Molecular modeling is an intricate and rewarding art, but it can also be fraught with challenges. One common difficulty is selecting and filtering conformations in large molecular systems efficiently. This is where SAMSON’s integration of the Node Specification Language (NSL) becomes a valuable asset. Today, we’ll focus on the powerful conformation attributes, which streamline conformation-related tasks.
What are conformation attributes?
Conformation attributes belong to the conformation attribute space (short name: co) in NSL and are designed specifically to work with conformation nodes. These attributes allow modelers to interrogate and manipulate specific conformations with precision. Some of these attributes are inherited from the more general node attribute space, while others are unique to the conformation context.
Inherited Attributes
1. name: This attribute matches the name of a conformation. You can filter conformations based on specific patterns or substrings. For example:
co.n "A": Matches conformations with the name “A”.co.n "L*": Matches conformations with names starting with “L”.
2. selected: This boolean attribute identifies whether a conformation is selected or not. It does not have a short name and is incredibly handy for refining selections. Examples include:
co.selected: Matches selected conformations.not co.selected: Matches unselected conformations.
3. selectionFlag: Another boolean attribute that builds on node.selectionFlag. Its short name is sf; practical examples are:
co.sf false: Matches conformations where the selection flag is set tofalse.co.sf: Matches conformations where the selection flag is set totrue.
Conformation-specific Attributes
numberOfAtoms: Unique to the conformation context, the numberOfAtoms attribute (short name: nat) allows users to filter conformations by their atom count. This is particularly useful when dealing with systems of varying sizes. Here are some examples:
co.nat > 100: Matches conformations that have more than 100 atoms.co.nat 100:200: Matches conformations containing between 100 and 200 atoms.
This attribute is invaluable for tasks like analyzing specific fragments, tracking conformations in simulations, or ensuring size constraints are met for downstream processing.
Why should you care?
Attributes in the conformation space empower molecular modelers by making it easier to refine searches and automate workflows. Need to retrieve conformations that meet specific criteria? Attributes such as co.nat or co.selected can help you achieve this in seconds, freeing up more time to focus on refining your designs or analyzing results. By mastering these attributes, you’ll become more efficient in handling complex molecular systems.
Where to go next
The conformation attributes in NSL are only a small subset of what this language can do within SAMSON. If you’re intrigued and want to dive deeper, check out the documentation page here to learn more about what SAMSON offers.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON today at https://www.samson-connect.net.