When working on complex biomolecular systems, it’s not always easy to stay organized. One common challenge molecular modelers face is identifying specific conformations of interest from large sets of data. For example, you may want to isolate conformations that contain a high number of atoms, so you can analyze their structural properties more closely, or prepare them for computationally intensive studies.
This is where the Node Specification Language (NSL) in SAMSON comes in handy. The NSL lets you quickly query and filter molecular data based on attributes like the number of atoms in a conformation, making tedious manual inspection unnecessary.
What Are Conformation Attributes?
In SAMSON, conformations are represented as nodes. Each conformation can have several attributes within the conformation (short: co) attribute space. One of the most useful of these, especially in high-throughput molecular modeling, is numberOfAtoms (short name: nat).
With co.nat, you can filter conformations based on how many atoms they contain, using intuitive expressions directly in the NSL.
Filter by Atom Count
You might want to focus only on conformations with a certain level of complexity—say, those made up of more than 100 atoms. Here’s how you can do that using NSL:
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co.nat > 100 |
This will return all conformations that contain more than 100 atoms. You don’t need to sort through your molecular document manually.
Need to go further? You can also specify a range. Want only conformations with between 100 and 200 atoms?
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co.nat 100:200 |
This flexibility allows you to adapt your queries to the task at hand—whether you’re filtering out molecules that are too small for your simulation or selecting a representative structural ensemble for visual comparison.
Organizing Large Documents
When working with tens or hundreds of structures, it’s easy for things to get chaotic. Using filters based on co.nat helps keep your modeling environment manageable. For instance, you can:
- Quickly isolate large conformations for further analysis
- Create automation pipelines based on size criteria
- Exclude small or irrelevant structures in one go
Making NSL Work for You
If you’re just getting started with NSL in SAMSON, working with conformation attributes is a simple yet powerful gateway. Especially in larger systems or workflows where you’re importing molecular data from simulations or structural datasets, being able to search with precision using co.nat can make a noticeable difference.
Even better, you can combine co.nat with other filters, like conformation name (co.n) or selection flags (co.sf), to tailor your query to your current modeling step.
To learn more about working with conformation attributes in SAMSON, visit the official documentation page: https://documentation.samson-connect.net/users/latest/nsl/conformation/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON from https://www.samson-connect.net.