or DNA structures, querying the number of chains in a folder becomes invaluable:
f.nc < 3: Matches folders with fewer than three chains.f.nc 2:4: Matches folders with two to four chains.
3. Number of Carbon Atoms (numberOfCarbons, f.nC)
You can refine searches based on the number of specific chemical elements, such as carbon atoms, using attributes like f.nC. For instance:
f.nC < 10: Matches folders with fewer than 10 carbon atoms.f.nC 10:20: Matches folders with 10 to 20 carbon atoms.
4. Partial Charges (partialCharge, f.pc)
To analyze total partial charges of molecular structures, f.pc simplifies the task. Queries like f.pc > 1.5 or f.pc 1.5:2.0 let you select folders with matching charge characteristics.
5. Residues, Segments, and Other Metrics
Advanced molecular analyses often involve filtering by residues, segments, or structural groups. Attributes like f.nr (number of residues), f.ns (number of segments), or f.nsg (number of structural groups) allow fine-grained control over your queries. For example:
f.nr > 100: Matches folders with more than 100 residues.f.nsg 10:12: Matches folders containing 10 to 12 structural groups.
Why Use NSL for Folder Queries?
The folder attributes in NSL make it simple to handle complex datasets. Rather than manually inspecting and sorting large systems, you can leverage NSL queries to quickly isolate folders of interest. This dramatically enhances productivity and ensures researchers focus more on insights than on tedious filtering tasks.
Learn More
Folder attributes are just one aspect of the powerful Node Specification Language. To dive deeper, visit the full documentation page and explore practical examples and additional attributes fit for any molecular modeling task.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.