Molecular modelers constantly face the challenge of efficiently querying and categorizing structural data within their models. Whether you’re working on a small organic molecule or a complex biomolecular assembly, identifying and organizing the diverse atomic and molecular properties can be tedious. This is where SAMSON’s Node Specification Language (NSL) and its structuralModel attribute space can save you valuable time.
What are Structural Model Attributes?
SAMSON’s structuralModel attribute space provides a structured way to match specific properties in structural models. By using these attributes, modelers can query characteristics such as the number of atoms, chains, residues, and more, with concise and intuitive syntax.
Why is this useful? For example, imagine you’re dealing with a molecular database and need to identify molecules containing more than 50 hydrogen atoms or structures with exactly 3 chains. With SAMSON, these queries are simple and human-readable.
Commonly Used Attributes at a Glance
Here are some commonly used structural attributes and examples of how they can simplify your tasks:
| Attribute | Short Name | Description | Examples |
|---|---|---|---|
| numberOfAtoms | nat |
Matches structural models with a specific number of atoms. | sm.nat > 100, sm.nat 100:200 |
| numberOfChains | nc |
Matches structural models with a specific number of chains. | sm.nc 2:4, sm.nc < 3 |
| numberOfHydrogens | nH |
Matches structural groups with a specific number of hydrogen atoms. | sm.nH < 10, sm.nH 10:20 |
| numberOfResidues | nr |
Matches structural models with a specific number of residues. | sm.nr > 130, sm.nr 100:130 |
| partialCharge | pc |
Matches models based on total partial charge. | sm.pc > 1.5, sm.pc 1.5:2.0 |
How It Works
The beauty of SAMSON’s structuralModel attributes is the combination of precision and simplicity they offer. With expressions such as ranges (100:200) or Boolean flags (true, false), modelers can craft complex queries. Many attributes, such as sm.nat (number of atoms) or sm.nc (number of chains), have straightforward examples available:
sm.nat < 1000: Finds structural models with fewer than 1000 atoms.sm.nm 2:4: Matches models containing between 2 and 4 molecules.sm.nsg > 10: Identifies models with more than 10 structural groups.
Best Practices
Here are a few quick tips to make the most of the structuralModel attribute space:
- Start small: Begin with simple queries to ensure you understand the syntax before building more complex expressions.
- Leverage short names: Familiarizing yourself with shorthand notations such as
natfornumberOfAtomscan save time and make your search expressions more concise. - Explore ranges: Use ranges (e.g.,
100:200) to narrow down your search efficiently.
Final Thought
SAMSON’s ability to query structural models using NSL attributes is a powerful feature for molecular modelers. By combining clear and intuitive expressions with precise matching capabilities, you can now focus on analysis rather than on manual data extraction. To learn more about structural model attributes and explore additional examples, visit the official documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.