When working with large molecular systems, structural models can become very complex — from polymers with multiple chains and residues to assemblies containing thousands of atoms. As your project grows, finding specific parts of your dataset can become difficult and time-consuming.
If you’re using SAMSON, the integrative platform for molecular design, you’ve likely encountered folders representing molecular structures. In large systems, these folders often contain several chains, atoms, residues, and more, making it challenging to isolate the exact subset you’re seeking. That’s where folder attributes in the Node Specification Language (NSL) come in. NSL allows you to perform precise queries to find what you’re looking for efficiently.
What Are Folder Attributes?
In SAMSON, folder attributes give you access to metadata about molecular structures stored in folders. These attributes can include the number of atoms, formal charge, partial charge, and counts of specific atom types such as carbons, hydrogens, nitrogens, and more.
For example:
f.nat > 100: selects all folders containing more than 100 atoms.f.nC 10:20: selects folders with 10 to 20 carbon atoms.f.fc 1: selects folders with a total formal charge equal to 1.
Why Molecular Modelers Find This Useful
Let’s say you’re simulating a protein-ligand complex and you want to quickly find structures with multiple chains, or maybe screen for systems with a particular number of sulfur atoms for disulfide-bond analysis. Instead of manually clicking through each folder in your document, you can execute a query like:
|
1 |
f.nc > 1 and f.nS > 2 |
This quickly narrows down your focus to structures with multiple chains and enough sulfur atoms to be candidates for disulfide bonding.
An Overview of Available Folder Attributes
| Attribute | Short name | Description |
|---|---|---|
numberOfAtoms |
f.nat |
Total number of atoms |
numberOfCarbons |
f.nC |
Carbon atom count |
numberOfChains |
f.nc |
Chain count (useful for proteins) |
numberOfHydrogens |
f.nH |
Hydrogen atom count |
numberOfMolecules |
f.nm |
Includes ligands, solvents, etc. |
numberOfResidues |
f.nr |
Useful for protein length screening |
formalCharge |
f.fc |
Total formal charge of the folder |
partialCharge |
f.pc |
Partial (non-integer) charge |
Combining Attributes for Complex Queries
Here’s an example to help you find specific systems among many:
|
1 |
f.nC 15:30 and f.nH < 60 and f.fc 0 |
This query finds folders with 15 to 30 carbon atoms, less than 60 hydrogen atoms, and zero formal charge — a possible filter for medium-sized neutral organic molecules.
Conclusion
Querying by folder attributes in NSL helps molecular modelers stay efficient, organized, and precise — particularly when dealing with complex systems. If you want better control over your structural model searches, mastering this tool will make your work significantly smoother.
To learn more about all folder attributes available in NSL, visit the SAMSON NSL folder attribute documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.