Understanding molecular attributes is key for molecular modelers who want to efficiently filter, categorize, and analyze molecular systems. SAMSON’s Node Specification Language (NSL) provides robust tools to define and leverage these attributes effectively. In this blog post, we’ll explore how molecule-specific attributes in SAMSON can simplify your workflow and save you time when managing complex molecular datasets.
The Importance of Molecular Attributes
When working with large molecular systems, clarity and precision are essential. Molecular attributes let you identify and manipulate molecule nodes based on their specific properties. For example, you might want to:
- Filter out molecules with fewer than 10 atoms.
- Identify molecules that are part of hidden structures.
- Locate molecules with a specific number of chains, residues, or atoms.
Thanks to SAMSON’s NSL, molecular modelers can easily access and use these attributes to focus on what matters most.
Molecular Attribute Categories
In SAMSON, molecular attributes belong to three categories:
- Attributes inherited from the node attribute space (e.g.,
visible,selected,name). - Attributes inherited from the structuralGroup attribute space (e.g.,
numberOfAtoms,formalCharge,numberOfHydrogens). - Attributes specific to the molecule attribute space (e.g.,
numberOfChains,numberOfResidues,numberOfSegments).
Examples of Useful Molecule Attributes
To highlight the potential of molecular attributes, here are some common use cases:
molecule.numberOfChains < 3: Matches molecules with fewer than three chains. This is particularly useful when working with macro-molecules like proteins.molecule.numberOfResidues > 100: Finds molecules that have more than 100 residues, allowing you to focus on particularly large molecules.molecule.numberOfSulfurs 2:5: Identifies molecules that contain between 2 and 5 sulfur atoms, which can be critical for analyzing disulfide bridge formations.not mol.selected: Filters molecules that are not currently selected in the workspace.
Boosting Productivity
The combination of molecule-specific and inherited attributes provides a versatile means of refining your molecular analysis. For example, you might combine different attributes to filter for molecules that are visible and contain more than a minimum number of atoms:
mol.v && mol.nat > 50: Matches visible molecules with more than 50 atoms.
By mastering these attributes, users can dramatically reduce the time taken to identify specific molecules in their projects, paving the way for smoother workflows and more targeted analyses.
Learn More
The examples above are just the tip of the iceberg. SAMSON’s documentation offers a full breakdown of all molecule attributes, their short names, possible values, and practical examples to get you started quickly.
Want to dive deeper? Visit the original documentation at https://documentation.samson-connect.net/users/latest/nsl/molecule/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.