Molecular modelers working with SAMSON know the importance of efficiently navigating, managing, and querying structural data with precision. SAMSON’s Node Specification Language (NSL) provides powerful tools to handle such data, and within this language, Path Attributes play a vital role when working with conformation nodes. In this blog post, we will explore the concept of Path Attributes, what they offer, and how they can be used to boost your productivity.
What Are Path Attributes?
Path attributes reside in the path attribute space of SAMSON’s Node Specification Language (NSL) and are specified using the short name p. These attributes are designed exclusively for paths, making them highly relevant for those analyzing conformation nodes in molecular structures.
The attributes are:
name (n): Inherited from the node attribute space, this allows matching by name.selected: Indicates whether a path is currently selected or not.selectionFlag (sf): Displays or modifies the selection flag for a path.numberOfAtoms (nat): Specific topath, this matches paths with specific numbers of atoms.
Why Are Path Attributes Valuable?
Consider a scenario where you are working with large molecular systems involving multiple paths or conformations. Efficient filtering and querying of these conformations can save time and provide clarity amidst complexity. This is where path attributes shine, as they allow you to search and categorize paths based on properties such as atom count, selection status, or name. You can make selections, analyze specific regions of your structure, or even automate repetitive tasks efficiently.
Examples and Practical Use Cases
Let’s look at how you can use these attributes through real examples:
1. Matching Paths by Name
The name attribute enables you to query paths with specific names. Use the short name n for this attribute.
- Match a specific name:
p.n "A" - Match names starting with a pattern:
p.n "L*"
2. Filtering Selected Paths
The selected attribute helps identify or exclude paths marked as selected.
- Query for selected paths:
p.selected - Exclude selected paths:
not p.selected
3. Counting Atoms in Paths
The numberOfAtoms attribute (p.nat) is a highly practical attribute when analyzing molecular conformations.
- Find paths with more than 100 atoms:
p.nat > 100 - Select paths with 100 to 200 atoms:
p.nat 100:200
This is particularly useful for narrowing down focus to smaller or larger conformations depending on your modeling goals.
Where to Start?
To get started with Path Attributes, it helps to experiment with simple queries directly in SAMSON. Combine attributes using logical operators and work your way through more complex filtering mechanisms.
For further examples, explanations, and advanced use cases, visit the official documentation page: Path Attributes in SAMSON.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at www.samson-connect.net.