As molecular modelers, ensuring precision in atom-level queries can often feel like threading a needle. Whether you’re analyzing molecular structures, identifying specific atomic environments, or customizing molecule manipulations, having a flexible and intuitive language for atom attributes is indispensable. Enter the NSL in the SAMSON molecular design platform, which simplifies this complexity with a robust set of atom attributes for various purposes.
What Are Atom Attributes?
Atom attributes in NSL allow you to target specific atom nodes with fine granularity. Whether you’re looking for atoms with particular chemical properties, identifying a subset based on geometrical arrangements, or working on specific categories like metals or hydrogens, there’s an attribute to assist you.
The attributes are located within the atom attribute space (denoted as a in short). These attributes enable powerful queries based on properties such as element type, position, chemical bonding, geometry, and other characteristics.
Key Attribute Categories
Let’s explore some of the key atom attributes that can streamline your molecular modeling efforts:
1. Elemental Attributes
Need to identify all oxygen atoms or differentiate non-metals from metalloids? The atom.element (a.e) and related elemental attributes come in handy:
atom.element Oxygen: Select all oxygen atoms.atom.symbol O: Alternatively, use the symbol to achieve the same result.
Need to broaden the query? Combine multiple elements:
a.e Carbon, Oxygen: Matches all carbon and oxygen atoms.
2. Geometrical Attributes
The geometrical arrangement of atoms plays a central role in properties like molecular reactivity and stability. Use atom.geometry (a.g) to identify atoms with specific geometries:
a.g tetrahedral: Matches atoms with tetrahedral geometry.a.g octahedral, dodecahedral: Filter atoms with octahedral or dodecahedral geometries.
3. Chemical Context: Functional and Bonding Insights
If you’re studying molecular interactions or customizing functional group queries, attributes like hybridization and hydrogen bonding reveal layers of chemical context:
a.hy sp2: Select SP2 hybridized atoms.a.hba: Identify hydrogen bond acceptors.a.hbd: Identify hydrogen bond donors.
4. Substructure and Residue Exploration
Navigating residues or substructures? Attributes like atom.residueSequenceNumber (a.resi) and atom.substructureSequenceNumber (a.sgi) simplify handling residue-based queries:
a.resi 42: Matches atoms in residue 42.a.sgi 20:40: Matches atoms in substructures numbered 20 to 40.
5. Specialized Categories
For more targeted insights, SAMSON’s NSL also accommodates attributes for categories like metals, noble gases, and transition metals:
a.met: Matches metallic atoms.a.transitionMetal: Focuses on transition metals specifically.
Why It Matters
If you’re ever bogged down by manually evaluating atom-based properties or targeting specific molecular fragments, you’d likely face challenges of efficiency and reproducibility. With NSL atom attributes, SAMSON empowers you to conduct precise queries that reduce manual guesswork.
Explore More!
With the extensive list of attributes available in SAMSON’s NSL, you can unlock new insights and optimize molecular workflows. Ready to explore them all? Visit the full documentation page at atom attributes documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.