Streamline Structural Model Selection with Node Specification Language

Molecular modeling often requires precise selection of structural models according to specific criteria, and filtering through large datasets can be daunting. In SAMSON, the Node Specification Language (NSL) empowers users to query structural models with unmatched precision, making this task significantly more efficient.

One essential aspect of NSL in SAMSON is the use of structural model attributes. These attributes allow molecular modelers to single out structural models based on features like the number of atoms, formal charge, visibility, and much more. Let’s dive into some key attributes and how to apply them effectively.

Inherited Attributes: Core Functionalities

Structural models inherit attributes from the general node attribute space in SAMSON. Here are some common ones:

  • Visibility: Check whether a structural model is visible (sm.v) or hidden (sm.h).
  • Ownership: Use attributes like hasMaterial (sm.hm) and ownsMaterial (sm.om) to determine material-related properties of nodes in your structural model.
  • Selection: The selectionFlag (sm.sf) or selected attribute indicates whether a node is selected, helping you focus on areas of interest.

For example, if you want to find structural models that are visible but not currently selected, you can use the following NSL query:

Specific Structural Model Attributes: Tailored Analysis

In addition to inherited attributes, SAMSON offers a rich space of structural-model-specific attributes. These include:

  • formalCharge (sm.fc): Filters structural models by their total formal charge. For example, sm.fc 6:8 would match models with a formal charge between 6 and 8.
  • numberOfAtoms (sm.nat): Query structural models by the number of atoms they contain. Use sm.nat < 1000 to find models with fewer than 1000 atoms.
  • numberOfChains (sm.nc): Matches models based on the number of chains. For example, sm.nc 2:4 isolates models with 2 to 4 chains.
  • numberOfCarbons and numberOfHydrogens (sm.nC, sm.nH): These attributes allow you to focus on models containing specific numbers of Carbon and Hydrogen atoms, respectively.
  • partialCharge (sm.pc): Employ this attribute to match models based on their partial charge, such as sm.pc > 1.5 for models with a partial charge exceeding 1.5.

The ability to combine these attributes in logical expressions allows you to create highly specific queries tailored to your modeling needs.

Practical Example: Targeting Specific Models

Let’s consider a practical scenario: You are investigating models with substantial hydrogen content and a moderate number of Carbon atoms. Here’s how you could find such models using NSL:

This query isolates structural models with more than 20 hydrogen atoms and between 15 to 25 carbon atoms. Such precise filtering saves considerable effort and ensures you focus on the most relevant data for your task.

Start Applying These Queries Today

The structured approach NSL brings to molecular modeling enables users to work more efficiently and with greater confidence. Whether you are a novice or an experienced molecular modeler, SAMSON’s NSL helps save hours digging through complex structures.

To further explore the wide range of structural model attributes available, visit the original documentation at https://documentation.samson-connect.net/users/latest/nsl/structuralModel/.

SAMSON and all SAMSON Extensions are free for non-commercial use. Learn more and download SAMSON at https://www.samson-connect.net.

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