Understanding Conformation Attributes for Molecular Design
For molecular modelers, working efficiently with specific node attributes is crucial when designing or analyzing complex molecular structures. The Conformation Attribute Space within SAMSON’s Node Specification Language (NSL) provides a structured way to define and query node attributes that are specific to molecular conformations.
This blog post highlights the conformation attributes supported by the NSL and explains how they can streamline molecular modeling workflows by enabling precise filtering and selection of conformations based on their properties.
What is the Conformation Attribute Space?
The conformation attribute space, abbreviated co, is a specialized attribute group in SAMSON’s NSL that applies exclusively to conformation nodes. Within this space, attributes inherited from general node specifications, as well as attributes unique to conformations, are accessible for use in molecular design and analysis contexts.
To help you get started, let’s take a closer look at these attributes, their possible values, and example usage for refining your queries:
Attributes Inherited from Node Specification
The conformation attribute space includes inherited attributes from general node specifications:
| Attribute Name | Short Name | Possible Values | Examples |
|---|---|---|---|
| name | n |
Strings in quotes | co.n "A"co.n "L*" |
| selected | true, false |
co.selectednot co.selected |
|
| selectionFlag | sf |
true, false |
co.sf falseco.sf |
The combination of these attributes provides flexibility to filter conformations based on naming conventions or their selected statuses. For example, using co.selected allows you to query only the conformations currently selected in a workspace.
Conformation-Specific Attribute: numberOfAtoms
In addition to inherited attributes, the conformation attribute space introduces the conformation-specific attribute numberOfAtoms, with short name nat. This attribute allows you to match conformations based on the number of atoms they contain.
Here’s how you can use numberOfAtoms effectively:
co.nat > 100: Matches and filters conformations with more than 100 atoms.co.nat 100:200: Matches conformations with the number of atoms falling within a range (100 to 200 in this example).
By targeting the number of atoms in conformations, you can significantly improve the precision of your queries, especially in large molecular structures where efficiency is key.
Start Using Conformation Attributes
Conformation attributes empower molecular modelers to refine workflows and enhance productivity when working with structural nodes in SAMSON. Whether you need to filter based on attribute names, selection statuses, or specific atom counts, the conformation attribute space is a powerful addition to your molecular modeling toolkit.
For more details, examples, and advanced usage guidelines, visit the official documentation at Conformation Attributes Documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at SAMSON Connect.