When working on molecular modeling, one of the most persistent challenges is filtering and identifying specific sets of structural models within a large dataset. For instance, you might need to isolate structural models based on the number of atoms, chains, or even specific atom types such as carbons or hydrogens. Thankfully, SAMSON‘s Node Specification Language (NSL) comes to the rescue with its well-defined structural model attributes. In this blog post, we’ll dive deep into these attributes, showing you how to leverage them to streamline your molecular design workflows.
The Concept of Structural Model Attributes
Structural model attributes let you express queries to match specific features of structural models. These attributes belong to the structuralModel attribute space, often shortened to sm, and they can include general attributes inherited from nodes and specific properties unique to structural models.
Inherited Attributes
Inherited attributes include aspects like visibility (sm.visible), selection (sm.selected), and material ownership (sm.ownsMaterial), which are common to many structural nodes. For example, filtering for visible structures can be achieved with queries like:
sm.visiblenot sm.visible
This can be particularly useful for adjusting your view or isolating segments of interest for further analysis.
Specific Structural Model Attributes
What makes structural model attributes especially powerful are the features specific to molecular data. Let’s explore a few important ones:
Number of Atoms
The attribute sm.nat allows you to select models by their total number of atoms:
sm.nat > 100: Selects models with more than 100 atoms.sm.nat 100:200: Selects models with between 100 and 200 atoms.
This is particularly helpful if you need to filter out overly complex models or focus on manageable ones.
Number of Carbons
sm.nC is designed for selecting models based on the number of carbon atoms, useful for organic chemists or material scientists:
sm.nC < 10: Matches models with fewer than 10 carbons.sm.nC 10:20: Finds models with 10 to 20 carbons.
Partial Charge
The sm.pc attribute targets models based on their partial charge, using real (floating-point) values:
sm.pc 1.5:2.0: Identifies models where the partial charge is within a specified range of 1.5 to 2.0.
This is a useful feature for molecular simulation experts looking to identify specific charged states.
Real-World Applications
Imagine you’re modeling a dataset of biomolecules and need to isolate all proteins with more than 3 chains. Using sm.nc > 3, you can easily filter and focus on larger structures for targeted analysis. Alternatively, you may restrict models to those with a specific number of residues (sm.nr 100:120) to focus on the relevant range for your study.
How to Get Started
To use these attributes effectively, you can integrate them into your SAMSON workflows when querying and visualizing models. These capabilities reduce the need for manual inspection, accelerate decision-making, and help you gain deeper insights into molecular data.
Learn more about structural model attributes and their use cases in SAMSON’s official documentation: here.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON from here.