For molecular modelers, efficiently analyzing and categorizing structural models in large datasets can often feel overwhelming. The good news is that SAMSON’s Node Specification Language (NSL) allows advanced filtering and querying of molecular structures using attributes from the structuralModel attribute space. Here, we take a deep dive into the Structural Model Attributes to help you make the most out of these capabilities.
What are Structural Model Attributes?
Structural model attributes in NSL allow you to query and filter specific structural models based on key characteristics. These attributes are accessible through the structuralModel attribute space, which has the short name sm, and they are specifically tailored to match only structural model nodes. Attributes include inherited ones (from the generic node attribute space) and attributes specifically defined for structuralModel.
The scope of these attributes spans from visibility states to structural composition details such as the number of atoms, residues, or specific elements—making it a versatile tool for modelers looking to generate insights from their molecular simulations.
Key Examples of Useful Attributes
Here’s a brief overview of some attributes and how they can be used effectively:
sm.nat(numberOfAtoms): This attribute matches structural models based on the number of atoms. For instance:sm.nat > 100: Matches all models that have more than 100 atoms.sm.nat 50:150: Matches all models with atom counts between 50 and 150.
sm.nC(numberOfCarbons): Ideal for isolating models based on the number of Carbon atoms.sm.nC < 10: Matches models with less than 10 Carbon atoms.
sm.fc(formalCharge): Use this to match models with a specific or range of formal charges.sm.fc 1: Matches structural models with a formal charge of 1.sm.fc 3:5: Matches models with a formal charge in the range of 3 to 5.
sm.nr(numberOfResidues): Helps in filtering models based on the number of residues.sm.nr > 150: Matches models with more than 150 residues.
Refine Your Workflow
The flexibility of these attributes allows users to design highly refined queries for molecular models. For example, combining attributes like sm.nat and sm.nC can allow the user to extract structural models with both a certain number of atoms and a specific range of Carbon atoms. This can be particularly useful for structurally complex systems like macromolecules or alloys where detailed queries are vital.
How to Get Started?
To start using these attributes, simply integrate them into your current molecular modeling pipeline within SAMSON. Whether you need insight into atomic compositions, residue counts, or other structural features, structuralModel attributes provide the filtering precision you need to make informed scientific decisions.
For the full reference on Structural Model Attributes, visit the official documentation. Explore additional examples and get started on building your own queries for structural models.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here and start integrating these tools into your molecular modeling projects today.