For molecular modelers dealing with conformations, querying specific paths efficiently can significantly speed up workflows and improve accuracy. SAMSON’s Path Attribute Space provides a streamlined way to define and manipulate path-related attributes, making molecular analysis more intuitive and precise.
The path attribute space (short name: p) in SAMSON focuses on conformation nodes and allows users to query or manipulate paths based on specific attributes. This blog post will explore key attributes from the path attribute space and examples of how to use them effectively.
Inherited Attributes
The Path Attribute Space inherits several useful attributes from the node attribute space:
- name (
n): This matches nodes by their name and supports wildcards. For instance:p.n "A"matches a path named ‘A’, whilep.n "L*"matches paths starting with ‘L’. - selected: Allows users to query whether a path is selected or not, e.g.,
p.selectedornot p.selected, though this attribute doesn’t have a short name. - selectionFlag (
sf): Indicates selection status with true/false values, likep.sforp.sf false.
Specific Path Attributes
In addition, the Path Attribute Space includes a specific attribute that is tailored for managing path-related data:
- numberOfAtoms (
nat): This attribute matches paths containing specific numbers of atoms. For example:p.nat > 100: Matches paths with more than 100 atoms.p.nat 100:200: Matches paths with 100 to 200 atoms.
By combining these specific and inherited attributes, users can construct highly customizable queries to filter or select molecular paths efficiently.
Why Use Path Attributes?
The ability to pinpoint paths with specific characteristics is essential for many molecular modeling tasks, such as analyzing complex conformations or isolating molecular pathways based on defined parameters. By using keywords and shorthand codes like p.nat and p.sf, SAMSON users can greatly reduce the time spent on repetitive tasks while improving precision during molecular design processes.
For example, suppose you are working on a molecular simulation where you want to isolate paths containing a precise number of atoms. Instead of manually searching, you can simply type p.nat 150 to find all paths with exactly 150 atoms. Similarly, if you are interested in paths that are already selected in the interface, a quick p.selected statement gets the job done.
Conclusion
By leveraging SAMSON’s Path Attribute Space, modelers can optimize their workflows and spend more time focusing on designing and understanding molecules. Whether you are filtering paths based on the number of atoms or selection flags, these tools add flexibility and clarity to molecular modeling tasks.
To explore these features in detail, visit the official documentation here: https://documentation.samson-connect.net/users/latest/nsl/path/.
SAMSON and all SAMSON Extensions are free for non-commercial use. Get started today at https://www.samson-connect.net.