For molecular modelers, navigating and managing molecular conformations effectively can often be a significant challenge. Whether you’re dealing with detailed structural analysis or large-scale molecular conformations, organizing and selecting relevant features is a frequent need. SAMSON provides a powerful solution through its ‘Conformation Attribute Space’ in the Node Specification Language (NSL), designed to simplify the process of querying and managing molecular conformations. In this blog post, we’ll explore how these attributes can help you work more effectively.
What are Conformation Attributes?
Conformation attributes in SAMSON streamline working with molecular conformations by providing specific attribute space called conformation (short name: co). It is tailored to match only conformation nodes and offer powerful property-based queries. Attributes here include inherited properties from the general node attribute space, as well as conformation-specific ones.
Key Inherited Attributes
Some of the inherited attributes from the node attribute space include:
name(n): Use this for identifying conformations by their names. Examples:co.n "A": Matches conformations named “A”.co.n "L*": Matches conformations with names starting with “L”.
selected: Indicates whether the conformation is selected. Examples:co.selected: Matches all selected conformations.not co.selected: Matches all unselected conformations.
selectionFlag(sf): Allows finer control over selection. Examples:co.sf false: Matches conformations with a false selection flag.co.sf: Matches conformations with a true selection flag.
Conformation-Specific Attribute: numberOfAtoms
In addition to the inherited attributes, the conformation attribute space also introduces a specific attribute—numberOfAtoms, abbreviated as nat. This attribute is particularly useful for limiting queries to conformations based on their atom counts. It supports integer values for precise and range-based matching:
co.nat > 100: Matches conformations containing more than 100 atoms.co.nat 100:200: Selects conformations with atom counts ranging between 100 and 200.
Why This Matters to Molecular Modelers
Efficiently filtering molecular conformations allows researchers to focus on specific structural properties during analysis or design. Whether identifying large conformations for complex modeling or narrowing down selected parts of a molecular system, the flexibility offered by these attributes simplifies complex workflows. By utilizing short names like co.nat or co.sf, you can write compact and efficient queries inside SAMSON, reducing guesswork and manual labor.
For those who need to manage molecular conformations on large scales, leveraging these attributes makes it easier to organize data meaningfully and work with just the conformations you need.
Learn More
If you would like to explore the full capabilities of conformation attributes in SAMSON, visit the official documentation page here. Mastering this tool will give you deeper control and insight over your molecular modeling tasks.
SAMSON and all SAMSON Extensions are free for non-commercial use. Start designing with SAMSON by downloading it from this link.